Acta Cryst. (2008). D64, 466–470
Acta Crystallographica Section D
Structure of acostatin, a dimeric disintegrin from
Southern copperhead (Agkistrodon contortrix
contortrix), at 1.7 A˚resolution
Stephen D. Swenson,cFrancis S.
Markland Jr,cJun-Yong Choe,d‡
Zhi-Jie Liue§ and Marc Allairea*
aNational Synchrotron Light Source, Brookhaven
National Laboratory, Building 725D, Upton,
NY 11973, USA,bChemistry Department,
University of Southern California, Los Angeles,
CA 90089, USA,cDepartment of Biochemistry
and Molecular Biology and Norris
Comprehensive Cancer Center, Keck School of
Medicine, University of Southern California,
Los Angeles, CA 90033, USA,dDivision of
Chemistry and Chemical Engineering, Howard
Hughes Medical Institute/California Institute of
Technology, Pasadena, CA 91125, USA, and
eDepartments of Biochemistry and Molecular
Biology and Chemistry, University of Georgia,
Athens, GA 30602, USA
‡ Present address: Department of Biochemistry
and Molecular Biology, Rosalind Franklin
University of Medicine and Science, The
Chicago Medical School, 3333 Green Bay Road,
North Chicago, IL 60064, USA.
§ Present address: National Laboratory of
Biomacromolecules, Institute of Biophysics,
Chinese Academy of Sciences, Beijing 100101,
People’s Republic of China.
Correspondence e-mail: email@example.com,
Received 5 November 2007
Accepted 22 January 2008
PDB Reference: acostatin, 3c05, r3c05sf.
Disintegrins are a family of small (4–14 kDa) proteins that bind to another class
of proteins, integrins. Therefore, as integrin inhibitors, they can be exploited as
anticancer and antiplatelet agents. Acostatin, an ?? heterodimeric disintegrin,
has been isolated from the venom of Southern copperhead (Agkistrodon
contortrix contortrix). The three-dimensional structure of acostatin has been
determined by macromolecular crystallography using the molecular-replace-
ment method. The asymmetric unit of the acostatin crystals consists of two
heterodimers. The structure has been refined to an Rworkand Rfreeof 18.6% and
21.5%, respectively, using all data in the 20–1.7 A˚ resolution range. The
structure of all subunits is similar and is well ordered into N-terminal and
C-terminal clusters with four intramolecular disulfide bonds. The overall fold
consists of short ?-sheets, each of which is formed by a pair of antiparallel ?-
strands connected by ?-turns and flexible loops of different lengths.
Conformational flexibility is found in the RGD loops and in the C-terminal
segment. The interaction of two N-terminal clusters via two intermolecular
disulfide bridges anchors the ?? chains of the acostatin dimers. The C-terminal
clusters of the heterodimer project inopposite directions and form a largerangle
between them in comparison with other dimeric disintegrins. Extensive
interactions are observed between two heterodimers, revealing an ????
acostatin tetramer. Further experiments are required to identify whether the
???? acostatin complex plays a functional role in vivo.
Disintegrins were discovered and isolated from the venom of snakes
and were given their name because of their biological function of
binding to another class of protein known as integrins. Disintegrins
contain a characteristic tripeptide motif, e.g. Arg-Gly-Asp (RGD),
that is critical for binding integrins. Disintegrins are among the most
potent known natural inhibitors of integrin function and are active at
nanomolar concentrations, whereas the activity of the short linear
RGD peptides is observed at the micromolar level. Disintegrins have
been found to inhibit platelet aggregation, angiogenesis, metastasis
and tumor growth (McLane et al., 1998; Markland, 1998). As such,
disintegrins can be explored as therapeutic agents against a number
of pathologies including Alzheimer’s disease, inflammation, auto-
immune diseases, virus infection, asthma, osteoporosis, thrombosis
and cancer (Marcinkiewicz, 2005).
Disintegrins are small disulfide-rich proteins and are isolated as
soluble monomers or dimers, as well as as domains of larger
membrane proteins such as the mammalian ADAM (a disintegrin
and metalloproteinase) family. The monomeric forms are subdivided
into short, medium and long disintegrins which contain ?50, ?70 and
?84 amino-acid residues and four, six or seven disulfide bridges,
respectively. Homodimeric and heterodimeric forms of disintegrins
are found with ?65 amino-acid residues per chain with four intra-
molecular and two intermolecular disulfide bridges. The disulfide-
bond pattern is highly conserved in each group. A functional classi-
fication for disintegrins based on the tripeptide motif and their
integrin-binding selectivity includes a subdivision into RGD-, MLD-
and KTS-disintegrins (Marcinkiewicz, 2005).
Comparisons of the three-dimensional structures of disintegrins
(Adler et al., 1991; Saudek et al., 1991; Senn & Klaus, 1993; Smith et
# 2008 International Union of Crystallography
Printed in Singapore – all rights reserved
al., 1996; Guo et al., 2001; Moreno-Murciano et al., 2003; Fujii et al.,
2003; Shin et al., 2003; Bilgrami et al., 2004, 2005; Monleo ´n et al., 2005;
Janes et al., 2005; Takeda et al., 2006; Igarashi et al., 2007) revealed a
remarkable similarity and a fold having an elongated overall shape.
The secondary structure of disintegrins is composed of a series of
short antiparallel ?-sheets, with the integrin-binding motif located at
the tip of one of the connecting loops. The C-terminus of each chain
was found to be structurally close to the integrin-binding loop.
Interactions between disintegrin subunits of dimers are mostly
observed within the N-terminal residues including two disulfide
bonds linking the two chains. In dimers the integrin-binding loops
containing the tripeptide motif point in opposite directions.
Structure–function studies of disintegrins have shown that the
disulfide bonding is essential for disintegrin structural integrity and
binding, whereas the RGD-flanking residues and C-terminus are
relevant for integrin-binding affinity and selection (Wierzbicka-
Patynowski et al., 1999; McLane et al., 2001; Yahalom et al., 2002).
Here, we present the three-dimensional structure of acostatin, a
heterodimeric disintegrin from the venom of the snake Agkistrodon
contortrix contortrix. The gene structure encoding the ?-chain
precursor of acostatin is consistent with the well known pre-peptide,
metalloprotease, spacer and disintegrin domains, whereas the ?-chain
has a short coding region encoding the disintegrin domain (Okuda et
al., 2002). Acostatin purified from the venom of the Southern
copperhead consists of a mature protein of 63 and 64 amino-acid
residues in the ?-chain and ?-chain, respectively, where both chains
contain the Arg-Gly-Asp (RGD) sequence motif. A predominant
form of purified acostatin has been identified in which the N-terminal
residue of the ?-chain is a pyroglutamic acid, lacking the initial
2.1. Crystallization and data collection
Crystals of acostatin purified from the venom of A. contortrix
contortrix were grown using the hanging-drop vapor-diffusion
method in which protein solution (?16.5 mg ml?1in 10 mM HEPES
pH 7.4, 14.7 mM NaCl) was mixed with an equal volume of reservoir
solution (1.8 M ammonium sulfate in 100 mM Tris buffer pH 8.5) as
previously described (Moiseeva et al., 2002). Crystal characterization
was performed using X-ray diffraction data collected at the SSRL
(Stanford Synchrotron Radiation Laboratory, Stanford, California,
USA). The final data set was collected from a flash-frozen crystal at
beamline 5.0.2 of the ALS (Advanced Light Source, Berkeley, Cali-
fornia, USA). Glycerol (12–15%) was added to the reservoir solution
as a cryoprotectant. Images were processed and scaled with HKL-
2000 (Otwinowski & Minor, 1997) and details of the data collection
and statistics are summarized in Table 1. The crystals belonged to
space group P212121with two acostatin dimers per asymmetric unit,
and diffracted to a resolution of 1.7 A˚. A monoclinic crystal form of
acostatin has been reported (Fujii et al., 2002).
2.2. Structure solution and refinement
Initial phase estimates were derived from a molecular-replacement
solution using the maximum-likelihood approach (Read, 2001) as
implemented in Phaser (McCoy et al., 2007). An initial homology
search model was generated using CCP4 tools (Collaborative
Computational Project, Number 4, 1994) and the program
CHAINSAW (Schwarzenbacher et al., 2004) with nonhomologous
side chains deleted to the C?atom. This model was built using the
trimestatin X-ray coordinates (PDB code 1j2l), truncated at the first
15 amino-acid residues and aligned with contortrostatin, another
homodimeric disintegrin also purified from this snake species and
thought to be the content of the crystals. The amino-acid sequences of
contortrostatin and the ?-chain of acostatin are identical. A clear
molecular-replacement solution was found with translational Z scores
of 10.20, 15.19, 19.56 and 20.81 identifying four subunits labeled
A, B, C and D and oriented so as to form the characteristic inter-
molecular disulfide bridges. The amino-acid sequence determined
from the X-ray crystallographic electron-density map and the
observed weight of 13 508 Da are consistent with the presence of the
predominant purified form of the heterodimeric acostatin. The
molecular-replacement solution obtained was used as a starting
model for automated model building using ARP/wARP (Perrakis et
al., 1999) and extended to 224 of the 252 amino-acid residues
contained in the Ile-lacking form of acostatin. Further model building
was performed using Coot (Emsley & Cowtan, 2004). The structure
was refined without noncrystallographic symmetry restraints with
REFMAC5 (Murshudov et al., 1997) using the Babinet scaling option
and a final overall weight of 0.45. Accessible surface area was
calculated with the CCP4 program AREAIMOL using a probe radius
of 1.4 A˚.
3. Results and discussion
The final crystallographic model consist of 1686 protein non-H atoms
from 224 amino-acid residues of two acostatin heterodimers, 293
water molecules, two sulfate ions and additional residual electron
densities tentatively modeled as ten water molecules and another
sulfate ion at a lower occupancy. The final refinement statistics are
summarized in Table 1. The model includes amino-acid residues 5–63
Acta Cryst. (2008). D64, 466–470Moiseeva et al.
Data-collection and refinement statistics.
Values in parentheses are for the highest resolution shell.
Crystal-to-detector distance (mm)
Oscillation range (?)
Exposure time (s)
Total angular rotation (?)
Unit-cell parameters (A˚)
Reflections with I > 3?(I) (%)
Molecules (dimers) per ASU
Working set of reflections (95%)
Test set of reflections (5%)
No. of protein non-H atoms
No. of water molecules
No. of sulfates
R.m.s.d. from ideal geometry
Bond lengths (A˚)
Bond angles (?)
Mean B factor (A˚2)
Ramachandran plot: (non-Gly, non-Pro) residues
in most favored regions (%)
ALS BL 5.0.2
ADSC CCD Q210
a = 37.45, b = 59.81, c = 121.31
for subunit A and 5–62 for subunit C of the Ile-lacking 62 amino-acid
residues (2–63) of the ?-chain of acostatin. The model also includes
amino-acid residues 4–62 for subunit B and 4–59 for subunit D of the
64 amino-acid residues of the ?-chain of acostatin. Electron densities
are connected for all backbone atoms at the 1? level except for
residues Arg43D–Gly44D and the tentatively assigned Lys61C–
His62C C-terminal residues. Residual electron densities are visible
and could potentially be explained on the basis of disorder in the
amino-terminal and carboxy-terminal residues and potential alter-
native conformations including the side chains of Met33B, Lys14C
and Glu35D. The model has been refined to crystallographic Rwork
and Rfreevalues of 18.6% and 21.5%, respectively, using all data in the
20.0–1.7 A˚ resolution range, with root-mean-square deviations
(r.m.s.d.s) in bond lengths and bond angles of 0.013 A˚and 1.3?,
respectively. The geometry of the model was analyzed with
MOLPROBITY (Davis et al., 2007) and showed 100% of the residues
to be in the core region of the Ramachandran plot. Additional
Moiseeva et al.
Acta Cryst. (2008). D64, 466–470
stereochemistry was analyzed using Coot and was found to be in
agreement with expected values. One outlier is found in the rotamer
conformation of Cys13 from all subunits. Fig. 1 shows representative
electron-density fit including Cys13 and a carboxy-terminal group at
residue Phe63 from the ?-type subunit A.
3.1. Acostatin subunit structures
The overall fold of all acostatin subunits (A, B, C, D) is similar and
is depicted for the heterodimer AB in Fig. 2(a). Each subunit struc-
ture can be divided into two distinct clusters: an amino-terminal
cluster (up to residue 19) and a carboxy-terminal cluster (residue 20
and beyond). In subunits A, B and D, the structure contains three
?-sheets each formed by a pair of antiparallel ?-strands consisting of
residues 8–9 with 14–15, residues 27–28 with 31–32 and residues 38–
40 with 49–50; in subunit C only thelatter two ?-sheets are found. The
?-strands are connected by ?-turns and flexible loops of different
lengths consisting of 4–10 residues. The typical intra-chain disulfide
bridges found in the disintegrin family are also observed in the
acostatin structure. For all subunits, the distances calculated between
the S atoms of the pairs of Cys residues 7–30, 21–27, 26–51 and 39–58
are all within expected disulfide-bond distances. The high content of
disulfide bridges in these polypeptides is likely to contribute to the
formation of a stable and well defined three-dimensional structure.
Electron-density fit of the model showing (a) observed differences in the amino-acid sequence of the ?- and ?-chains of acostatin represented by subunits A and B,
respectively, (b) all Cys13 residues identified as rotamer outliers and (c) the carboxyl group of the C-terminal residue Phe63 of subunit A. This figure was prepared using
PyMOL (DeLano, 2002).
Comparison of the structure of the
?- and ?-chains of acostatin does not
(Fig. 2b). The r.m.s.d. for the super-
imposition of the C?atoms (residues
5–59) of the ?-chains (A/C) and the ?-
chains (B/D) are 0.88 and 1.02 A˚,
respectively. In comparison, super-
imposition of mixed chain types gives
r.m.s.d.s of 1.03 A˚(A/B), 1.04 A˚(A/
D), 1.12 A˚(C/D) and 1.57 A˚(B/C).
For all overlays, the deviations are
mainly located in the region of resi-
dues 38–50, designated as the Arg-
with the largest deviation of 4.3 A˚at
Asp45 when comparing subunits B
and C. We also observed that the
C-terminal residues 60–62 visible in
subunits A, B and C and located
adjacent to the RGD loops are found
in different orientations. Most of the
counted for by crystal contacts. The
comparison of the acostatin fold with
the previously determined disintegrin
structures of the monomeric trimes-
tatin, the schistatin homodimer and
the heterodimer from Echis carinatus
does not indicate any major structural
rearrangements, as expected from
their homologous sequences (Fig. 3).
The calculated r.m.s.d. of 1.2–1.5 A˚in
the superimposition of acostatin with
other disintegrin structures is com-
parable to the overlay of the different
chain types of acostatin. Additional
conformational differences are also
observed in the N-terminal residues.
can be ac-
3.2. The ab acostatin dimer
between the ?- and ?-chains in both
the AB and CD dimers. The N-term-
inal clusters of each pair of subunits
are responsible for dimer formation
(Fig. 2a). In both heterodimers, we
observed that the distances calculated
between the S atoms of Cys residue 8
in one chain and Cys residue 13 in the
other chain are all within expected
disulfide-bond distances. This pattern
of disulfide bridges is identical to the
pattern of intermolecular disulfide
bonds observed in the homodimer of
schistatin (Bilgrami et al., 2004) and
the heterodimer from the E. carinatus
disintegrin (Bilgrami et al., 2005).
These two intermolecular disulfide
bridges per heterodimer certainly
contribute to the stability and rigidity
Acta Cryst. (2008). D64, 466–470Moiseeva et al.
Sequence alignment of acostatin with trimestatin, schistatin and the E. carinatus heterodimer.
(a) Overall structure of the acostatin heterodimer represented by a C?tracing of subunits A (in blue) and B (in magenta)
with disulfide bridges inyellowand the side chains of the RGD binding loops. (b) Superimposition of the C?tracing of the
acostatin ABCD subunits (A subunit in green, B in blue, C in purple and D in orange). (c) Superimposition of the C?
tracing of acostatin AB (green) and CD (blue) dimers on the dimer from E. carinatus (red). (d) Overall structure of the
tetrameric arrangement of all acostatin subunits represented by a C?tracing. (e) The electrostatic surface of the acostatin
tetramer on the scale ?10 kT/e. The color map is from red (negative electrostatic potential) to blue (positive electrostatic
potential). The figure was prepared in PyMOL (DeLano, 2002) and the electrostatic potential was calculated using APBS
(Baker et al., 2001).
of the dimer. In addition, two hydrogen-bond distances are observed Download full-text
in the heterodimer AB between the side-chain N atoms of Asn5 and
the carbonyl O atoms of Ala10. In heterodimer CD the side chains of
Asn5 adopt a different rotamer conformation and the carbonyl O
atoms of Ala10 and the N atoms of Cys7 are found to interact with
the same water molecules. Overall, 8.3% and 9.7% of the accessible
surface area of the subunits is buried in the formation of the AB and
CD dimers, respectively.
The overall fold of the acostatin AB and CD dimers is essentially
similar. Superimposition of the dimers gives a calculated r.m.s.d. on
C?atoms of 1.82 A˚. We observed that dimerization through the
N-terminal domains takes place such that the C-terminal domains are
facing away from each other. The C-terminal domains in the
heterodimeric acostatin are widely separated from each other: the
distances between the tips of the C-terminal domains at the C?atoms
of Asp45 are 69.5 and 69.8 A˚for the AB and CD dimers, respectively.
With such an orientation of the N- and C-terminal regions, it is not
surprising to find that the slight differences between the heterodimers
are located in this RGD-containing segment. Comparison of the
acostatin dimers with previously reported dimeric disintegrins reveals
a major overall difference. We observed that the dimerization
through the N-terminal clusters generated a different hinge region
between the C-terminal domains (Fig. 2c), with a larger angle in the
acostatin dimers. This larger angular hinge moves the tips of the
C-terminal domains in acostatin further apart. In comparison, the
calculated distances between the C?atoms of Asp45 in schistatin and
the E. carinatus heterodimeric disintegrin are 57.7 and 59.1 A˚,
3.3. An abba acostatin tetramer
We observed considerable interactions between the acostatin AB
and CD heterodimers, as shown in Figs. 2(d) and 2(e). A substantial
part (8.2%) of the accessible surface area of the subunits, mostly
spread over the N- and C-terminal clusters of the ? chains (B and D),
is buried in this heterodimer–heterodimer interaction. We identified
two regions of hydrophobic interaction involving residue Leu15 in
subunit B with Phe32 and Ile54 in subunit D and vice versa. Two
hydrogen bonds are also formed, with the carbonyl O atom of Ser19
interacting with the side-chain N atom of Gln20. Two additional
hydrogen bonds are formed between subunits B and C; one involved
the side-chain carboxyl group of Glu35 (subunit B) and the N atom of
Leu15 (subunit C) and the other is made between the carbonyl O
atom of Asn52 (subunit B) and the side-chain amino group of Lys14
(subunit C). These residues adopt a different conformation in the
A/D subunits and the interactions found between them are mediated
through a network of water molecules. The surface complementa-
rities of the AB and CD dimers suggest the possibility of a tetrameric
form of acostatin that is best represented by an ???? acostatin
tetramer. In the tetrameric form the RGD loops are all pointing in
different and almost orthogonal directions. The distance between the
C?atoms of Asp45 of the ?-chains is 40.9 A˚and that between the ?-
chains is 80.6 A˚. The equivalent distances measured between the AD
and BC subunits are 40.5 and 38.7 A˚, respectively. This tetrameric
arrangement is new among known disintegrin structures but could be
an artifact of crystallization. Further experiments are required to
identify whether this ???? acostatin complex plays a functional role
We thank the SSRL, the ALS and their staff for providing access to
the beamline facility. This work was supported in part by funds
provided to MA by the Department of Energy under contract No.
DEAC02-98CH10866, the National Institutes of Health/National
Institute of General Medical Sciences under agreement Y1 GM-0080-
03 and the Brookhaven National Laboratory/Laboratory Directed
Research and Development Program. RB acknowledges partial
support from the National Science Foundation (grant CHE-98-16294)
as well as from the Zumberge Research Innovation Fund of the
University of Southern California.
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