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- PDB-5thp: Rhodocetin in complex with the integrin alpha2-A domain -

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Basic information

Entry
Database: PDB / ID: 5thp
TitleRhodocetin in complex with the integrin alpha2-A domain
Components
  • (Snaclec rhodocetin subunit ...) x 2
  • Integrin alpha-2
KeywordsCELL ADHESION / C-type lectin / integrin / venom / coagulation
Function / homology
Function and homology information


collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / positive regulation of cell projection organization / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / positive regulation of smooth muscle contraction ...collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / positive regulation of cell projection organization / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / positive regulation of smooth muscle contraction / skin morphogenesis / CHL1 interactions / response to L-ascorbic acid / basal part of cell / collagen-activated signaling pathway / positive regulation of phagocytosis, engulfment / Laminin interactions / hepatocyte differentiation / Platelet Adhesion to exposed collagen / focal adhesion assembly / mammary gland development / heparan sulfate proteoglycan binding / mesodermal cell differentiation / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / integrin complex / positive regulation of smooth muscle cell migration / MET activates PTK2 signaling / cell adhesion mediated by integrin / Syndecan interactions / response to amine / response to muscle activity / cell-substrate adhesion / positive regulation of collagen biosynthetic process / positive regulation of epithelial cell migration / ECM proteoglycans / detection of mechanical stimulus involved in sensory perception of pain / Integrin cell surface interactions / collagen binding / laminin binding / axon terminus / extracellular matrix organization / positive regulation of smooth muscle cell proliferation / positive regulation of cell adhesion / positive regulation of translation / animal organ morphogenesis / cell-matrix adhesion / integrin-mediated signaling pathway / cellular response to estradiol stimulus / cellular response to mechanical stimulus / female pregnancy / cell-cell adhesion / integrin binding / blood coagulation / amyloid-beta binding / toxin activity / virus receptor activity / response to hypoxia / cell adhesion / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / : / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / C-type lectin, conserved site / C-type lectin domain signature. / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor ...: / : / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / C-type lectin, conserved site / C-type lectin domain signature. / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Snaclec rhodocetin subunit gamma / Snaclec rhodocetin subunit delta / Integrin alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Calloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.006 Å
AuthorsMcDougall, M. / Orriss, G.L. / Stetefeld, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Heart and Stroke Foundation Canada, Grant-in-Aid programG-14-0006025 Canada
CitationJournal: PLoS Biol. / Year: 2017
Title: Dramatic and concerted conformational changes enable rhodocetin to block alpha 2 beta 1 integrin selectively.
Authors: Eble, J.A. / McDougall, M. / Orriss, G.L. / Niland, S. / Johanningmeier, B. / Pohlentz, G. / Meier, M. / Karrasch, S. / Estevao-Costa, M.I. / Martins Lima, A. / Stetefeld, J.
History
DepositionSep 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Snaclec rhodocetin subunit gamma
B: Snaclec rhodocetin subunit delta
C: Integrin alpha-2
D: Snaclec rhodocetin subunit gamma
E: Snaclec rhodocetin subunit delta
F: Integrin alpha-2
G: Snaclec rhodocetin subunit gamma
H: Snaclec rhodocetin subunit delta
I: Integrin alpha-2
J: Snaclec rhodocetin subunit gamma
K: Snaclec rhodocetin subunit delta
L: Integrin alpha-2
M: Snaclec rhodocetin subunit gamma
N: Snaclec rhodocetin subunit delta
O: Integrin alpha-2
P: Snaclec rhodocetin subunit gamma
Q: Snaclec rhodocetin subunit delta
R: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,928108
Polymers326,13118
Non-polymers3,79790
Water3,927218
1
A: Snaclec rhodocetin subunit gamma
B: Snaclec rhodocetin subunit delta
C: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,97518
Polymers54,3553
Non-polymers62015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Snaclec rhodocetin subunit gamma
E: Snaclec rhodocetin subunit delta
F: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,26725
Polymers54,3553
Non-polymers91222
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Snaclec rhodocetin subunit gamma
H: Snaclec rhodocetin subunit delta
I: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,09219
Polymers54,3553
Non-polymers73716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Snaclec rhodocetin subunit gamma
K: Snaclec rhodocetin subunit delta
L: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,85814
Polymers54,3553
Non-polymers50311
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Snaclec rhodocetin subunit gamma
N: Snaclec rhodocetin subunit delta
O: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,89917
Polymers54,3553
Non-polymers54414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: Snaclec rhodocetin subunit gamma
Q: Snaclec rhodocetin subunit delta
R: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,83715
Polymers54,3553
Non-polymers48212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.763, 130.763, 251.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Snaclec rhodocetin subunit ... , 2 types, 12 molecules ADGJMPBEHKNQ

#1: Protein
Snaclec rhodocetin subunit gamma


Mass: 15741.510 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: D2YW39
#2: Protein
Snaclec rhodocetin subunit delta


Mass: 14875.982 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: D2YW40

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Protein , 1 types, 6 molecules CFILOR

#3: Protein
Integrin alpha-2 / CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / ...CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / VLA-2 subunit alpha


Mass: 23737.738 Da / Num. of mol.: 6 / Fragment: UNP residues 170-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2, CD49B / Production host: Escherichia coli (E. coli) / References: UniProt: P17301

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Non-polymers , 6 types, 308 molecules

#4: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris pH 8.0, 2.65M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.006→19.87 Å / Num. obs: 83038 / % possible obs: 99.3 % / Redundancy: 5.3 % / Net I/σ(I): 11.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GPR

3gpr


Resolution: 3.006→19.867 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.52 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.27 4301 5.18 %random exclusion
Rwork0.2206 ---
obs0.2237 82982 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.006→19.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20622 0 170 218 21010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221250
X-RAY DIFFRACTIONf_angle_d0.55428886
X-RAY DIFFRACTIONf_dihedral_angle_d11.54212396
X-RAY DIFFRACTIONf_chiral_restr0.043080
X-RAY DIFFRACTIONf_plane_restr0.0033682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0094-3.0610.37322220.31713887X-RAY DIFFRACTION93
3.061-3.11650.36492290.31123886X-RAY DIFFRACTION94
3.1165-3.17610.31472130.30223917X-RAY DIFFRACTION95
3.1761-3.24060.31272200.30083923X-RAY DIFFRACTION95
3.2406-3.31070.38431740.29273937X-RAY DIFFRACTION96
3.3107-3.38720.37022050.27973938X-RAY DIFFRACTION95
3.3872-3.47140.35231980.26473945X-RAY DIFFRACTION95
3.4714-3.56460.31562390.27083909X-RAY DIFFRACTION94
3.5646-3.66870.32482170.25263927X-RAY DIFFRACTION95
3.6687-3.78620.30852250.24693905X-RAY DIFFRACTION95
3.7862-3.92020.2381880.24573942X-RAY DIFFRACTION95
3.9202-4.07560.27032640.22153885X-RAY DIFFRACTION94
4.0756-4.25890.25322350.20333905X-RAY DIFFRACTION94
4.2589-4.48050.2292380.19173935X-RAY DIFFRACTION94
4.4805-4.75670.18851980.17843942X-RAY DIFFRACTION95
4.7567-5.11670.22522030.18563929X-RAY DIFFRACTION95
5.1167-5.61850.27131980.20453959X-RAY DIFFRACTION95
5.6185-6.40180.26172050.21283935X-RAY DIFFRACTION95
6.4018-7.95720.282210.20873963X-RAY DIFFRACTION95
7.9572-18.4930.21712090.16653992X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7146-0.17390.14273.997-0.25773.97970.28670.6787-0.1316-0.0329-0.16110.02130.61440.6741-0.09940.8090.2366-0.20370.9696-0.06920.6761-124.9052393.546-28.2963
20.6685-0.42670.42581.1913-0.24922.11490.12710.58590.1337-0.0199-0.37140.3953-0.4553-0.39530.19670.82090.3244-0.2170.9848-0.02080.8276-141.7647415.2724-31.3897
33.40410.7284-1.11372.52080.64440.3389-0.21130.5599-0.096-0.30120.0311-0.1779-0.03120.02030.21250.88590.1068-0.04230.76810.04620.4849-112.171422.3575-18.7188
43.53970.0542.68962.55010.34932.9025-0.18860.2591-0.526-0.14190.2315-0.10120.09420.64170.00020.47830.11160.13340.8120.0340.539-54.8648461.4876-14.9339
52.3879-0.68561.08851.06470.51392.36630.00370.1744-0.5340.07710.32350.42410.3723-0.127-0.38020.52940.01140.16670.92590.2451.017-81.9635456.4262-18.3128
60.61970.2581-0.06180.767-0.13012.0842-0.3128-0.42030.02080.4490.13380.2269-0.0775-0.06770.23560.84490.35750.16020.85030.18260.9408-74.7839485.7736-4.5912
71.38070.8416-0.7283.1777-1.93022.3760.4130.3867-0.00270.5424-0.23580.446-0.4252-0.068-0.13090.79570.1331-0.07410.5273-0.0790.5557-127.0624402.70036.172
81.7566-1.09780.56611.1555-1.4862.0460.30240.038-0.51270.27630.05120.37230.3578-0.2112-0.35020.81760.1604-0.18430.5854-0.11181.11-132.0185376.22829.4167
93.59551.12390.14462.9806-1.87321.8380.32610.693-0.46380.2769-0.2517-0.66850.50680.5027-0.09590.83470.299-0.26050.7538-0.22240.7196-103.0612382.7882-4.2001
102.85540.3817-1.32531.9764-0.16320.47970.1838-0.79210.17830.4514-0.13930.294-0.3820.3461-0.07550.911-0.40720.16161.0548-0.11890.5558-60.2456.0934-43.041
112.13280.9564-2.41442.4072-2.46434.7485-0.15860.1766-0.12710.18940.36970.60730.2094-0.6004-0.1380.8194-0.29220.29190.9744-0.081.0805-75.2111435.4155-40.7168
121.0854-1.6081-0.21934.11590.14794.35460.1418-0.3055-0.1323-0.1762-0.02950.08420.35330.5985-0.14640.5727-0.15070.02860.70730.07020.538-47.4416428.0559-52.571
132.34460.24040.60131.7583-1.78832.7254-0.4957-0.1341.30990.6669-0.4131-0.5966-0.7158-0.39970.77520.9791-0.0222-0.52160.7054-0.14381.2802-112.4323470.154425.1481
143.8991-1.10331.00241.0361-0.17863.24940.1574-0.0015-0.1725-0.0449-0.1117-0.00230.52260.2295-0.03110.76380.0403-0.24350.48090.06910.7044-99.7026445.898527.4082
151.48040.37750.56262.6663-0.26372.6610.06430.52860.52120.0489-0.4627-0.17080.37210.3580.34980.52950.0153-0.07390.68340.15920.7815-112.6418452.5059-2.7266
161.20870.08130.57133.2095-1.01881.3536-0.10830.29920.3343-0.4296-0.6808-1.47270.38750.70960.72520.60850.05610.0361.02360.5321.2814-118.1251476.0794-33.762
171.1493-1.3621-0.21154.0788-2.42394.5478-0.26460.1882-0.1752-0.04480.10050.11820.067-0.34650.1520.5421-0.2146-0.09330.98160.36870.8723-142.665488.8551-36.025
182.294-0.7341-0.24482.3031-2.93264.4238-0.3555-0.03840.38070.5724-0.0772-0.596-0.8645-0.21590.34850.58420.0373-0.27270.5404-0.02710.8688-136.037475.9979-5.9137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 133)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 122)
3X-RAY DIFFRACTION3(chain 'C' and resid 172 through 363)
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 133)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 122)
6X-RAY DIFFRACTION6(chain 'F' and resid 172 through 364)
7X-RAY DIFFRACTION7(chain 'G' and resid 2 through 133)
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 122)
9X-RAY DIFFRACTION9(chain 'I' and resid 173 through 363)
10X-RAY DIFFRACTION10(chain 'J' and resid 3 through 133)
11X-RAY DIFFRACTION11(chain 'K' and resid 15 through 122)
12X-RAY DIFFRACTION12(chain 'L' and resid 174 through 362)
13X-RAY DIFFRACTION13(chain 'M' and resid 2 through 133)
14X-RAY DIFFRACTION14(chain 'N' and resid 1 through 122)
15X-RAY DIFFRACTION15(chain 'O' and resid 171 through 362)
16X-RAY DIFFRACTION16(chain 'P' and resid 2 through 133)
17X-RAY DIFFRACTION17(chain 'Q' and resid 1 through 122)
18X-RAY DIFFRACTION18(chain 'R' and resid 171 through 362)

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