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- PDB-4dmu: Crystal structure of the von Willebrand factor A3 domain in compl... -

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Basic information

Entry
Database: PDB / ID: 4dmu
TitleCrystal structure of the von Willebrand factor A3 domain in complex with a collagen III derived triple-helical peptide
Components
  • Collagen III derived triple-helical peptide
  • von Willebrand factor
KeywordsSTRUCTURAL PROTEIN/PROTEIN BINDING / dinucleotide binding fold / collagen binding / platelet activation / hemostasis / plasma / STRUCTURAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


Weibel-Palade body / Defective F8 binding to von Willebrand factor / hemostasis / Platelet Adhesion to exposed collagen / platelet alpha granule / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / immunoglobulin binding ...Weibel-Palade body / Defective F8 binding to von Willebrand factor / hemostasis / Platelet Adhesion to exposed collagen / platelet alpha granule / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / immunoglobulin binding / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / Integrin signaling / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor, type A domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBrondijk, T.H.C. / Huizinga, E.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Implications for collagen I chain registry from the structure of the collagen von Willebrand factor A3 domain complex.
Authors: Brondijk, T.H. / Bihan, D. / Farndale, R.W. / Huizinga, E.G.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen III derived triple-helical peptide
B: von Willebrand factor
C: Collagen III derived triple-helical peptide
D: von Willebrand factor
E: Collagen III derived triple-helical peptide
F: von Willebrand factor
G: Collagen III derived triple-helical peptide
H: von Willebrand factor
I: Collagen III derived triple-helical peptide
J: von Willebrand factor
K: Collagen III derived triple-helical peptide
L: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,10316
Polymers168,71812
Non-polymers3844
Water0
1
A: Collagen III derived triple-helical peptide
B: von Willebrand factor


Theoretical massNumber of molelcules
Total (without water)28,1202
Polymers28,1202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-9 kcal/mol
Surface area12470 Å2
MethodPISA
2
C: Collagen III derived triple-helical peptide
D: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2163
Polymers28,1202
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-25 kcal/mol
Surface area12380 Å2
MethodPISA
3
E: Collagen III derived triple-helical peptide
F: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2163
Polymers28,1202
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-24 kcal/mol
Surface area12360 Å2
MethodPISA
4
G: Collagen III derived triple-helical peptide
H: von Willebrand factor


Theoretical massNumber of molelcules
Total (without water)28,1202
Polymers28,1202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-10 kcal/mol
Surface area12420 Å2
MethodPISA
5
I: Collagen III derived triple-helical peptide
J: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2163
Polymers28,1202
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-27 kcal/mol
Surface area12380 Å2
MethodPISA
6
K: Collagen III derived triple-helical peptide
L: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2163
Polymers28,1202
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-24 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.614, 187.614, 89.373
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
12B
22D
32F
42H
52J
62L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 300
2114C1 - 300
3114E1 - 300
4114G1 - 300
5114I1 - 300
6114K1 - 300
1124B1600 - 2000
2124D1600 - 2000
3124F1600 - 2000
4124H1600 - 2000
5124J1600 - 2000
6124L1600 - 2000

NCS ensembles :
ID
1
2

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Components

#1: Protein
Collagen III derived triple-helical peptide


Mass: 7742.494 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: synthetic peptide covers part of human collagen III sequence
#2: Protein
von Willebrand factor / / vWF / von Willebrand antigen 2 / von Willebrand antigen II


Mass: 20377.223 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VWF, F8VWF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04275
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM cacodylate, pH 6.5, 1.20 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.518
11h+k,-k,-l20.482
ReflectionResolution: 2.8→46.9 Å / Num. all: 41019 / Num. obs: 41019 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7 % / Biso Wilson estimate: 67.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4679 / % possible all: 73.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATZ & 4DMT

1atz

4dmt


Resolution: 2.8→46.32 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.883 / SU B: 48.367 / SU ML: 0.395 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 2090 5.1 %RANDOM - not-related by twinning
Rwork0.20154 ---
obs0.20416 38880 92.23 %-
all-38880 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.995 Å2
Baniso -1Baniso -2Baniso -3
1--19.75 Å20 Å20 Å2
2---19.75 Å20 Å2
3---39.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11631 0 20 0 11651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02212032
X-RAY DIFFRACTIONr_bond_other_d0.0020.028326
X-RAY DIFFRACTIONr_angle_refined_deg1.6492.09416568
X-RAY DIFFRACTIONr_angle_other_deg0.922320129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51251581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89223.455385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.633151584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2661572
X-RAY DIFFRACTIONr_chiral_restr0.080.21857
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02313311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022047
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.261.58051
X-RAY DIFFRACTIONr_mcbond_other0.11.53166
X-RAY DIFFRACTIONr_mcangle_it0.433213049
X-RAY DIFFRACTIONr_scbond_it0.89733981
X-RAY DIFFRACTIONr_scangle_it1.3794.53519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A963medium positional0.270.5
11C963medium positional0.260.5
11E963medium positional0.240.5
11G963medium positional0.30.5
11I963medium positional0.270.5
11K963medium positional0.310.5
22B2345medium positional0.260.5
22D2345medium positional0.230.5
22F2345medium positional0.250.5
22H2345medium positional0.260.5
22J2345medium positional0.230.5
22L2345medium positional0.240.5
11A963medium thermal0.282
11C963medium thermal0.322
11E963medium thermal0.32
11G963medium thermal0.312
11I963medium thermal0.372
11K963medium thermal0.232
22B2345medium thermal0.312
22D2345medium thermal0.322
22F2345medium thermal0.282
22H2345medium thermal0.322
22J2345medium thermal0.432
22L2345medium thermal0.352
LS refinement shellResolution: 2.799→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 169 -
Rwork0.233 1926 -
obs--65.04 %
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)
15.5571-0.6525-0.15434.5447-0.12412.9082-0.0789-0.11510.12530.32320.1583-0.6768-0.19780.4812-0.07940.6471-0.0746-0.06520.5268-0.07940.303932.771699.90240.9487
23.69790.8788-3.40635.9101-4.047212.1379-0.1446-0.4629-0.08750.64090.1499-0.1526-0.2868-0.475-0.00530.69770.0451-0.06560.5795-0.06850.336339.795182.5088-5.5954
34.4986-0.0335-0.65044.64150.96294.9410.0597-0.13770.07040.09440.0941-0.4729-0.22650.2845-0.15380.576-0.0494-0.04660.2641-0.0090.13299.284275.55330.518
46.79970.9342-7.91132.73650.168821.73630.54260.35520.41760.28210.39830.1265-0.8283-1.0654-0.94090.50130.0229-0.08730.1485-0.01040.1961-1.876560.6353-6.0206
54.28720.2857-0.11945.3214-0.20496.43720.09230.23310.02310.00210.05670.4512-0.4958-0.4889-0.1490.78780.1326-0.05760.3237-0.02960.1975-13.864176.810949.268
66.3555-1.1232-8.35541.68691.861515.8680.31830.09220.1251-0.35910.09960.0188-0.47560.1646-0.41790.6173-0.0866-0.10830.2149-0.04810.2842-3.844560.824255.6139
74.4085-0.40170.33713.5153-1.49512.3221-0.16030.2546-0.4394-0.50190.2012-0.31060.37360.1557-0.04090.8677-0.13380.05820.765-0.1610.497320.424180.909249.521
82.5651.2351-3.53544.6665-6.915722.4237-0.28840.40620.1081-0.2101-0.381-0.564-0.4910.28690.66940.8822-0.04260.12630.8062-0.01410.394738.735981.012655.8839
93.66980.31570.24063.59660.26774.715-0.09840.27650.1724-0.04030.0819-0.3224-0.15280.38130.01650.3079-0.0140.02510.28080.02420.13799.642932.73013.8732
106.23-0.644610.13973.3613-1.865327.9152-0.0521-0.25730.196-0.2361-0.12520.28190.0049-0.54040.17730.20780.02520.13530.18090.03690.2305-1.643947.933810.8366
114.38220.308-0.41356.3424-1.7165.02420.0285-0.1617-0.01380.13190.1440.857-0.1193-0.6371-0.17250.3362-0.02750.06210.4207-0.03490.1263-13.047131.643945.0027
126.35610.94328.09912.10260.442127.40140.1534-0.08140.10350.2268-0.15130.0888-0.2681-0.184-0.00210.43760.04830.13880.1711-0.0020.2454-3.774647.683437.8542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1686 - 1873
2X-RAY DIFFRACTION2A3 - 226
3X-RAY DIFFRACTION2A227
4X-RAY DIFFRACTION3D1686 - 1873
5X-RAY DIFFRACTION4C3 - 226
6X-RAY DIFFRACTION4C227
7X-RAY DIFFRACTION5F1686 - 1873
8X-RAY DIFFRACTION6E3 - 226
9X-RAY DIFFRACTION6E227
10X-RAY DIFFRACTION7H1687 - 1873
11X-RAY DIFFRACTION8G3 - 226
12X-RAY DIFFRACTION8G227
13X-RAY DIFFRACTION9J1683 - 1873
14X-RAY DIFFRACTION10I3 - 226
15X-RAY DIFFRACTION10I227
16X-RAY DIFFRACTION11L1686 - 1873
17X-RAY DIFFRACTION12K2 - 226
18X-RAY DIFFRACTION12K227

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