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- PDB-6n29: Crystal structure of monomeric von Willebrand Factor D`D3 assembly -

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Basic information

Entry
Database: PDB / ID: 6n29
TitleCrystal structure of monomeric von Willebrand Factor D`D3 assembly
Componentsvon Willebrand factor
KeywordsBLOOD CLOTTING / von Willebrand Factor
Function / homology
Function and homology information


Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Defective VWF binding to collagen type I / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Weibel-Palade body / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of intracellular signal transduction / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / 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 / blood coagulation / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / protein-folding chaperone binding / 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 / Von Willebrand factor-like domain / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / Von Willebrand factor-like domain / : / 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. / von Willebrand factor type C domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor type A domain / Laminin / Laminin / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsDong, X. / Arndt, J.W. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)CA-31798 United States
CitationJournal: Blood / Year: 2019
Title: The von Willebrand factor D'D3 assembly and structural principles for factor VIII binding and concatemer biogenesis.
Authors: Dong, X. / Leksa, N.C. / Chhabra, E.S. / Arndt, J.W. / Lu, Q. / Knockenhauer, K.E. / Peters, R.T. / Springer, T.A.
History
DepositionNov 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / reflns_shell
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _reflns_shell.Rmerge_I_obs
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: von Willebrand factor
B: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,09812
Polymers106,6602
Non-polymers1,43910
Water1,802100
1
A: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1807
Polymers53,3301
Non-polymers8506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9185
Polymers53,3301
Non-polymers5894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.690, 174.690, 104.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein von Willebrand factor / vWF


Mass: 53329.832 Da / Num. of mol.: 2 / Mutation: Q852R, C1009A, C1142A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VWF, F8VWF / Production host: Homo sapiens (human) / References: UniProt: P04275
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
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: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 5.5% (w/v) PEG8000, 10% (w/v) PEG1000, 0.2 M calcium acetate and 0.1 M Tris-acetate, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 55726 / % possible obs: 98.7 % / Redundancy: 14.1 % / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 10.9 % / Rmerge(I) obs: 5.19 / Mean I/σ(I) obs: 0.41 / Num. unique obs: 3570 / CC1/2: 0.114 / % possible all: 87.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→48.45 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.17
RfactorNum. reflection% reflection
Rfree0.2415 2101 3.78 %
Rwork0.2018 --
obs0.2033 55604 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7261 0 87 100 7448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057563
X-RAY DIFFRACTIONf_angle_d0.70710315
X-RAY DIFFRACTIONf_dihedral_angle_d10.4934717
X-RAY DIFFRACTIONf_chiral_restr0.0481157
X-RAY DIFFRACTIONf_plane_restr0.0051348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.55810.38051210.37043071X-RAY DIFFRACTION87
2.5581-2.62210.40431370.36933471X-RAY DIFFRACTION97
2.6221-2.69290.43221370.39413498X-RAY DIFFRACTION99
2.6929-2.77220.39291410.36633575X-RAY DIFFRACTION100
2.7722-2.86160.37011390.32393571X-RAY DIFFRACTION100
2.8616-2.96390.3781420.29163575X-RAY DIFFRACTION100
2.9639-3.08260.30611400.26973582X-RAY DIFFRACTION100
3.0826-3.22280.2781400.25453571X-RAY DIFFRACTION100
3.2228-3.39270.2831420.23753604X-RAY DIFFRACTION100
3.3927-3.60520.24611410.2193617X-RAY DIFFRACTION100
3.6052-3.88350.22491430.19623620X-RAY DIFFRACTION100
3.8835-4.27410.2231420.17423622X-RAY DIFFRACTION100
4.2741-4.8920.1751430.13833649X-RAY DIFFRACTION100
4.892-6.16140.20591450.16723708X-RAY DIFFRACTION100
6.1614-48.45940.21571480.17353769X-RAY DIFFRACTION97
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)
12.68090.16880.77548.69883.82387.03450.6878-1.4909-0.28991.24410.0039-0.74610.4464-0.5634-0.65791.08140.209-0.0631.21970.03970.8974-40.5056138.453187.5186
29.3617-6.6103-6.37924.78925.08838.7990.59232.14690.0894-0.2626-1.52171.06-0.9481-2.14340.73740.88190.28070.10141.2446-0.04951.3145-19.4258127.96871.9812
33.88270.2385-2.0164.3503-0.13748.5857-0.0234-0.2713-0.34550.48020.1331-0.12651.13960.5784-0.08420.57080.1028-0.00980.4944-0.08480.54139.8833110.005570.7286
43.0187-0.4521.07483.4924-1.06477.19950.1524-0.17740.17630.24790.2084-0.4186-0.64570.6967-0.33410.5473-0.03970.1090.733-0.15010.631410.7442124.814488.2632
56.35061.9582-1.43311.7075-0.63716.24470.1257-0.43660.6049-0.26440.2004-0.4253-1.49390.581-0.2821.0177-0.24570.27550.7046-0.19990.944718.8281136.397662.0787
69.52783.28270.53833.96133.48683.9831-0.07440.3398-0.1444-1.1750.1931-0.5964-0.70110.517-0.12910.74980.0440.13770.77760.05160.601313.193119.996440.9849
76.9892-1.2629-3.88099.36122.80926.90530.14880.76660.9549-1.21580.18010.0481-0.5604-0.3834-0.28651.04610.36260.21781.11020.29531.051549.5446.598917.5401
88.4029-6.9369-3.37087.08823.76345.9048-1.3984-0.3703-0.97511.34080.3782-0.49621.02140.98410.84111.11450.31250.09970.79560.02361.270137.30467.616931.4601
93.7253-0.19280.52774.15062.3846.50160.02640.1560.0075-0.2675-0.06120.3078-0.5471-0.42480.03580.4460.04780.0470.4165-0.05130.455721.593198.13230.8184
105.3473-0.9899-0.12994.0783-0.59354.36920.30730.46730.3097-0.53160.1678-0.4822-0.34640.7142-0.4530.7251-0.06960.120.6156-0.15060.56338.185597.332415.052
113.77413.53990.59718.6852.79456.38070.2717-0.1665-0.15650.24540.0809-1.2294-0.42831.0533-0.3650.6359-0.1241-0.07220.8656-0.11240.893147.7415104.562242.2006
127.04315.8947-5.56286.689-5.5084.95690.1859-0.5420.45240.60310.0820.3771-0.83480.4883-0.36181.20850.07360.00110.698-0.09370.674430.684699.560861.9688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 764:828
2X-RAY DIFFRACTION2chain A and resseq 829:864
3X-RAY DIFFRACTION3chain A and resseq 865:1037
4X-RAY DIFFRACTION4chain A and resseq 1038:1126
5X-RAY DIFFRACTION5chain A and resseq 1127:1197
6X-RAY DIFFRACTION6chain A and resseq 1198:1252
7X-RAY DIFFRACTION7chain B and resseq 764:828
8X-RAY DIFFRACTION8chain B and resseq 829:864
9X-RAY DIFFRACTION9chain B and resseq 865:1037
10X-RAY DIFFRACTION10chain B and resseq 1038:1126
11X-RAY DIFFRACTION11chain B and resseq 1127:1197
12X-RAY DIFFRACTION12chain B and resseq 1198:1252

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