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- PDB-3gxb: Crystal structure of VWF A2 domain -

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Basic information

Entry
Database: PDB / ID: 3gxb
TitleCrystal structure of VWF A2 domain
Componentsvon Willebrand factor
KeywordsCELL ADHESION / VWA-like fold / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Extracellular matrix / Glycoprotein / Hemostasis / Isopeptide bond / Secreted / von Willebrand disease
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 / positive regulation of intracellular signal transduction / 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 / 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 / collagen-containing extracellular matrix / 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, 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 (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 signature. / 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 / molecular replacement / Resolution: 1.9 Å
AuthorsZhou, Y.F. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural specializations of A2, a force-sensing domain in the ultralarge vascular protein von Willebrand factor.
Authors: Zhang, Q. / Zhou, Y.F. / Zhang, C.Z. / Zhang, X. / Lu, C. / Springer, T.A.
History
DepositionApr 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,0207
Polymers41,6332
Non-polymers1,3875
Water7,296405
1
A: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4623
Polymers20,8161
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5584
Polymers20,8161
Non-polymers7423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.110, 60.810, 56.350
Angle α, β, γ (deg.)90.00, 99.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 6 / Auth seq-ID: 1495 - 1671 / Label seq-ID: 1 - 177

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein von Willebrand factor / vWF / von Willebrand antigen 2 / von Willebrand antigen II


Mass: 20816.400 Da / Num. of mol.: 2 / Fragment: ADAMTS13 cleavage domain, residues 1495-1671
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F8VWF, VWF / Plasmid: pLEXm / References: UniProt: P04275
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 2
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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 277 K / pH: 7.2
Details: 0.1 M Bis-Tris pH 7.2, 0.2 M lithium sulfate, 25 % PEG3350, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→27.82 Å / Num. obs: 28792 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.104
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 2 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FE8

1fe8


Resolution: 1.9→27.82 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.21 / SU B: 8.079 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1466 5.1 %RANDOM
Rwork0.183 ---
obs0.185 27317 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.25 Å2
2---0.46 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 89 405 3286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223414
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.011.9974698
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1585446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64424.261176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51915590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8421533
X-RAY DIFFRACTIONr_chiral_restr0.0620.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212729
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3151.52027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6223345
X-RAY DIFFRACTIONr_scbond_it1.04731387
X-RAY DIFFRACTIONr_scangle_it1.8344.51336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1403 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.365
loose thermal0.8210
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 122 -
Rwork0.266 1962 -
obs--98.44 %
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)
12.5206-0.4106-1.00751.14450.44911.2630.0325-0.03690.0629-0.0555-0.05220.0680.0013-0.0450.01970.0084-0.0005-0.00310.0065-0.00620.0083-5.9891.61232.6157
21.14580.2759-0.75431.53250.33112.1238-0.01030.01150.0157-0.160.0115-0.03840.03260.0047-0.00130.0215-0.00050.00570.00020.00010.00181.0265-1.5029-3.4873
30.9211-0.0606-0.56230.98520.61811.48690.01340.0723-0.0683-0.0302-0.04080.05150.1282-0.11790.02740.0306-0.0079-0.01050.0105-0.00420.0098-4.3814-6.624-1.162
40.53140.3493-0.53111.0997-0.40423.6457-0.0288-0.136-0.03170.0967-0.0137-0.19560.20450.170.04260.0280.0201-0.01980.0423-0.00480.04789.2859-9.26075.8373
50.65990.20510.25480.4519-0.19030.8873-0.03-0.08760.04320.0768-0.007-0.1280.05640.13950.0370.06880.0356-0.03820.0824-0.04050.07366.3439-0.250910.7319
64.4086-0.1845-0.12531.195-0.05912.07190.0355-0.25410.10850.18190.0029-0.0227-0.04760.1719-0.03840.0349-0.0098-0.00470.03-0.00690.0056-0.02419.41112.7863
77.7432-0.1638-0.73882.72240.59372.093-0.10360.15520.028-0.0660.1055-0.11720.05540.0328-0.00190.0133-0.00490.00180.0079-0.00360.00570.326912.5776-0.9958
82.58290.9705-1.44131.3052-0.77441.5714-0.1186-0.0170.00570.1050.0614-0.06120.0643-0.03020.05720.0310.0104-0.00790.0057-0.00590.008617.618-22.658831.9492
98.5587-0.1434-2.56581.7332-1.44582.0748-0.0773-0.1315-0.11230.18050.0202-0.0534-0.09720.02920.05720.06510.0106-0.03680.0035-0.00410.025628.3279-27.638133.4053
101.26780.2155-0.30651.4545-0.22640.7319-0.0694-0.06330.11050.06040.0452-0.0641-0.06070.03280.02420.01540.0039-0.01450.0064-0.00720.017122.2566-14.819627.5912
114.92932.667-2.57454.9732-1.77625.4734-0.2880.4660.0187-0.50760.2941-0.24190.1406-0.0004-0.00610.068-0.02670.0340.06330.00210.024227.9938-19.274515.4035
121.58140.51450.00171.380.70320.4344-0.1030.3294-0.0483-0.21590.10520.0374-0.0658-0.0145-0.00220.1013-0.0335-0.03790.09050.01340.07787.9658-21.535420.8607
130.9482-0.297-0.03731.20760.40762.1383-0.01760.09-0.1217-0.04670.00810.1058-0.04-0.05640.00950.0078-0.0035-0.00420.012-0.00810.022412.5344-30.001821.2775
143.03550.3006-1.32812.73730.19465.0668-0.0549-0.1507-0.06620.03170.0094-0.17990.01780.1270.04550.00470.0035-0.00220.00860.00250.019423.6435-34.036529.08
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1495 - 1521
2X-RAY DIFFRACTION2A1522 - 1545
3X-RAY DIFFRACTION3A1546 - 1579
4X-RAY DIFFRACTION4A1580 - 1597
5X-RAY DIFFRACTION5A1598 - 1624
6X-RAY DIFFRACTION6A1625 - 1654
7X-RAY DIFFRACTION7A1655 - 1671
8X-RAY DIFFRACTION8B1495 - 1518
9X-RAY DIFFRACTION9B1519 - 1528
10X-RAY DIFFRACTION10B1529 - 1593
11X-RAY DIFFRACTION11B1594 - 1606
12X-RAY DIFFRACTION12B1607 - 1619
13X-RAY DIFFRACTION13B1620 - 1654
14X-RAY DIFFRACTION14B1655 - 1671

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