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- PDB-4nt5: Crystal structure of human von Willebrand factor CTCK domain -

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Basic information

Entry
Database: PDB / ID: 4nt5
TitleCrystal structure of human von Willebrand factor CTCK domain
Componentsvon Willebrand factor
KeywordsPROTEIN BINDING / cystine knot / dimerization of VWF
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 / Weibel-Palade body / 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 / 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 / Weibel-Palade body / 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 / 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 / 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 (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.281 Å
AuthorsZhou, Y.F. / Springer, T.A.
CitationJournal: Blood / Year: 2014
Title: Highly reinforced structure of a C-terminal dimerization domain in von Willebrand factor.
Authors: Zhou, Y.F. / Springer, T.A.
History
DepositionDec 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Derived calculations
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_symm_contact / struct_conn
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8338
Polymers12,0661
Non-polymers7677
Water1086
1
A: von Willebrand factor
hetero molecules

A: von Willebrand factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,66516
Polymers24,1322
Non-polymers1,53414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_445z-1/4,-y-1/4,x+1/41
Buried area4880 Å2
ΔGint-99 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.340, 135.340, 135.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-3002-

ZN

21A-3003-

SO4

31A-3003-

SO4

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Components

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


Mass: 12065.751 Da / Num. of mol.: 1
Fragment: C-terminal cystine knot domain, unp residues 2721-2813
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F8VWF, VWF / Plasmid: ET8 home made / Cell line (production host): HEK293S Gnt1 / 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.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 8.56 Å3/Da / Density % sol: 85.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 1.3 M Lithium Sulfate, 0.1 M Bicine, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.28237 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28237 Å / Relative weight: 1
ReflectionResolution: 3.281→47.85 Å / Num. all: 12294 / Num. obs: 12292 / % possible obs: 99.9 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.219 / Rsym value: 0.228 / Net I/σ(I): 10.87
Reflection shellResolution: 3.28→3.37 Å / Redundancy: 10.27 % / Rmerge(I) obs: 5.79 / Mean I/σ(I) obs: 0.43 / Num. unique all: 931 / Rsym value: 6.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHASERin phenix.autosolphasing
PHENIX(phenix.refine: dev_1426)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.281→47.85 Å / SU ML: 0.64 / Phase error: 28.39 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 534 7.56 %random selection of 8% of reflections.
Rwork0.2244 ---
obs0.2261 12292 99.97 %-
all-12294 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.281→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms711 0 40 6 757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003775
X-RAY DIFFRACTIONf_angle_d0.461040
X-RAY DIFFRACTIONf_dihedral_angle_d11.198284
X-RAY DIFFRACTIONf_chiral_restr0.02115
X-RAY DIFFRACTIONf_plane_restr0.003132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2805-3.45350.45851250.3991647X-RAY DIFFRACTION100
3.4535-3.66980.34621300.33741629X-RAY DIFFRACTION100
3.6698-3.9530.29811340.26741597X-RAY DIFFRACTION100
3.953-4.35050.22011310.20771634X-RAY DIFFRACTION100
4.3505-4.97950.16621200.1661627X-RAY DIFFRACTION100
4.9795-6.27140.21911400.19441614X-RAY DIFFRACTION100
6.2714-47.8550.24471490.21241615X-RAY DIFFRACTION100
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)
14.6366-0.9785-5.15275.42996.36892.0182-2.5891-2.5786-0.4942.41552.3427-4.60280.78082.21030.52611.5290.0026-0.40611.86770.42031.60912.1247-8.953940.8793
23.85734.61764.01687.20736.22285.12680.84850.1694-1.6111-0.1418-0.3789-0.55680.26740.1635-0.4051.01710.16030.11621.02890.05851.186417.3247-2.771220.7459
37.48245.1013-1.36183.5178-0.0941.11742.0594-2.7388-1.47410.3924-2.8575-1.5781-1.04640.33090.75021.5996-0.2508-0.02161.58850.76311.7066-3.7543-21.994539.5326
48.58414.06460.54116.8296-3.69296.17240.4552-0.904-1.24290.3424-1.2865-0.54980.60470.36610.96961.08620.09920.23410.82980.11180.86557.5758-2.433323.6218
57.78124.7982-4.42492.0424-7.75045.33912.756-2.0479-1.69091.0364-2.6464-0.969-0.7193-0.6788-0.67441.3361-0.0673-0.05791.32660.24411.56950.6719-10.142435.301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2721 through 2727 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2728 through 2749 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2750 through 2765 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2766 through 2801 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2802 through 2813 )

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