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- PDB-1fe8: CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A3 DOMAIN IN COMPL... -

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Entry
Database: PDB / ID: 1fe8
TitleCRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A3 DOMAIN IN COMPLEX WITH A FAB FRAGMENT OF IGG RU5 THAT INHIBITS COLLAGEN BINDING
Components
  • (IMMUNOGLOBULIN IGG ...) x 2
  • VON WILLEBRAND FACTOR
KeywordsIMMUNE SYSTEM / Collagen binding / conformational changes / epitope / von Willebrand factor A-type domain
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 / Fc-gamma receptor I complex binding / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / immunoglobulin complex, circulating ...Weibel-Palade body / Defective F8 binding to von Willebrand factor / hemostasis / Platelet Adhesion to exposed collagen / platelet alpha granule / Fc-gamma receptor I complex binding / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / immunoglobulin complex, circulating / cell-substrate adhesion / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin binding / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / complement activation, classical pathway / antigen binding / 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 / antibacterial humoral response / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Ig gamma-2A chain C region, A allele / von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å
AuthorsBouma, B. / Huizinga, E.G. / Schiphorst, M.E. / Sixma, J.J. / Kroon, J. / Gros, P.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Identification of the collagen-binding site of the von Willebrand factor A3-domain.
Authors: Romijn, R.A. / Bouma, B. / Wuyster, W. / Gros, P. / Kroon, J. / Sixma, J.J. / Huizinga, E.G.
#1: Journal: Structure / Year: 1997
Title: Crystal structure of the A3 domain of human von Willebrand factor: implications for collagen binding
Authors: Huizinga, E.G. / van der Plas, R.M. / Kroon, J. / Sixma, J.J. / Gros, P.
#2: Journal: To be Published
Title: Binding of von Willebrand Factor to collagen type III: role of specific amino acids in the collagen binding domain and effects of neighbouring domains
Authors: van der Plas, R.M. / Gomes, L. / Marquart, J.A. / Vink, T. / Meijers, J.C.M. / de Groot, P.G. / Sixma, J.J. / Huizinga, E.G.
#3: Journal: J.Biol.Chem. / Year: 1997
Title: The von Willebrand Factor A3 domain does not contain a metal ion-dependent adhesion site motif
Authors: Bienkowska, J. / Cruz, M. / Atiemo, A. / Handin, R. / Liddington, R.
History
DepositionJul 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / 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 / pdbx_unobs_or_zero_occ_atoms / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VON WILLEBRAND FACTOR
H: IMMUNOGLOBULIN IGG RU5
L: IMMUNOGLOBULIN IGG RU5
B: VON WILLEBRAND FACTOR
I: IMMUNOGLOBULIN IGG RU5
M: IMMUNOGLOBULIN IGG RU5
C: VON WILLEBRAND FACTOR
J: IMMUNOGLOBULIN IGG RU5
N: IMMUNOGLOBULIN IGG RU5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,59415
Polymers199,9139
Non-polymers1,6816
Water15,817878
1
A: VON WILLEBRAND FACTOR
H: IMMUNOGLOBULIN IGG RU5
L: IMMUNOGLOBULIN IGG RU5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3636
Polymers66,6383
Non-polymers7263
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-19 kcal/mol
Surface area25310 Å2
MethodPISA
2
B: VON WILLEBRAND FACTOR
I: IMMUNOGLOBULIN IGG RU5
M: IMMUNOGLOBULIN IGG RU5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2265
Polymers66,6383
Non-polymers5892
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-22 kcal/mol
Surface area25650 Å2
MethodPISA
3
C: VON WILLEBRAND FACTOR
J: IMMUNOGLOBULIN IGG RU5
N: IMMUNOGLOBULIN IGG RU5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0054
Polymers66,6383
Non-polymers3671
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-25 kcal/mol
Surface area25540 Å2
MethodPISA
4
A: VON WILLEBRAND FACTOR
H: IMMUNOGLOBULIN IGG RU5
L: IMMUNOGLOBULIN IGG RU5
B: VON WILLEBRAND FACTOR
I: IMMUNOGLOBULIN IGG RU5
M: IMMUNOGLOBULIN IGG RU5
C: VON WILLEBRAND FACTOR
J: IMMUNOGLOBULIN IGG RU5
N: IMMUNOGLOBULIN IGG RU5
hetero molecules

A: VON WILLEBRAND FACTOR
H: IMMUNOGLOBULIN IGG RU5
L: IMMUNOGLOBULIN IGG RU5
B: VON WILLEBRAND FACTOR
I: IMMUNOGLOBULIN IGG RU5
M: IMMUNOGLOBULIN IGG RU5
C: VON WILLEBRAND FACTOR
J: IMMUNOGLOBULIN IGG RU5
N: IMMUNOGLOBULIN IGG RU5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,18930
Polymers399,82618
Non-polymers3,36312
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area53030 Å2
ΔGint-128 kcal/mol
Surface area137100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.8, 183.6, 131.8
Angle α, β, γ (deg.)90.0, 116.2, 90.0
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein VON WILLEBRAND FACTOR /


Mass: 21025.176 Da / Num. of mol.: 3 / Fragment: COLLAGEN BINDING DOMAIN A3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P04275

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Antibody , 2 types, 6 molecules HIJLMN

#2: Antibody IMMUNOGLOBULIN IGG RU5


Mass: 22420.012 Da / Num. of mol.: 3 / Fragment: FAB FRAGMENT HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863*PLUS
#3: Antibody IMMUNOGLOBULIN IGG RU5


Mass: 23192.434 Da / Num. of mol.: 3 / Fragment: FAB FRAGMENT LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 2 types, 5 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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

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Non-polymers , 2 types, 879 molecules

#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: iso-propanol, MPD, cacodylate, sodium chloride, Tris , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
213 %(v/v)isopropanol1reservoirprecipitant
322 %(v/v)MPD1reservoirprecipitant
4100 mMcacodylic acid1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8469
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8469 Å / Relative weight: 1
ReflectionResolution: 2.03→29.9 Å / Num. all: 143255 / Num. obs: 143245 / % possible obs: 85.9 % / Observed criterion σ(I): -3.5 / Redundancy: 4.2 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.4
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.404 / Num. unique all: 8424 / % possible all: 51.5
Reflection
*PLUS
Num. obs: 143255
Reflection shell
*PLUS
% possible obs: 51.5 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
CNSphasing
RefinementResolution: 2.03→29.9 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: used maximum likelihood refinement against structure factors
RfactorNum. reflection% reflectionSelection details
Rfree0.264 7206 -RANDOM
Rwork0.227 ---
all0.229 143245 --
obs0.229 143245 85.9 %-
Refinement stepCycle: LAST / Resolution: 2.03→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13889 0 105 878 14872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.41
X-RAY DIFFRACTIONx_torsion_deg26
X-RAY DIFFRACTIONx_torsion_impr_deg0.77
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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