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- PDB-5ou9: Crystal structure of Glycoprotein VI in complex with collagen-pep... -

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Basic information

Entry
Database: PDB / ID: 5ou9
TitleCrystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3
Components
  • (GPO)3
  • Platelet glycoprotein VI
KeywordsBLOOD CLOTTING / Platelet / glycoprotein / GPVI / collagen-binding / platelet activation / GPO3 / CRP
Function / homology
Function and homology information


collagen type I trimer / cellular response to vitamin E / tooth mineralization / cellular response to fluoride / collagen receptor activity / Anchoring fibril formation / intramembranous ossification / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization ...collagen type I trimer / cellular response to vitamin E / tooth mineralization / cellular response to fluoride / collagen receptor activity / Anchoring fibril formation / intramembranous ossification / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Defective VWF binding to collagen type I / platelet-derived growth factor binding / immune response-regulating signaling pathway / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / bone trabecula formation / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / Extracellular matrix organization / embryonic skeletal system development / cartilage development involved in endochondral bone morphogenesis / tetraspanin-enriched microdomain / Collagen biosynthesis and modifying enzymes / skin morphogenesis / collagen-activated tyrosine kinase receptor signaling pathway / endochondral ossification / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of platelet aggregation / collagen fibril organization / response to steroid hormone / face morphogenesis / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / Scavenging by Class A Receptors / GP1b-IX-V activation signalling / Syndecan interactions / enzyme-linked receptor protein signaling pathway / blood vessel development / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Collagen degradation / Non-integrin membrane-ECM interactions / negative regulation of cell-substrate adhesion / response to hyperoxia / protein localization to nucleus / ECM proteoglycans / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / response to cAMP / GPVI-mediated activation cascade / collagen binding / cellular response to fibroblast growth factor stimulus / cellular response to retinoic acid / visual perception / protein tyrosine kinase binding / cellular response to epidermal growth factor stimulus / secretory granule / skeletal system development / Cell surface interactions at the vascular wall / cellular response to amino acid stimulus / cellular response to glucose stimulus / response to hydrogen peroxide / sensory perception of sound / response to insulin / platelet activation / platelet aggregation / cellular response to mechanical stimulus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / osteoblast differentiation / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / cellular response to tumor necrosis factor / protein transport / response to estradiol / signaling receptor activity / protease binding / : / positive regulation of cell migration / membrane raft / response to xenobiotic stimulus / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / cell surface / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain ...Fibrillar collagen, C-terminal / Fibrillar collagen C-terminal domain / Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. / Fibrillar collagens C-terminal domain / : / : / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Collagen alpha-1(I) chain / Platelet glycoprotein VI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFeitsma, L.J. / Huizinga, E.G.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organization for Scientific ResearchECHO 700.58.006 Netherlands
CitationJournal: To be Published
Title: Structural insights into collagen-binding by platelet receptor Glycoprotein VI
Authors: Feitsma, L.J. / Brondijk, T.H.C. / Jarvis, G. / Hagemans, D. / Bihan, D. / Jerah, N. / Versteeg, M. / Farndale, R.W. / Huizinga, E.G.
History
DepositionAug 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: 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
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: Platelet glycoprotein VI
B: Platelet glycoprotein VI
C: (GPO)3
D: (GPO)3
E: (GPO)3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,78010
Polymers44,9135
Non-polymers8665
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-14 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.720, 59.720, 319.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide / Sugars , 3 types, 7 molecules ABCDE

#1: Protein Platelet glycoprotein VI / GPVI / Glycoprotein 6


Mass: 19719.215 Da / Num. of mol.: 2 / Mutation: -102-105 -131-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GP6 / Cell line (production host): HEK293-EBNA1-S / Production host: Homo sapiens (human) / References: UniProt: Q9HCN6
#2: Protein/peptide (GPO)3


Mass: 1824.985 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02452*PLUS
#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

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Non-polymers , 3 types, 44 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M MMT-buffer pH 9.0 25% (w/v) PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.5→79.93 Å / Num. obs: 21273 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 56.4 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.113 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.971 / Num. unique obs: 2503 / CC1/2: 0.646 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLM1.0.7data reduction
Aimless0.1.30data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OU7

5ou7


Resolution: 2.5→79.93 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 24.728 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.264 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26027 1064 5 %RANDOM
Rwork0.22791 ---
obs0.22955 20113 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.524 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.5→79.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 52 41 3181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023284
X-RAY DIFFRACTIONr_bond_other_d0.0020.023013
X-RAY DIFFRACTIONr_angle_refined_deg1.5642.0544509
X-RAY DIFFRACTIONr_angle_other_deg1.15737046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2835.024413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90822.414116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2515437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2621524
X-RAY DIFFRACTIONr_chiral_restr0.1270.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0223607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02653
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_it1.4954.181645
X-RAY DIFFRACTIONr_mcbond_other1.4954.1771644
X-RAY DIFFRACTIONr_mcangle_it2.7656.252049
X-RAY DIFFRACTIONr_mcangle_other2.7656.2532050
X-RAY DIFFRACTIONr_scbond_it1.0434.1731639
X-RAY DIFFRACTIONr_scbond_other1.0434.1751640
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9516.2472458
X-RAY DIFFRACTIONr_long_range_B_refined4.14947.8783211
X-RAY DIFFRACTIONr_long_range_B_other4.10547.8183203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 82 -
Rwork0.361 1440 -
obs--100 %
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)
10.62420.6831-0.01233.2238-2.27642.18430.0936-0.1293-0.02330.3046-0.0689-0.0085-0.3289-0.025-0.02470.1963-0.0730.00740.51910.180.0692-23.86913.769-24.451
22.22381.50532.5511.6661.794.2988-0.0602-0.17760.0089-0.11110.0758-0.166-0.2807-0.4312-0.01560.3403-0.0364-0.09420.20030.03480.1435-12.5656.72819.752
33.2293.38642.42449.92665.99926.8938-0.18420.34730.0190.32060.07490.484-0.0219-0.35840.10940.0994-0.0549-0.00350.48070.22070.1909-30.469-5.81-8.615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 178
2X-RAY DIFFRACTION2B0 - 173
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION3D1 - 21
5X-RAY DIFFRACTION3E1 - 21

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