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- PDB-7r58: Crystal structure of the GPVI-glenzocimab complex -

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Basic information

Entry
Database: PDB / ID: 7r58
TitleCrystal structure of the GPVI-glenzocimab complex
Components
  • Fab heavy chain
  • Fab light chain
  • Platelet glycoprotein VI
KeywordsBLOOD CLOTTING
Function / homology
Function and homology information


collagen receptor activity / immune response-regulating signaling pathway / tetraspanin-enriched microdomain / collagen-activated tyrosine kinase receptor signaling pathway / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of platelet aggregation / enzyme-linked receptor protein signaling pathway / collagen binding / GPVI-mediated activation cascade ...collagen receptor activity / immune response-regulating signaling pathway / tetraspanin-enriched microdomain / collagen-activated tyrosine kinase receptor signaling pathway / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of platelet aggregation / enzyme-linked receptor protein signaling pathway / collagen binding / GPVI-mediated activation cascade / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / platelet activation / platelet aggregation / transmembrane signaling receptor activity / signaling receptor activity / membrane raft / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins ...: / 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
THIOCYANATE ION / Platelet glycoprotein VI
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsJandrot-Perrus, M. / Lebozec, K. / Rose, N. / Welin, M. / Billiald, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Blood Adv / Year: 2023
Title: Targeting platelet GPVI with glenzocimab: a novel mechanism for inhibition.
Authors: Billiald, P. / Slater, A. / Welin, M. / Clark, J.C. / Loyau, S. / Pugniere, M. / Jiacomini, I.G. / Rose, N. / Lebozec, K. / Toledano, E. / Francois, D. / Watson, S.P. / Jandrot-Perrus, M.
History
DepositionFeb 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Platelet glycoprotein VI
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,60812
Polymers70,9263
Non-polymers6829
Water14,034779
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.669, 93.195, 110.42
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 22570.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GP6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HCN6

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab heavy chain


Mass: 24250.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab light chain


Mass: 24105.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 788 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 % PEG 3350 0.2 M KSCN 0.1 M Bis-Tris propane pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→49.43 Å / Num. obs: 56379 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.995 / Rpim(I) all: 0.072 / Rrim(I) all: 0.265 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.95 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3695 / CC1/2: 0.598 / Rpim(I) all: 0.512 / Rrim(I) all: 1.851

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AZE,3GWK,5OU7

5aze

3gwk

5ou7


Resolution: 1.902→49.43 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 2780 -RANDOM
Rwork0.1862 ---
obs0.1885 56311 100 %-
Displacement parametersBiso mean: 22.87 Å2
Baniso -1Baniso -2Baniso -3
1-3.9176 Å20 Å20 Å2
2---0.5026 Å20 Å2
3----3.415 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.902→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 41 779 5539
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084990HARMONIC2
X-RAY DIFFRACTIONt_angle_deg16816HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1647SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes833HARMONIC5
X-RAY DIFFRACTIONt_it4990HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion649SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4825SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.03
X-RAY DIFFRACTIONt_other_torsion16.15
LS refinement shellResolution: 1.902→1.92 Å
RfactorNum. reflection% reflection
Rfree0.2527 61 -
Rwork0.2853 --
obs--97.82 %

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