5OU9 | pdb_00005ou9

Crystal structure of Glycoprotein VI in complex with collagen-peptide (GPO)3

• PDB DOI: https://doi.org/10.2210/pdb5OU9/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-08-23 Released: 2018-09-05 
• Deposition Author(s): Feitsma, L.J., Huizinga, E.G.
• Funding Organization(s): Netherlands Organization for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Structural insights into collagen-binding by platelet receptor Glycoprotein VI

Feitsma, L.J., Brondijk, T.H.C., Jarvis, G., Hagemans, D., Bihan, D., Jerah, N., Versteeg, M., Farndale, R.W., Huizinga, E.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.78 kDa 
• Atom Count: 3,203 
• Modeled Residue Count: 411 
• Deposited Residue Count: 425 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet glycoprotein VI	A, B	181	Homo sapiens	Mutation(s): 0  Gene Names: GP6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCN6 (Homo sapiens) Explore Q9HCN6  Go to UniProtKB:  Q9HCN6
PHAROS:  Q9HCN6 GTEx:  ENSG00000088053
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q9HCN6-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
(GPO)3	C, D, E	21	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02452 (Homo sapiens) Explore P02452  Go to UniProtKB:  P02452
PHAROS:  P02452 GTEx:  ENSG00000108821

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	G [auth A], J [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
CL	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	C, D, E	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.72	α = 90
b = 59.72	β = 90
c = 319.72	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Feitsma, L.J., Huizinga, E.G.

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Funding Organization	Location	Grant Number
Netherlands Organization for Scientific Research	Netherlands	ECHO 700.58.006

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary