5EIV

Crystal structure of complex of osteoclast-associated immunoglobulin-like receptor (OSCAR) and a synthetic collagen consensus peptide

• PDB DOI: https://doi.org/10.2210/pdb5EIV/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2015-10-30 Released: 2015-11-25 
• Deposition Author(s): Zhou, L., Blaszczyk, M., Chirgadze, D., Bihan, D., Farndale, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.220 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A6B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 59.01 kDa 
• Atom Count: 4,106 
• Modelled Residue Count: 504 
• Deposited Residue Count: 553 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Osteoclast-associated immunoglobulin-like receptor	A, B	203	Homo sapiens	Mutation(s): 1  Gene Names: OSCAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYS5 (Homo sapiens) Explore Q8IYS5  Go to UniProtKB:  Q8IYS5
PHAROS:  Q8IYS5 GTEx:  ENSG00000170909

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-PRO-HYP-GLY-PRO-HYP-GLY-PRO-HYP-GLY-PRO-ALA-GLY-PHE-HYP-GLY-PRO-HYP-GLY-PRO-HYP	C, D, E, F, G, H	21	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PRO-GLY-PRO-PRO-GLY-PRO-PRO	I, J, K	7	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth A], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	M [auth A], Q [auth B], S [auth B], U [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	V [auth F]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	N [auth A], O [auth A], W [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	R [auth B], T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.220 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.707	α = 90
b = 136.585	β = 90.05
c = 70.584	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Zhou, L., Blaszczyk, M., Chirgadze, D., Bihan, D., Farndale, R.W.

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2016-02-17
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Refinement description, Structure summary