8H7J | pdb_00008h7j

The crystal structure of CD163 SRCR5-9

• PDB DOI: https://doi.org/10.2210/pdb8H7J/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Sus scrofa
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2022-10-20 Released: 2023-10-25 
• Deposition Author(s): Luo, Z.P., Li, R., Ma, H.F.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 

Literature

The crystal structure of CD163 SRCR5-9

Ma, H.F., Li, R., Luo, Z.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 62.86 kDa 
• Atom Count: 4,397 
• Modeled Residue Count: 555 
• Deposited Residue Count: 563 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scavenger receptor cysteine-rich type 1 protein M130	A	563	Sus scrofa	Mutation(s): 0  Gene Names: CD163, M130
UniProt
Find proteins for Q2VL90 (Sus scrofa) Explore Q2VL90  Go to UniProtKB:  Q2VL90
Glycosylation
Glycosylation Sites: 5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G64181RO GlyCosmos:  G64181RO GlyGen:  G64181RO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.328	α = 90
b = 60.085	β = 114.12
c = 85.424	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Luo, Z.P., Li, R., Ma, H.F.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary