4I0P

HLA-DO in complex with HLA-DM

• PDB DOI: https://doi.org/10.2210/pdb4I0P/pdb
• Entry: 4I0P supersedes: 3USA

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2012-11-18 Released: 2012-12-26 
• Deposition Author(s): Guce, A.I., Mortimer, S.E., Stern, L.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 172.08 kDa 
• Atom Count: 12,064 
• Modelled Residue Count: 1,488 
• Deposited Residue Count: 1,498 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA-DMA protein	A, E	188	Homo sapiens	Mutation(s): 0  Gene Names: 3108, HLA-DMA
UniProt
Find proteins for Q6ICR9 (Homo sapiens) Explore Q6ICR9  Go to UniProtKB:  Q6ICR9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DM beta chain	B, F	191	Homo sapiens	Mutation(s): 0  Gene Names: 3109, DMB, HLA-DMB, RING7
UniProt & NIH Common Fund Data Resources
Find proteins for P28068 (Homo sapiens) Explore P28068  Go to UniProtKB:  P28068
PHAROS:  P28068 GTEx:  ENSG00000242574

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DO alpha chain	C, G	181	Homo sapiens	Mutation(s): 0  Gene Names: 3111, HLA-DNA, HLA-DOA, HLA-DZA
UniProt & NIH Common Fund Data Resources
Find proteins for P06340 (Homo sapiens) Explore P06340  Go to UniProtKB:  P06340
PHAROS:  P06340 GTEx:  ENSG00000204252

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DO beta chain	D, H	189	Homo sapiens	Mutation(s): 0  Gene Names: 3112, HLA-DOB
UniProt & NIH Common Fund Data Resources
Find proteins for P13765 (Homo sapiens) Explore P13765  Go to UniProtKB:  P13765
PHAROS:  P13765 GTEx:  ENSG00000241106

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth C], K [auth D], M [auth E], O [auth G], P [auth G], Q [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE	R [auth H]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	L [auth D], N [auth F], T [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	S [auth H]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.26	α = 90
b = 147.1	β = 106.49
c = 95.959	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Guce, A.I., Mortimer, S.E., Stern, L.J.
• This entry supersedes: 3USA

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2013-01-16
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary