6CQJ

Crystal structure of DR1 presenting the RQ13 peptide

• PDB DOI: https://doi.org/10.2210/pdb6CQJ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, HIV-1 M:B_HXB2R
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-03-15 Released: 2018-06-06 
• Deposition Author(s): Farenc, C., Gras, S., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.249 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 135.97 kDa 
• Atom Count: 9,642 
• Modelled Residue Count: 1,125 
• Deposited Residue Count: 1,152 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A, D, G	182	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DRB1-1 beta chain	B, E, H	189	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Capsid protein p24	C, F, I	13	HIV-1 M:B_HXB2R	Mutation(s): 0
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth A], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	K [auth A], M [auth B], P [auth E], Q [auth G]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	N [auth D], R [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017	J	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.249 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.684	α = 61.56
b = 82.017	β = 88.2
c = 83.05	γ = 86.47

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Farenc, C., Gras, S., Rossjohn, J.

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2018-06-27
  Changes: Data collection, Database references, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary