7KEI | pdb_00007kei

DQA1*01:02/DQB1*06:02 in complex with a hemagglutinin peptide from the H1N1 pandemic flu virus.

• PDB DOI: https://doi.org/10.2210/pdb7KEI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, H1N1 subtype
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2020-10-10 Released: 2021-10-13 
• Deposition Author(s): Birtley, J.R., Stern, L.J., Mellins, E.D., Jiang, W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DQA1*01:02/DQB1*06:02 in complex with a flu peptide.

Birtley, J.R., Stern, L.J., Mellins, E.D., Jiang, W.

To be published.

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

Macromolecule Content 

• Total Structure Weight: 50.92 kDa 
• Atom Count: 3,761 
• Modeled Residue Count: 382 
• Deposited Residue Count: 441 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II HLA-DQ-alpha chain	A	206	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQA1
UniProt
Find proteins for Q30066 (Homo sapiens) Explore Q30066  Go to UniProtKB:  Q30066
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DQ beta 1 chain	B	210	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SU54 (Homo sapiens) Explore Q5SU54  Go to UniProtKB:  Q5SU54
GTEx:  ENSG00000179344

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HA peptide from 2009 H1N1 pandemic flu virus.	C	25	H1N1 subtype	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-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	D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth H]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.31	α = 90
b = 58.255	β = 96.08
c = 67.507	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): Birtley, J.R., Stern, L.J., Mellins, E.D., Jiang, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5 U01 AI101990

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary