7NUI | pdb_00007nui

Crystal structure of HLA-B*08:01 in complex with ELRSRYWAI viral peptide

• PDB DOI: https://doi.org/10.2210/pdb7NUI/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens, Influenza A virus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-03-12 Released: 2021-04-14 
• Deposition Author(s): Mavridis, G., Giastas, P., Mpakali, A.
• Funding Organization(s): Hellenic Foundation for Research and Innovation (HFRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HLA-B*08:01 in complex with ELRSRYWAI viral peptide

Mavridis, G.

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)

Macromolecule Content 

• Total Structure Weight: 45.36 kDa 
• Atom Count: 3,260 
• Modeled Residue Count: 384 
• Deposited Residue Count: 385 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA-B*08:01 heavy chain	A	276	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GLU-LEU-ARG-SER-ARG-TYR-TRP-ALA-ILE	C [auth D]	9	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)) Explore Q9Q0U8  Go to UniProtKB:  Q9Q0U8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.236	α = 90
b = 40.206	β = 101.53
c = 125.978	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Mavridis, G., Giastas, P., Mpakali, A.

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Funding Organization	Location	Grant Number
Hellenic Foundation for Research and Innovation (HFRI)	Greece	157

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary