4WU7 | pdb_00004wu7

HLA-A24 in complex with HIV-1 Nef134-8(2F)

• PDB DOI: https://doi.org/10.2210/pdb4WU7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-31 Released: 2015-05-06 
• Deposition Author(s): Shimizu, A., Yamagata, A., Fukai, S., Iwamoto, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.287 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Nef134-8 epitope presented by HLA-A24

Kato, J., Kawana, A., Shimizu, A., Zhu, D., Han, C., Nakamura, H., Koibuchi, T., Sato, Y., Yamagata, A., Fukai, S., Gao, G.F., Brumme, Z.L., Iwamoto, A.

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 2  

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

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

Macromolecule Content 

• Total Structure Weight: 88.91 kDa 
• Atom Count: 6,477 
• Modeled Residue Count: 762 
• Deposited Residue Count: 764 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-24 alpha chain	A, D	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	99	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
8-Mer peptide from Protein Nef	C, F	8	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04601 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04601  Go to UniProtKB:  P04601

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.287 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.714	α = 90
b = 87.02	β = 90
c = 152.227	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data reduction
MOLREP	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Shimizu, A., Yamagata, A., Fukai, S., Iwamoto, A.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary