Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.09 kDa 
• Atom Count: 5259 
• Modelled Residue Count: 612 
• Deposited Residue Count: 622 
• Unique protein chains: 4

1SJH

HLA-DR1 complexed with a 13 residue HIV capsid peptide

• DOI: 10.2210/pdb1SJH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct, Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-03-03 Released: 2004-08-17 
• Deposition Author(s): Zavala-Ruiz, Z., Strug, I., Walker, B.D., Norris, P.J., Stern, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.245 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

A hairpin turn in a class II MHC-bound peptide orients residues outside the binding groove for T cell recognition.

Zavala-Ruiz, Z., Strug, I., Walker, B.D., Norris, P.J., Stern, L.J.

(2004) Proc Natl Acad Sci U S A 101: 13279-13284

• PubMed: 15331779 
• DOI: 10.1073/pnas.0403371101
• Primary Citation of Related Structures:  
  1SJE, 1SJH


• PubMed Abstract: 
  

T cells generally recognize peptide antigens bound to MHC proteins through contacts with residues found within or immediately flanking the seven- to nine-residue sequence accommodated in the MHC peptide-binding groove. However, some T cells require peptide residues outside this region for activation, the structural basis for which is unknown. Here, we have investigated a HIV Gag-specific T cell clone that requires an unusually long peptide antigen for activation. The crystal structure of a minimally antigenic 16-mer bound to HLA-DR1 shows that the peptide C-terminal region bends sharply into a hairpin turn as it exits the binding site, orienting peptide residues outside the MHC-binding region in position to interact with a T cell receptor. Peptide truncation and substitution studies show that both the hairpin turn and the extreme C-terminal residues are required for T cell activation. These results demonstrate a previously unrecognized mode of MHC-peptide-T cell receptor interaction.

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Organizational Affiliation: 

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A	180	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DRB1-1 beta chain	B	190	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
NIH Common Fund Data Resources
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GAG polyprotein	C	13	synthetic construct	Mutation(s): 0
Find proteins for P12495 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)) Explore P12495  Go to UniProtKB:  P12495

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterotoxin type C-3	D	239	Staphylococcus aureus	Mutation(s): 4  Gene Names: entC3, SAV2009, SA1817
Find proteins for P0A0L5 (Staphylococcus aureus) Explore P0A0L5  Go to UniProtKB:  P0A0L5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.245 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.464	α = 90
b = 172.464	β = 90
c = 121.461	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-03 
• Released Date: 2004-08-17 
Deposition Author(s): Zavala-Ruiz, Z., Strug, I., Walker, B.D., Norris, P.J., Stern, L.J.

Revision History  

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-04-04
  Changes: Data collection
• Version 1.5: 2020-02-05
  Changes: Derived calculations, Source and taxonomy