6LF9

Crystal structure of pSLA-1*1301 complex with dodecapeptide RVEDVTNTAEYW

• PDB DOI: https://doi.org/10.2210/pdb6LF9/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Sus scrofa, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-11-30 Released: 2021-03-17 
• Deposition Author(s): Wei, X.H., Wang, S., Zhang, N.Z., Xia, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

Peptidomes and Structures Illustrate How SLA-I Micropolymorphism Influences the Preference of Binding Peptide Length.

Wei, X.H., Wang, S., Zhang, N.Z., Xia, C.

(2022) Front Immunol 

• DOI: https://doi.org/10.3389/fimmu.2022.820881

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)

Biological Assembly 3  

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

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

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 176.49 kDa 
• Atom Count: 12,718 
• Modelled Residue Count: 1,528 
• Deposited Residue Count: 1,528 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A [auth D], D [auth A], G, J	273	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for B1PJU7 (Sus scrofa) Explore B1PJU7  Go to UniProtKB:  B1PJU7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B [auth E], E [auth B], H, K	97	Sus scrofa	Mutation(s): 0  Gene Names: B2M
UniProt
Find proteins for Q07717 (Sus scrofa) Explore Q07717  Go to UniProtKB:  Q07717

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP	C [auth F], F [auth C], I, L	12	synthetic construct	Mutation(s): 0
UniProt
Find proteins for P16082 (Equine infectious anemia virus (strain WSU5)) Explore P16082  Go to UniProtKB:  P16082

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.169	α = 90
b = 44.24	β = 90.03
c = 199.631	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Wei, X.H., Wang, S., Zhang, N.Z., Xia, C.

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2022-03-23
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary