7K80

KIR3DL1*001 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide

• PDB DOI: https://doi.org/10.2210/pdb7K80/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21, Homo sapiens
• Mutation(s): No 


• Deposited: 2020-09-24 Released: 2020-12-09 
• Deposition Author(s): MacLachlan, B.J., Rossjohn, J., Vivian, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 157 kDa 
• Atom Count: 11,001 
• Modelled Residue Count: 1,333 
• Deposited Residue Count: 1,366 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A5H2UYS3 (Homo sapiens) Explore A0A5H2UYS3  Go to UniProtKB:  A0A5H2UYS3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	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
ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP	C, F	8	synthetic construct	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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Killer cell immunoglobulin-like receptor 3DL1	G, H	299	Homo sapiens	Mutation(s): 0  Gene Names: KIR3DL1, CD158E, NKAT3, NKB1
UniProt & NIH Common Fund Data Resources
Find proteins for P43629 (Homo sapiens) Explore P43629  Go to UniProtKB:  P43629
PHAROS:  P43629 GTEx:  ENSG00000167633

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	O [auth G], P [auth G], Q [auth G], R [auth H], S [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACT	J [auth A], K [auth D], L [auth D], M [auth E], N [auth E]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	I [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.265	α = 82.47
b = 85.017	β = 85.97
c = 94.832	γ = 77.92

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): MacLachlan, B.J., Rossjohn, J., Vivian, J.P.

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references
• Version 1.2: 2021-02-17
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description