7FI5

Crystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D

• PDB DOI: https://doi.org/10.2210/pdb7FI5/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-07-30 Released: 2022-08-31 
• Deposition Author(s): Cai, W., Peng, S., Xu, T., Tian, Y., Li, Y., Liu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.258 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Crystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D

Cai, W., Peng, S., Xu, T., Tian, Y., Li, Y., Liu, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 64.31 kDa 
• Atom Count: 4,247 
• Modelled Residue Count: 518 
• Deposited Residue Count: 553 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NKG2-D type II integral membrane protein	A, B	139	Homo sapiens	Mutation(s): 0  Gene Names: KLRK1, D12S2489E, NKG2D
UniProt & NIH Common Fund Data Resources
Find proteins for P26718 (Homo sapiens) Explore P26718  Go to UniProtKB:  P26718
PHAROS:  P26718 GTEx:  ENSG00000213809

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I polypeptide-related sequence A	C	275	Homo sapiens	Mutation(s): 5  Gene Names: MICA, PERB11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q29983 (Homo sapiens) Explore Q29983  Go to UniProtKB:  Q29983
PHAROS:  Q29983

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.258 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.379	α = 90
b = 123.379	β = 90
c = 180.834	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Cai, W., Peng, S., Xu, T., Tian, Y., Li, Y., Liu, J.

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary