7FI8 | pdb_00007fi8

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

PDB DOI: https://doi.org/10.2210/pdb7FI8/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.267 (Depositor), 0.262 (DCC)
R-Value Work:
0.204 (Depositor), 0.207 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7FI8

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 64.05 kDa
Atom Count: 4,150
Modeled Residue Count: 510
Deposited Residue Count: 553
Unique protein chains: 2

Macromolecules

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26718
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q29983
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.267 (Depositor), 0.262 (DCC)
R-Value Work: 0.204 (Depositor), 0.207 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.481	α = 90
b = 121.481	β = 90
c = 102.063	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2022-08-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-08-31
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.