5F70 | pdb_00005f70

Crystal structures of human TIM members

PDB DOI: https://doi.org/10.2210/pdb5F70/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2015-12-07 Released: 2016-02-03
Deposition Author(s): Gao, G.F., Lu, G., Wang, H., Qi, J.
Funding Organization(s): National Natural Science foundation of China, Strategic Priority Research Program of the Chinese Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.259 (Depositor), 0.257 (DCC)
R-Value Work:
0.197 (Depositor), 0.193 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5F70

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

Literature

Crystal structures of human TIM members: Ebolavirus entry-enhancing receptors

Wang, H., Qi, J.X., Liu, N.N.

(2015) Chin Sci Bull 60: 3438-3453

DOI: https://doi.org/10.1360/N972015-01255

Macromolecule Content

Total Structure Weight: 11.4 kDa
Atom Count: 881
Modeled Residue Count: 103
Deposited Residue Count: 103
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatitis A virus cellular receptor 1	A	103	Homo sapiens	Mutation(s): 0 Gene Names: TIMD1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96D42 (Homo sapiens) Explore Q96D42 Go to UniProtKB: Q96D42
PHAROS: Q96D42 GTEx: ENSG00000113249
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96D42
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.259 (Depositor), 0.257 (DCC)
R-Value Work: 0.197 (Depositor), 0.193 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.787	α = 90
b = 33.773	β = 90
c = 86.875	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data processing
SCALEPACK	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement
HKL-2000	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-02-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science foundation of China	China	81590761
Strategic Priority Research Program of the Chinese Academy of Sciences	China	XDB08020100

Revision History (Full details and data files)

Version 1.0: 2016-02-03
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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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.