5F7H

Human T-cell immunoglobulin and mucin domain protein 4 (hTIM-4) complex with phosphoserine

• PDB DOI: https://doi.org/10.2210/pdb5F7H/pdb

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


• Deposited: 2015-12-08 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.278 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77.36 kDa 
• Atom Count: 5,468 
• Modelled Residue Count: 674 
• Deposited Residue Count: 678 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell immunoglobulin and mucin domain-containing protein 4	A [auth B], B [auth A], C, D, E, F	113	Homo sapiens	Mutation(s): 0  Gene Names: TIMD4, TIM4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96H15 (Homo sapiens) Explore Q96H15  Go to UniProtKB:  Q96H15
PHAROS:  Q96H15 GTEx:  ENSG00000145850

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SEP	H [auth B], J [auth A], L [auth C], N [auth D], P [auth E], R [auth F]	PHOSPHOSERINE C3 H8 N O6 P BZQFBWGGLXLEPQ-REOHCLBHSA-N
CA	G [auth B], I [auth A], K [auth C], M [auth D], O [auth E], Q [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.278 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.444	α = 90
b = 65.034	β = 108.55
c = 68.851	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

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Gao, G.F., Lu, G., Wang, H., Qi, J.

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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  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description