5DZO

Crystal structure of human T-cell immunoglobulin and mucin domain protein 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.301 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

TIM-1 acts a dual-attachment receptor for Ebolavirus by interacting directly with viral GP and the PS on the viral envelope.

Yuan, S.Cao, L.Ling, H.Dang, M.Sun, Y.Zhang, X.Chen, Y.Zhang, L.Su, D.Wang, X.Rao, Z.

(2015) Protein Cell 6: 814-824

  • DOI: 10.1007/s13238-015-0220-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ebolavirus can cause hemorrhagic fever in humans with a mortality rate of 50%-90%. Currently, no approved vaccines and antiviral therapies are available. Human TIM1 is considered as an attachment factor for EBOV, enhancing viral infection through int ...

    Ebolavirus can cause hemorrhagic fever in humans with a mortality rate of 50%-90%. Currently, no approved vaccines and antiviral therapies are available. Human TIM1 is considered as an attachment factor for EBOV, enhancing viral infection through interaction with PS located on the viral envelope. However, reasons underlying the preferable usage of hTIM-1, but not other PS binding receptors by filovirus, remain unknown. We firstly demonstrated a direct interaction between hTIM-1 and EBOV GP in vitro and determined the crystal structures of the Ig V domains of hTIM-1 and hTIM-4. The binding region in hTIM-1 to EBOV GP was mapped by chimeras and mutation assays, which were designed based on structural analysis. Pseudovirion infection assays performed using hTIM-1 and its homologs as well as point mutants verified the location of the GP binding site and the importance of EBOV GP-hTIM-1 interaction in EBOV cellular entry.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hepatitis A virus cellular receptor 1
A
107Homo sapiensMutation(s): 0 
Gene Names: HAVCR1 (KIM1, TIM1, TIMD1)
Find proteins for Q96D42 (Homo sapiens)
Go to Gene View: HAVCR1
Go to UniProtKB:  Q96D42
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.301 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.157 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 50.739α = 90.00
b = 50.739β = 90.00
c = 84.162γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology 973 ProjectChina2014CB542800

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-02-10
    Type: Database references