3ZGQ | pdb_00003zgq

Crystal structure of human interferon-induced protein IFIT5

• PDB DOI: https://doi.org/10.2210/pdb3ZGQ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-19 Released: 2013-01-23 
• Deposition Author(s): Katibah, G.E., Lee, H.J., Huizar, J.P., Vogan, J.M., Alber, T., Collins, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.178 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

TRNA Binding, Structure, and Localization of the Human Interferon-Induced Protein Ifit5.

Katibah, G.E., Lee, H.J., Huizar, J.P., Vogan, J.M., Alber, T., Collins, K.

(2013) Mol Cell 49: 743

• PubMed: 23317505 
• DOI: https://doi.org/10.1016/j.molcel.2012.12.015
• Primary Citation Related Structures: 
  3ZGQ


• PubMed Abstract: 
  

  Interferon-induced proteins, including the largely uncharacterized interferon-induced tetratricopeptide repeat (IFIT) protein family, provide defenses against pathogens. Differing from expectations for tetratricopeptide repeat (TPR) proteins and from human IFIT1, IFIT2, and IFIT3, we show that human IFIT5 recognizes cellular RNA instead of protein partners. In vivo and in vitro, IFIT5 bound to endogenous 5'-phosphate-capped RNAs, including transfer RNAs. The crystal structure of IFIT5 revealed a convoluted intramolecular packing of eight TPRs as a fold that we name the TPR eddy. Additional, non-TPR structural elements contribute to an RNA binding cleft. Instead of general cytoplasmic distribution, IFIT5 concentrated in actin-rich protrusions from the apical cell surface colocalized with the RNA-binding retinoic acid-inducible gene-I (RIG-I). These findings establish compartmentalized cellular RNA binding activity as a mechanism for IFIT5 function and reveal the TPR eddy as a scaffold for RNA recognition.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.04 kDa 
• Atom Count: 4,152 
• Modeled Residue Count: 475 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERFERON-INDUCED PROTEIN WITH TETRATRICOPEPTIDE REPEATS 5	A	482	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13325 (Homo sapiens) Explore Q13325  Go to UniProtKB:  Q13325
PHAROS:  Q13325 GTEx:  ENSG00000152778

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.178 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.833	α = 90
b = 71.793	β = 90
c = 116.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Katibah, G.E., Lee, H.J., Huizar, J.P., Vogan, J.M., Alber, T., Collins, K.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-03-06
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary