2X04

Crystal structure of the PABC-TNRC6C complex

• PDB DOI: https://doi.org/10.2210/pdb2X04/pdb

• Classification: PEPTIDE/RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-04 Released: 2010-01-19 
• Deposition Author(s): Jinek, M., Fabian, M.R., Coyle, S.M., Sonenberg, N., Doudna, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.186 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Structural Insights Into the Human Gw182-Pabc Interaction in Microrna-Mediated Deadenylation

Jinek, M., Fabian, M.R., Coyle, S.M., Sonenberg, N., Doudna, J.A.

(2010) Nat Struct Mol Biol 17: 238

• PubMed: 20098421 
• DOI: https://doi.org/10.1038/nsmb.1768
• Primary Citation of Related Structures:  
  2X04


• PubMed Abstract: 
  

  GW182-family proteins are essential for microRNA-mediated translational repression and deadenylation in animal cells. Here we show that a conserved motif in the human GW182 paralog TNRC6C interacts with the C-terminal domain of polyadenylate binding protein 1 (PABC) and present the crystal structure of the complex. Mutations at the complex interface impair mRNA deadenylation in mammalian cell extracts, suggesting that the GW182-PABC interaction contributes to microRNA-mediated gene silencing.

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Organizational Affiliation: 

Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.57 kDa 
• Atom Count: 1,671 
• Modelled Residue Count: 186 
• Deposited Residue Count: 196 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYADENYLATE-BINDING PROTEIN 1	A, B	80	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P11940 (Homo sapiens) Explore P11940  Go to UniProtKB:  P11940
PHAROS:  P11940 GTEx:  ENSG00000070756

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRINUCLEOTIDE REPEAT-CONTAINING GENE 6C PROTEIN	C, D	18	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCJ0 (Homo sapiens) Explore Q9HCJ0  Go to UniProtKB:  Q9HCJ0
PHAROS:  Q9HCJ0 GTEx:  ENSG00000078687

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.186 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.11	α = 90
b = 72.23	β = 119.76
c = 37.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Jinek, M., Fabian, M.R., Coyle, S.M., Sonenberg, N., Doudna, J.A.

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other