3QB5 | pdb_00003qb5

Human C3PO complex in the presence of MnSO4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3QB5

This is version 1.2 of the entry. See complete history

Literature

Structure of C3PO and mechanism of human RISC activation.

Ye, X.Huang, N.Liu, Y.Paroo, Z.Huerta, C.Li, P.Chen, S.Liu, Q.Zhang, H.

(2011) Nat Struct Mol Biol 18: 650-657

  • DOI: https://doi.org/10.1038/nsmb.2032
  • Primary Citation Related Structures: 
    3PJA, 3QB5

  • PubMed Abstract: 

    Assembly of the RNA-induced silencing complex (RISC) consists of loading duplex (guide-passenger) siRNA onto Argonaute (Ago2) and removing the passenger strand. Ago2 contributes critically to RISC activation by nicking the passenger strand. Here we reconstituted duplex siRNA-initiated RISC activity using recombinant human Ago2 (hAgo2) and C3PO, indicating that C3PO has a critical role in hAgo2-RISC activation. Consistently, genetic depletion of C3PO compromised RNA silencing in mammalian cells. We determined the crystal structure of hC3PO, which reveals an asymmetric octamer barrel consisting of six translin and two TRAX subunits. This asymmetric assembly is critical for the function of C3PO as an endonuclease that cleaves RNA at the interior surface. The current work supports a Dicer-independent mechanism for human RISC activation, in which Ago2 directly binds duplex siRNA and nicks the passenger strand, and then C3PO activates RISC by degrading the Ago2-nicked passenger strand.


  • Organizational Affiliation
    • Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Macromolecule Content 

  • Total Structure Weight: 112.31 kDa 
  • Atom Count: 7,062 
  • Modeled Residue Count: 861 
  • Deposited Residue Count: 974 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Translin
A, B, C
228Homo sapiensMutation(s): 0 
Gene Names: TSN
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15631 (Homo sapiens)
Explore Q15631 
Go to UniProtKB:  Q15631
PHAROS:  Q15631
GTEx:  ENSG00000211460 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15631
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Translin-associated protein XD [auth K]290Homo sapiensMutation(s): 0 
Gene Names: TSNAXTRAX
UniProt & NIH Common Fund Data Resources
Find proteins for Q99598 (Homo sapiens)
Explore Q99598 
Go to UniProtKB:  Q99598
PHAROS:  Q99598
GTEx:  ENSG00000116918 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99598
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth K],
K
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4

Query on PO4



Download:Ideal Coordinates CCD File
F [auth C],
I [auth K]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN

Query on MN



Download:Ideal Coordinates CCD File
H [auth K]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.166α = 90
b = 98.166β = 90
c = 446.466γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description