Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 49.96 kDa 
• Atom Count: 3482 
• Modelled Residue Count: 398 
• Deposited Residue Count: 427 
• Unique protein chains: 1

1W9H

The Structure of a Piwi protein from Archaeoglobus fulgidus.

• PDB DOI: 10.2210/pdb1W9H/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-10-13 Released: 2005-01-13 
• Deposition Author(s): Parker, J.S., Roe, S.M., Barford, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.237 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Crystal Structure of a Piwi Protein Suggests Mechanisms for Sirna Recognition and Slicer Activity

Parker, J.S., Roe, S.M., Barford, D.

(2004) EMBO J 23: 4727

• PubMed: 15565169 
• DOI: 10.1038/sj.emboj.7600488
• Primary Citation of Related Structures:  
  1W9H


• PubMed Abstract: 
  

RNA silencing regulates gene expression through mRNA degradation, translation repression and chromatin remodelling. The fundamental engines of RNA silencing are RISC and RITS complexes, whose common components are 21-25 nt RNA and an Argonaute protein containing a PIWI domain of unknown function. The crystal structure of an archaeal Piwi protein (AfPiwi) is organised into two domains, one resembling the sugar-binding portion of the lac repressor and another with similarity to RNase H. Invariant residues and a coordinated metal ion lie in a pocket that surrounds the conserved C-terminus of the protein, defining a key functional region in the PIWI domain. Furthermore, two Asp residues, conserved in the majority of Argonaute sequences, align spatially with the catalytic Asp residues of RNase H-like catalytic sites, suggesting that in eukaryotic Argonaute proteins the RNase H-like domain may possess nuclease activity. The conserved region around the C-terminus of the PIWI domain, which is required for small interfering RNA (siRNA) binding to AfPiwi, may function as the receptor site for the obligatory 5' phosphate of siRNAs, thereby specifying the cleavage position of the target mRNA.

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Organizational Affiliation: 

Section of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, London, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL PROTEIN AF1318	A	427	Archaeoglobus fulgidus	Mutation(s): 0
UniProt
Find proteins for O28951 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28951  Go to UniProtKB:  O28951

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
NI	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	I [auth A], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.237 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.09	α = 90
b = 137.863	β = 90
c = 51.663	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SnB	phasing
SHARP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-13 
• Released Date: 2005-01-13 
Deposition Author(s): Parker, J.S., Roe, S.M., Barford, D.

Revision History  

• Version 1.0: 2005-01-13
  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: 2017-07-05
  Changes: Refinement description