2W42 | pdb_00002w42

THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT DNA DUPLEX.

• PDB DOI: https://doi.org/10.2210/pdb2W42/pdb
• NAKB: 2W42

• Classification: PROTEIN/DNA COMPLEX
• Organism(s): Archaeoglobus fulgidus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-11-19 Released: 2008-12-09 
• Deposition Author(s): Parker, J.S., Roe, S.M., Barford, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Enhancement of the Seed-Target Recognition Step in RNA Silencing by a Piwi-Mid Domain Protein

Parker, J.S., Parizotto, E.A., Wang, M., Roe, S.M., Barford, D.

(2009) Mol Cell 33: 204

• PubMed: 19187762 
• DOI: https://doi.org/10.1016/j.molcel.2008.12.012
• Primary Citation Related Structures: 
  2W42


• PubMed Abstract: 
  

  Target recognition in RNA silencing is governed by the "seed sequence" of a guide RNA strand associated with the PIWI/MID domain of an Argonaute protein in RISC. Using a reconstituted in vitro target recognition system, we show that a model PIWI/MID domain protein confers position-dependent tightening and loosening of guide-strand-target interactions. Over the seed sequence, the interaction affinity is enhanced up to approximately 300-fold. Enhancement is achieved through a reduced entropy penalty for the interaction. In contrast, interactions 3' of the seed are inhibited. We quantified mismatched target recognition inside and outside the seed, revealing amplified discrimination at the third position in the seed mediated by the PIWI/MID domain. Thus, association of the guide strand with the PIWI/MID domain generates an enhanced affinity anchor site over the seed that can promote fidelity in target recognition and stabilize and guide the assembly of the active silencing complex.

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Organizational Affiliation: 
• Institute of Cancer Research, Chester Beatty Laboratories, London, UK. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 108.4 kDa 
• Atom Count: 7,235 
• Modeled Residue Count: 806 
• Deposited Residue Count: 886 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE UNCHARACTERIZED PROTEIN	A, B	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*CP*GP*AP*CP*GP*CP)-3'	C [auth P], E [auth R]	8	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*CP*GP*AP*AP*TP*TP)-3'	D [auth Q], F [auth S]	8	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	G [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.838	α = 75.8
b = 61.384	β = 75.86
c = 103.54	γ = 79.47

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Parker, J.S., Roe, S.M., Barford, D.

Revision History  

• Version 1.0: 2008-12-09
  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: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description