Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 18956.06 
• Atom Count: 1163 
• Residue Count: 138 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3O3I

Crystal Structure of human Hiwi1 PAZ domain (residues 277-399) in complex with 14-mer RNA (12-bp + 2-nt overhang) containing 2'-OH at its 3'-end

• DOI: 10.2210/pdb3O3I/pdb
• NDB: NA0639

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2010-07-24 Released: 2011-01-12 
• Deposition Author(s): Tian, Y., Simanshu, D.K., Ma, J.-B., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.801 Å
• R-Value Free: 0.297 
• R-Value Work: 0.243 

Literature

Inaugural Article: Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains.

Tian, Y., Simanshu, D.K., Ma, J.B., Patel, D.J.

(2011) Proc.Natl.Acad.Sci.USA 108: 903-910

• PubMed: 21193640 
• DOI: 10.1073/pnas.1017762108
• Primary Citation of Related Structures:  
  3O7X, 3O7V, 3O6E


• PubMed Abstract: 
  

Argonaute and Piwi proteins are key players in the RNA silencing pathway, with the former interacting with micro-RNAs (miRNAs) and siRNAs, whereas the latter targets piwi-interacting RNAs (piRNAs) that are 2'-O-methylated (2(')-OCH(3)) at their 3' ends. Germline-specific piRNAs and Piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. Humans contain four Piwi family proteins designated Hiwi1, Hiwi2, Hiwi3, and Hili. We report on the structures of Hili-PAZ (Piwi/Argonaute/Zwille) domain in the free state and Hiwi1 PAZ domain bound to self-complementary 14-mer RNAs (12-bp + 2-nt overhang) containing 2(')-OCH(3) and 2'-OH at their 3' ends. These structures explain the molecular basis underlying accommodation of the 2(')-OCH(3) group within a preformed Hiwi1 PAZ domain binding pocket, whose hydrophobic characteristics account for the preferential binding of 2(')-OCH(3) over 2'-OH 3' ends. These results contrast with the more restricted binding pocket for the human Ago1 PAZ domain, which exhibits a reverse order, with preferential binding of 2'-OH over 2(')-OCH(3) 3' ends.

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Organizational Affiliation: 

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Piwi-like protein 1	X	124	Homo sapiens	Mutation(s): 0  Gene Names: PIWIL1 (HIWI) EC: 3.1.26.-
Find proteins for Q96J94 (Homo sapiens) Go to Gene View: PIWIL1 Go to UniProtKB:  Q96J94

Entity ID: 2
Molecule	Chains	Length	Organism
RNA (5'-R(*GP*CP*GP*AP*AP*UP*AP*UP*UP*CP*GP*CP*UP*U)-3')	A	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.801 Å
• R-Value Free: 0.297 
• R-Value Work: 0.243 
• Space Group: P 4₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 44.303	α = 90.00
b = 44.303	β = 90.00
c = 147.707	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
HKL-2000	data reduction
DENZO	data reduction
REFMAC	refinement
ADSC	data collection
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-24 
• Released Date: 2011-01-12 
• Deposition Author(s): Tian, Y., Simanshu, D.K., Ma, J.-B., Patel, D.J.

Revision History 

• Version 1.0: 2011-01-12
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-11-08
  Type: Refinement description