Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.19 kDa 
• Atom Count: 1,177 
• Modelled Residue Count: 129 
• Deposited Residue Count: 158 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 1SI3

Crystal structure of the PAZ domain of human eIF2c1 in complex with a 9-mer siRNA-like duplex

• PDB DOI: 10.2210/pdb1SI3/pdb
• NDB: PR0112

• Classification: GENE REGULATION/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-02-27 Released: 2004-05-25 
• Deposition Author(s): Ye, K., Ma, J.B., Patel, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.304 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 

Literature

Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain.

Ma, J.B., Ye, K., Patel, D.J.

(2004) Nature 429: 318-322

• PubMed: 15152257 
• DOI: 10.1038/nature02519
• Primary Citation of Related Structures:  
  1SI2, 1SI3


• PubMed Abstract: 
  

Short RNAs mediate gene silencing, a process associated with virus resistance, developmental control and heterochromatin formation in eukaryotes. RNA silencing is initiated through Dicer-mediated processing of double-stranded RNA into small interfering RNA (siRNA). The siRNA guide strand associates with the Argonaute protein in silencing effector complexes, recognizes complementary sequences and targets them for silencing. The PAZ domain is an RNA-binding module found in Argonaute and some Dicer proteins and its structure has been determined in the free state. Here, we report the 2.6 A crystal structure of the PAZ domain from human Argonaute eIF2c1 bound to both ends of a 9-mer siRNA-like duplex. In a sequence-independent manner, PAZ anchors the 2-nucleotide 3' overhang of the siRNA-like duplex within a highly conserved binding pocket, and secures the duplex by binding the 7-nucleotide phosphodiester backbone of the overhang-containing strand and capping the 5'-terminal residue of the complementary strand. On the basis of the structure and on binding assays, we propose that PAZ might serve as an siRNA-end-binding module for siRNA transfer in the RNA silencing pathway, and as an anchoring site for the 3' end of guide RNA within silencing effector complexes.

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Organizational Affiliation: 

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York 10021, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2C 1	B [auth A]	149	Homo sapiens	Mutation(s): 3  Gene Names: EIF2C1, AGO1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL18 (Homo sapiens) Explore Q9UL18  Go to UniProtKB:  Q9UL18
PHAROS:  Q9UL18

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3'	A [auth B]	9	N/A

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	B [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.304 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.799	α = 90
b = 99.799	β = 90
c = 34.933	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): Ye, K., Ma, J.B., Patel, D.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance