3ALR

Crystal structure of Nanos

• PDB DOI: https://doi.org/10.2210/pdb3ALR/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-06 Released: 2011-02-02 
• Deposition Author(s): Hashimoto, H., Hara, K., Hishiki, A., Kawaguchi, S., Shichijo, N., Nakamura, K., Unzai, S., Tamaru, Y., Shimizu, T., Sato, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.208 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Crystal structure of zinc-finger domain of Nanos and its functional implications

Hashimoto, H., Hara, K., Hishiki, A., Kawaguchi, S., Shichijo, N., Nakamura, K., Unzai, S., Tamaru, Y., Shimizu, T., Sato, M.

(2010) EMBO Rep 11: 848-853

• PubMed: 20948543 
• DOI: https://doi.org/10.1038/embor.2010.155
• Primary Citation of Related Structures:  
  3ALR


• PubMed Abstract: 
  

  Nanos is an RNA-binding protein that is involved in the development and maintenance of germ cells. In combination with Pumilio, Nanos binds to the 3' untranslated region of a messenger RNA and represses its translation. Nanos has two conserved Cys-Cys-His-Cys zinc-finger motifs that are indispensable for its function. In this study, we have determined the crystal structure of the zinc-finger domain of zebrafish Nanos, for the first time revealing that Nanos adopts a novel zinc-finger structure. In addition, Nanos has a conserved basic surface that is directly involved in RNA binding. Our results provide the structural basis for further studies to clarify Nanos function.

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Organizational Affiliation: 

Graduate School of Nanobioscience, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47.29 kDa 
• Atom Count: 2,105 
• Modelled Residue Count: 250 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanos protein	A, B, C, D	106	Danio rerio	Mutation(s): 0  Gene Names: nanos
UniProt
Find proteins for Q90WW1 (Danio rerio) Explore Q90WW1  Go to UniProtKB:  Q90WW1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth C], K [auth C], L [auth D], M [auth D], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.208 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.961	α = 90
b = 100.961	β = 90
c = 71.577	γ = 120

Software Package:

Software Name	Purpose
SERGUI	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-02 
Deposition Author(s): Hashimoto, H., Hara, K., Hishiki, A., Kawaguchi, S., Shichijo, N., Nakamura, K., Unzai, S., Tamaru, Y., Shimizu, T., Sato, M.

Revision History  

• Version 1.0: 2011-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.3: 2024-03-13
  Changes: Advisory, Data collection, Database references, Derived calculations