3ALR | pdb_00003alr

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.208 (Depositor), 0.209 (DCC)
R-Value Work:
0.163 (Depositor), 0.189 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/embor.2010.155
Primary Citation 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.

Organizational Affiliation

Graduate School of Nanobioscience, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, Japan. hash@tsurumi.yokohama-cu.ac.jp

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q90WW1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth B] I [auth B] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.208 (Depositor), 0.209 (DCC)
R-Value Work: 0.163 (Depositor), 0.189 (DCC)
R-Value Observed: 0.165 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2011-02-02

Deposition Author(s):

Revision History (Full details and data files)

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