[English] 日本語
Yorodumi
- PDB-2rre: Structure and function of the N-terminal nucleolin binding domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rre
TitleStructure and function of the N-terminal nucleolin binding domain of nuclear valocine containing protein like 2 (NVL2) harboring a nucleolar localization signal
ComponentsPutative uncharacterized protein
KeywordsNUCLEAR PROTEIN / nucleolar localization signal / RNA binding / alternatively spliced domain
Function / homology
Function and homology information


regulation of protein localization to nucleolus / nuclear exosome (RNase complex) / preribosome binding / telomerase holoenzyme complex / positive regulation of telomerase activity / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / positive regulation of protein binding / nucleolus ...regulation of protein localization to nucleolus / nuclear exosome (RNase complex) / preribosome binding / telomerase holoenzyme complex / positive regulation of telomerase activity / ribosomal large subunit biogenesis / rRNA processing / ribosome biogenesis / positive regulation of protein binding / nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Arc Repressor Mutant, subunit A - #2010 / NVL2, nucleolin binding domain / NVL2, N-terminal domain superfamily / Nucleolin binding domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...Arc Repressor Mutant, subunit A - #2010 / NVL2, nucleolin binding domain / NVL2, N-terminal domain superfamily / Nucleolin binding domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Arc Repressor Mutant, subunit A / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleolin_bd domain-containing protein / Nuclear valosin-containing protein-like
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 5
AuthorsFujiwara, Y. / Fujiwara, K. / Goda, N. / Iwaya, N. / Tenno, T. / Shirakawa, M. / Hiroaki, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and function of the N-terminal nucleolin binding domain of nuclear valosin-containing protein-like 2 (NVL2) harboring a nucleolar localization signal
Authors: Fujiwara, Y. / Fujiwara, K. / Goda, N. / Iwaya, N. / Tenno, T. / Shirakawa, M. / Hiroaki, H.
History
DepositionAug 3, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)9,1091
Polymers9,1091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Putative uncharacterized protein / NVL2


Mass: 9108.525 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: The PRESAT-vector: asymmetric T-vector for high-throughput screening of soluble protein domains for structural proteomics. Goda N, Tenno T, Takasu H, Hiroaki H, Shirakawa M. Protein Sci. ...Description: The PRESAT-vector: asymmetric T-vector for high-throughput screening of soluble protein domains for structural proteomics. Goda N, Tenno T, Takasu H, Hiroaki H, Shirakawa M. Protein Sci. 2004 Mar;13(3):652-8.PMID: 14978305
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CRW9, UniProt: Q9DBY8*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: 20 structure ensemble
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HN(CA)CB
1423D H(CCO)NH
1513D 1H-15N NOESY
1623D 1H-13C NOESY
1723D HNCO

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM [U-99% 15N] NVL2 N-terminal domain; 95% H2O/5% D2O95% H2O/5% D2O
20.6mM [U-99% 13C; U-99% 15N] NVL2 N-terminal domain; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMNVL2 N-terminal domain-1[U-99% 15N]1
0.6 mMNVL2 N-terminal domain-2[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 25 / pH: 6.4 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX8002
GE AvanceGEAVANCE6003

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.0.17Guntert, Mumenthaler and Wuthrichrefinement
CNS1.2refinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 5

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more