[English] 日本語
Yorodumi
- PDB-2llh: NMR structure of Npm1_c70 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2llh
TitleNMR structure of Npm1_c70
ComponentsNucleophosmin
KeywordsDNA BINDING PROTEIN / CHAPERONE / NUCLEOLAR / ONCOPROTEIN
Function / homology
Function and homology information


regulation of mRNA stability involved in cellular response to UV / regulation of eIF2 alpha phosphorylation by dsRNA / regulation of endoribonuclease activity / negative regulation of centrosome duplication / positive regulation of cell cycle G2/M phase transition / regulation of endodeoxyribonuclease activity / regulation of centriole replication / granular component / negative regulation of protein kinase activity by regulation of protein phosphorylation / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation ...regulation of mRNA stability involved in cellular response to UV / regulation of eIF2 alpha phosphorylation by dsRNA / regulation of endoribonuclease activity / negative regulation of centrosome duplication / positive regulation of cell cycle G2/M phase transition / regulation of endodeoxyribonuclease activity / regulation of centriole replication / granular component / negative regulation of protein kinase activity by regulation of protein phosphorylation / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / SARS-CoV-1-host interactions / regulation of centrosome duplication / Tat protein binding / spindle pole centrosome / ALK mutants bind TKIs / Nuclear import of Rev protein / centrosome cycle / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / nucleocytoplasmic transport / protein kinase inhibitor activity / ribosomal large subunit binding / macrophage differentiation / ribosomal small subunit binding / ribosomal large subunit export from nucleus / NF-kappaB binding / core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / Deposition of new CENPA-containing nucleosomes at the centromere / SUMOylation of transcription cofactors / ribosome assembly / ribosomal large subunit biogenesis / positive regulation of translation / intracellular protein transport / protein-DNA complex / PKR-mediated signaling / protein import into nucleus / positive regulation of NF-kappaB transcription factor activity / cellular response to UV / cellular senescence / Signaling by ALK fusions and activated point mutants / unfolded protein binding / intracellular protein localization / nucleosome assembly / ribosomal small subunit biogenesis / DNA-binding transcription factor binding / molecular adaptor activity / histone binding / transcription coactivator activity / rRNA binding / chromatin remodeling / ribonucleoprotein complex / negative regulation of cell population proliferation / focal adhesion / DNA repair / positive regulation of cell population proliferation / centrosome / chromatin binding / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / nucleolus / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Nucleophosmin, C-terminal / Nucleophosmin C-terminal domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsBanci, L. / Bertini, I. / Brunori, M. / Di Matteo, A. / Federici, L. / Gallo, A. / Lo Sterzo, C. / Mori, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of Nucleophosmin DNA-binding Domain and Analysis of Its Complex with a G-quadruplex Sequence from the c-MYC Promoter.
Authors: Gallo, A. / Lo Sterzo, C. / Mori, M. / Di Matteo, A. / Bertini, I. / Banci, L. / Brunori, M. / Federici, L.
History
DepositionNov 9, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)8,5151
Polymers8,5151
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 / 400target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Nucleophosmin / NPM / Nucleolar phosphoprotein B23 / Nucleolar protein NO38 / Numatrin


Mass: 8514.803 Da / Num. of mol.: 1 / Fragment: Nucleolar localization region residues 225-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPM1, NPM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06748

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D HBHA(CO)NH
1723D HN(CO)CA
1823D HN(CA)CO
1923D (H)CCH-TOCSY
11012D 1H-1H NOESY
11123D 1H-13C NOESY
11213D 1H-15N NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-15N] protein, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-13C; U-15N] protein, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-15N]1
20 mMsodium phosphate-21
0.5 mMentity-3[U-13C; U-15N]2
20 mMsodium phosphate-42
Sample conditionsIonic strength: 20 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE5003

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA2.1Keller and Wuthrichchemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
PSVSBhattacharya and Montelionevalidation
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

+
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://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