[English] 日本語
Yorodumi
- PDB-2l9r: Solution NMR Structure of Homeobox domain of Homeobox protein Nkx... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l9r
TitleSolution NMR Structure of Homeobox domain of Homeobox protein Nkx-3.1 from homo sapiens, Northeast Structural Genomics Consortium Target HR6470A
ComponentsHomeobox protein Nkx-3.1
KeywordsTRANSCRIPTION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative / transcription factor / Methods Development
Function / homology
Function and homology information


MADS box domain binding / positive regulation of androgen secretion / salivary gland development / dorsal aorta development / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of epithelial cell proliferation involved in prostate gland development / epithelial cell proliferation involved in salivary gland morphogenesis / branching involved in prostate gland morphogenesis / pharyngeal system development / epithelial cell proliferation involved in prostate gland development ...MADS box domain binding / positive regulation of androgen secretion / salivary gland development / dorsal aorta development / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of epithelial cell proliferation involved in prostate gland development / epithelial cell proliferation involved in salivary gland morphogenesis / branching involved in prostate gland morphogenesis / pharyngeal system development / epithelial cell proliferation involved in prostate gland development / metanephros development / cysteine-type endopeptidase activator activity involved in apoptotic process / cellular response to steroid hormone stimulus / branching morphogenesis of an epithelial tube / androgen receptor signaling pathway / response to testosterone / site of DNA damage / positive regulation of cell division / cellular response to interleukin-1 / somitogenesis / transcription regulator inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of mitotic cell cycle / nuclear estrogen receptor binding / histone deacetylase binding / male gonad development / cellular response to xenobiotic stimulus / nuclear receptor activity / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / cellular response to tumor necrosis factor / regulation of protein localization / heart development / cellular response to hypoxia / DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / DNA damage response / positive regulation of gene expression / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily ...: / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeobox protein Nkx-3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Xiao, R. / Lee, H.-W. / Hamilton, K. / Ciccosanti, C. / Wang, H.B. / Acton, T.B. / Everett, J.K. / Huang, Y.J. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Homeobox domain of Homeobox protein Nkx-3.1 from homo sapiens, Northeast Structural Genomics Consortium Target HR6470A
Authors: Liu, G. / Xiao, R. / Lee, H.-W. / Hamilton, K. / Ciccosanti, C. / Wang, H.B. / Acton, T.B. / Everett, J.K. / Huang, Y.J. / Montelione, G.T.
History
DepositionFeb 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Jun 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 1.4May 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: Homeobox protein Nkx-3.1


Theoretical massNumber of molelcules
Total (without water)8,3711
Polymers8,3711
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 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Homeobox protein Nkx-3.1 / Homeobox protein NK-3 homolog A


Mass: 8370.620 Da / Num. of mol.: 1 / Fragment: DNA binding Homeobox residues 132-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NKX3-1, NKX3.1, NKX3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q99801

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.69 mM [U-100% 13C; U-100% 15N] HR6470A, 90% H2O/10% D2O90% H2O/10% D2O
20.65 mM [U-5% 13C; U-100% 15N] HR6470A, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.69 mMHR6470A-1[U-100% 13C; U-100% 15N]1
0.65 mMHR6470A-2[U-5% 13C; U-100% 15N]2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: distance geometry, torsion angle dynamics, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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