[English] 日本語
Yorodumi
- PDB-2ld5: Solution NMR-derived complex structure of Hoxa13 DNA binding doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ld5
TitleSolution NMR-derived complex structure of Hoxa13 DNA binding domain bound to DNA
Components
  • DNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*TP*TP*TP*TP*AP*TP*TP*TP*G)-3')
  • Homeobox protein Hox-A13
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


endothelial cell fate specification / positive regulation of mesenchymal cell apoptotic process / regulation of BMP signaling pathway / branching involved in prostate gland morphogenesis / endothelial cell morphogenesis / male genitalia development / tissue homeostasis / embryonic forelimb morphogenesis / intermediate filament cytoskeleton / ventricular septum development ...endothelial cell fate specification / positive regulation of mesenchymal cell apoptotic process / regulation of BMP signaling pathway / branching involved in prostate gland morphogenesis / endothelial cell morphogenesis / male genitalia development / tissue homeostasis / embryonic forelimb morphogenesis / intermediate filament cytoskeleton / ventricular septum development / artery morphogenesis / inner ear development / anatomical structure morphogenesis / vasculogenesis / cis-regulatory region sequence-specific DNA binding / positive regulation of mitotic nuclear division / animal organ morphogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Homeobox protein Hox1A3 N-terminal / Hox protein A13 N terminal / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily ...Homeobox protein Hox1A3 N-terminal / Hox protein A13 N terminal / 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
DNA / DNA (> 10) / Homeobox protein Hox-A13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZhang, Y.
CitationJournal: Plos One / Year: 2011
Title: Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.
Authors: Zhang, Y. / Larsen, C.A. / Stadler, H.S. / Ames, J.B.
History
DepositionMay 14, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Homeobox protein Hox-A13
B: DNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3')
C: DNA (5'-D(P*GP*AP*TP*TP*TP*TP*AP*TP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)15,3743
Polymers15,3743
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Homeobox protein Hox-A13 / Homeobox protein Hox-1.10


Mass: 8670.194 Da / Num. of mol.: 1 / Fragment: Homeobox DNA binding residues 320-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hox-1.10, Hoxa13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62424
#2: DNA chain DNA (5'-D(*CP*AP*AP*AP*TP*AP*AP*AP*AP*TP*C)-3')


Mass: 3334.239 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*GP*AP*TP*TP*TP*TP*AP*TP*TP*TP*G)-3')


Mass: 3369.217 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 1H-13C NOESY

-
Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] sodium phosphate, 100% D2O
Solvent system: 100% D2O
SampleConc.: 0.5 mM / Component: sodium phosphate-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.025 / pH: 6.0 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

+
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