[English] 日本語
Yorodumi
- PDB-2k40: NMR structure of HESX-1 homeodomain double mutant R31L/E42L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k40
TitleNMR structure of HESX-1 homeodomain double mutant R31L/E42L
ComponentsHomeobox expressed in ES cells 1
KeywordsDNA BINDING PROTEIN / THERMOSTABLE HOMEODOMAIN VARIANT / Developmental protein / Disease mutation / DNA-binding / Dwarfism / Homeobox / Nucleus / Polymorphism / Transcription / Transcription regulation
Function / homology
Function and homology information


nose development / otic vesicle formation / : / pituitary gland development / : / chromatin => GO:0000785 / forebrain morphogenesis / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding ...nose development / otic vesicle formation / : / pituitary gland development / : / chromatin => GO:0000785 / forebrain morphogenesis / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Homeobox expressed in ES cells 1 / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...Homeobox expressed in ES cells 1 / 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 expressed in ES cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsSolution structure of the thermostable double mutant R31L/E42L of human HESX-1 homeodomain
AuthorsAsensio, J. / Torrado, M. / Gonzalez, C. / Bastida, A.
CitationJournal: To be Published
Title: The role of conserved salt-bridges on homeodomain stability
Authors: Asensio, J. / Torrado, M. / Gonzalez, C. / Bastida, A. / Corzana, F.
History
DepositionMay 26, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Homeobox expressed in ES cells 1


Theoretical massNumber of molelcules
Total (without water)8,1271
Polymers8,1271
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein Homeobox expressed in ES cells 1 / Homeobox protein ANF / hAnf


Mass: 8127.353 Da / Num. of mol.: 1
Fragment: DNA binding domain of Human transcription factor Hesx-I (UNP residues 108-174)
Mutation: R31L, E42L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HESX1, HANF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBX0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: SOLUTION STRUCTURE OF THE THERMOSTABLE DOUBLE MUTANT R31L/E42L OF HUMAN HESX-1 HOMEODOMAIN
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1312D 1H-1H TOCSY
1422D 1H-1H TOCSY
1512D DQF-COSY
1622D DQF-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM HESX-I HOMEODOMAIN, 90% H2O/10% D2O90% H2O/10% D2O
20.600 mM HESX-I HOMEODOMAIN, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.6 mMHESX-I HOMEODOMAIN1
0.600 mMHESX-I HOMEODOMAIN2
Sample conditionsIonic strength: 0.1 NaCl / pH: 6.0 / Pressure: ambient atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Varian UnityVarianUNITY5003

-
Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
DYANAGuntert, Braun and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / 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