[English] 日本語
Yorodumi
- PDB-1i11: SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i11
TitleSOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE
ComponentsTRANSCRIPTION FACTOR SOX-5
KeywordsDNA BINDING PROTEIN / HMG BOX / DNA BENDING / DNA RECOGNITION / CHROMATIN / DNA SEQUENCE SPECIFIC / TESTIS DETERMINING.
Function / homology
Function and homology information


positive regulation of mesenchymal stem cell differentiation / regulation of timing of neuron differentiation / central nervous system neuron differentiation / positive regulation of cartilage development / asymmetric neuroblast division / positive regulation of chondrocyte differentiation / cartilage development / cartilage condensation / oligodendrocyte differentiation / cell fate commitment ...positive regulation of mesenchymal stem cell differentiation / regulation of timing of neuron differentiation / central nervous system neuron differentiation / positive regulation of cartilage development / asymmetric neuroblast division / positive regulation of chondrocyte differentiation / cartilage development / cartilage condensation / oligodendrocyte differentiation / cell fate commitment / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / cellular response to transforming growth factor beta stimulus / in utero embryonic development / transcription regulator complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Transcription factor SOX-6 / High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor SOX-5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / SIMULATING ANNEALING
AuthorsCary, P.D. / Read, C.M. / Davis, B. / Driscoll, P.C. / Crane-Robinson, C.
CitationJournal: Protein Sci. / Year: 2001
Title: Solution structure and backbone dynamics of the DNA-binding domain of mouse Sox-5.
Authors: Cary, P.D. / Read, C.M. / Davis, B. / Driscoll, P.C. / Crane-Robinson, C.
History
DepositionJan 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSCRIPTION FACTOR SOX-5


Theoretical massNumber of molelcules
Total (without water)9,8251
Polymers9,8251
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein TRANSCRIPTION FACTOR SOX-5


Mass: 9825.412 Da / Num. of mol.: 1 / Fragment: HMG BOX
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SOX-5 / Organ: TESTISTesticle / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P35710

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H NOESY
1242D 1H NOESY
1332D 15N-1H HMQC-J
1413D 15N-1H NOESY
NMR detailsText: This Structure was determined using a combination of 2D and 3D NMR spectra. THE 30 STRUCTURES ARE ALIGNED OVER ALL BACKBONE ATOMS FOR RESIDUES 10-25 AND 32-43. MODEL 1 IS THE MINIMUM ENERGY AND ...Text: This Structure was determined using a combination of 2D and 3D NMR spectra. THE 30 STRUCTURES ARE ALIGNED OVER ALL BACKBONE ATOMS FOR RESIDUES 10-25 AND 32-43. MODEL 1 IS THE MINIMUM ENERGY AND REFERENCE STRUCTURE FOR THE OTHER 29 STRUCTURES.

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12-3 mM [U-100% 15N] Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution23 mM Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 100% D2Osample_2100% D2O
solution31 mM [U-100% 15N] Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 90% H2O/10% D2Osample_390% H2O/10% D2O
solution43 mM Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 90% H2O/10% D2Osample_490% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSox-5 HMG Box[U-100% 15N]2-31
75 mMpotassium phosphate buffernatural abundance1
0.5 mMDTTnatural abundance1
3 mMSox-5 HMG Boxnatural abundance2
75 mMpotassium phosphate buffernatural abundance2
0.5 mMDTTnatural abundance2
1 mMSox-5 HMG Box[U-100% 15N]13
75 mMpotassium phosphate buffernatural abundance3
0.5 mMDTTnatural abundance3
3 mMSox-5 HMG Boxnatural abundance4
75 mMpotassium phosphate buffernatural abundance4
0.5 mMDTTnatural abundance4
Sample conditionsIonic strength: 75 mM KPO4 / pH: 6.20 / Pressure: Ambient / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
GE OMEGAGEOMEGA6001
Bruker AMBrukerAM6002
Varian UNITYPLUSVarianUNITYPLUS5003

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Felix2.3Molecular Simulationsdata analysis
NMRView3JOHNSON, BRUCE A.data analysis
Insight II97Molecular Simulationsdata analysis
RefinementMethod: SIMULATING ANNEALING / Software ordinal: 1
Details: Structures are based on a total of 1383 nonredundant distance NOE restraints, 61 dihedral angle restraints and 24 paired distance restraints for hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 30

+
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