[English] 日本語
Yorodumi
- PDB-1j3d: Solution structure of the C-terminal domain of the HMGB2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j3d
TitleSolution structure of the C-terminal domain of the HMGB2
ComponentsHigh mobility group protein 2
KeywordsDNA BINDING PROTEIN / HMG-BOX
Function / homology
Function and homology information


Apoptosis induced DNA fragmentation / non-sequence-specific DNA binding, bending / positive regulation of DNA ligase activity / spermatid nucleus differentiation / DNA geometric change / regulation of stem cell proliferation / inflammatory response to antigenic stimulus / supercoiled DNA binding / response to steroid hormone / DNA binding, bending ...Apoptosis induced DNA fragmentation / non-sequence-specific DNA binding, bending / positive regulation of DNA ligase activity / spermatid nucleus differentiation / DNA geometric change / regulation of stem cell proliferation / inflammatory response to antigenic stimulus / supercoiled DNA binding / response to steroid hormone / DNA binding, bending / positive regulation of DNA binding / transcription factor binding / DNA topological change / regulation of neurogenesis / cis-regulatory region sequence-specific DNA binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / four-way junction DNA binding / condensed chromosome / double-strand break repair via nonhomologous end joining / male gonad development / chemotaxis / nucleosome assembly / single-stranded DNA binding / double-stranded DNA binding / spermatogenesis / DNA recombination / defense response to Gram-negative bacterium / response to lipopolysaccharide / defense response to Gram-positive bacterium / protein domain specific binding / negative regulation of gene expression / innate immune response / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / nucleus / cytoplasm
Similarity search - Function
HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain ...HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / : / High mobility group box domain / DNA Binding (I), subunit A / HMG-box domain / 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
High mobility group protein B2
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodSOLUTION NMR / simulated annealing
AuthorsKurita, J. / Shimahara, H. / Yoshida, M. / Tate, S.
CitationJournal: To be Published
Title: Strucutral comparison of two HMG-boxes in the non-histone protein HMG-2 with in the HMG-1
Authors: Kurita, J. / Shimahara, H. / Yoshida, M. / Tate, S.
History
DepositionJan 23, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: High mobility group protein 2


Theoretical massNumber of molelcules
Total (without water)8,9551
Polymers8,9551
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)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein High mobility group protein 2 / High mobility group B2 / HMG2 / HMGB2


Mass: 8955.344 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): pET / References: UniProt: P17741

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1332D NOESY
142CT HMQC
254IPAP
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM C-terminal Domain U-15N,13C; 50mM Acetate buffer Na95% H2O/5% D2O
21mM C-terminal Domain non-label; 50mM Acetate buffer Na95% H2O/5% D2O
31mM C-terminal Domain U-15N; 50mM phosphate buffer Na87.5% H2O, 5% D2O, 7.5% bicelle
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15ambient 298 K
26.4ambient 303 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA1.1Nilgesstructure solution
X-PLOR3.851Brungerrefinement
NMRPipe2001.157.17.50Delaglioprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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