[English] 日本語
Yorodumi
- PDB-1hsn: THE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hsn
TitleTHE STRUCTURE OF THE HMG BOX AND ITS INTERACTION WITH DNA
ComponentsHIGH MOBILITY GROUP PROTEIN 1
KeywordsDNA-BINDING
Function / homology
Function and homology information


regulation of T cell mediated immune response to tumor cell / negative regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / positive regulation of DNA ligation / apoptotic cell clearance / DNA binding, bending / endoplasmic reticulum-Golgi intermediate compartment / condensed chromosome / autophagy ...regulation of T cell mediated immune response to tumor cell / negative regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / positive regulation of DNA ligation / apoptotic cell clearance / DNA binding, bending / endoplasmic reticulum-Golgi intermediate compartment / condensed chromosome / autophagy / chemotaxis / DNA recombination / adaptive immune response / endosome / inflammatory response / innate immune response / DNA repair / extracellular region / nucleus / plasma membrane
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
BETA-MERCAPTOETHANOL / High mobility group protein B1
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodSOLUTION NMR
AuthorsRead, C.M. / Cary, P.D. / Crane-Robinson, C. / Driscoll, P.C. / Carillo, M.O.M. / Norman, D.G.
Citation
Journal: To be Published
Title: The Structure of the Hmg Box and its Interaction with DNA
Authors: Read, C.M. / Cary, P.D. / Crane-Robinson, C. / Driscoll, P.C. / Carillo, M.O.M. / Norman, D.G.
#1: Journal: Nucleic Acids Res. / Year: 1993
Title: Solution Structure of a DNA-Binding Domain from Hmg1
Authors: Read, C.M. / Cary, P.D. / Crane-Robinson, C. / Driscoll, P.C. / Norman, D.G.
History
DepositionNov 17, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIGH MOBILITY GROUP PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9212
Polymers8,8431
Non-polymers781
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)49 / -
Representative

-
Components

#1: Protein HIGH MOBILITY GROUP PROTEIN 1


Mass: 8843.149 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: INSERT DERIVED BY PCR / Plasmid: PGEX-2T GENE: INSERT DERIVED BY PCR / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P07156
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
X-PLOR3phasing
NMR software
NameVersionDeveloperClassification
SIMULATED ANNEALINGNILGESrefinement
X-PLOR3BRUNGERrefinement
NMR ensembleConformers submitted total number: 49

+
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