[English] 日本語
Yorodumi
- PDB-1hmf: STRUCTURE OF THE HMG BOX MOTIF IN THE B-DOMAIN OF HMG1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hmf
TitleSTRUCTURE OF THE HMG BOX MOTIF IN THE B-DOMAIN OF HMG1
ComponentsHIGH MOBILITY GROUP PROTEIN FRAGMENT-B
KeywordsDNA-BINDING
Function / homology
Function and homology information


positive regulation of myeloid progenitor cell differentiation / Apoptosis induced DNA fragmentation / male-specific defense response to bacterium / open form four-way junction DNA binding / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / Pyroptosis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / TAK1-dependent IKK and NF-kappa-B activation ...positive regulation of myeloid progenitor cell differentiation / Apoptosis induced DNA fragmentation / male-specific defense response to bacterium / open form four-way junction DNA binding / crossed form four-way junction DNA binding / positive regulation of myeloid cell apoptotic process / Pyroptosis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / TAK1-dependent IKK and NF-kappa-B activation / Regulation of TLR by endogenous ligand / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / positive regulation of myeloid cell differentiation / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / neutrophil clearance / T-helper 1 cell activation / toll-like receptor 2 signaling pathway / myeloid dendritic cell activation / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of macrophage inflammatory protein 1 alpha production / glycolipid binding / positive regulation of dendritic cell differentiation / bent DNA binding / positive regulation of toll-like receptor 9 signaling pathway / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of glycogen catabolic process / non-sequence-specific DNA binding, bending / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / eye development / induction of positive chemotaxis / RAGE receptor binding / positive regulation of mesenchymal cell proliferation / positive regulation of interleukin-1 production / V(D)J recombination / cellular response to interleukin-7 / endothelial cell proliferation / inflammatory response to antigenic stimulus / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / psychomotor behavior / macrophage activation involved in immune response / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of innate immune response / positive regulation of monocyte chemotaxis / positive regulation of vascular endothelial cell proliferation / apoptotic cell clearance / positive regulation of activated T cell proliferation / regulation of nucleotide-excision repair / positive regulation of smooth muscle cell migration / toll-like receptor 4 signaling pathway / DNA binding, bending / Neutrophil degranulation / T-helper 1 cell differentiation / MyD88-dependent toll-like receptor signaling pathway / supercoiled DNA binding / phosphatidylserine binding / positive regulation of wound healing / positive regulation of sprouting angiogenesis / negative regulation of DNA replication / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of type II interferon production / myoblast proliferation / positive regulation of interferon-alpha production / negative regulation of blood vessel endothelial cell migration / positive regulation of interleukin-10 production / response to glucose / lung development / cellular response to interleukin-1 / positive regulation of blood vessel endothelial cell migration / positive regulation of myoblast differentiation / protein kinase activator activity / positive regulation of interleukin-12 production / transcription repressor complex / positive regulation of mitotic cell cycle / condensed chromosome / four-way junction DNA binding / peptide binding / DNA polymerase binding / response to type II interferon / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of autophagy / response to glucocorticoid / cytokine activity / positive regulation of interleukin-8 production / positive regulation of interleukin-1 beta production / positive regulation of neuron projection development / lipopolysaccharide binding / circadian rhythm / cell morphogenesis / response to insulin
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 B1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR
AuthorsWeir, H.M. / Kraulis, P.J. / Hill, C.S. / Raine, A.R.C. / Laue, E.D. / Thomas, J.O.
CitationJournal: EMBO J. / Year: 1993
Title: Structure of the HMG box motif in the B-domain of HMG1.
Authors: Weir, H.M. / Kraulis, P.J. / Hill, C.S. / Raine, A.R. / Laue, E.D. / Thomas, J.O.
History
DepositionMar 7, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: HIGH MOBILITY GROUP PROTEIN FRAGMENT-B


Theoretical massNumber of molelcules
Total (without water)8,7911
Polymers8,7911
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 / -
Representative

-
Components

#1: Protein HIGH MOBILITY GROUP PROTEIN FRAGMENT-B


Mass: 8791.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P63159

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameVersionClassification
X-PLOR2model building
X-PLOR2refinement
X-PLOR2phasing
NMR softwareName: X-PLOR / Version: 2.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers 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