[English] 日本語
Yorodumi
- PDB-2rtu: Solution structure of oxidized human HMGB1 A box -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rtu
TitleSolution structure of oxidized human HMGB1 A box
ComponentsHigh mobility group protein B1
KeywordsDNA BINDING PROTEIN / disulfide bond / High Mobility Group Box 1
Function / homology
Function and homology information


regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation / positive regulation of myeloid cell differentiation / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of dendritic cell differentiation / C-X-C chemokine binding / positive regulation of toll-like receptor 9 signaling pathway / negative regulation of CD4-positive, alpha-beta T cell differentiation / neutrophil clearance / positive regulation of glycogen catabolic process / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / RAGE receptor binding / positive regulation of interleukin-1 production / eye development / Regulation of TLR by endogenous ligand / bubble DNA binding / V(D)J recombination / alphav-beta3 integrin-HMGB1 complex / myeloid cell differentiation / myeloid progenitor cell differentiation / Apoptosis induced DNA fragmentation / inflammatory response to antigenic stimulus / regulation of nucleotide-excision repair / macrophage activation involved in immune response / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / positive regulation of monocyte chemotactic protein-1 production / cellular response to interleukin-7 / endothelial cell proliferation / positive regulation of chemokine (C-X-C motif) ligand 2 production / glycogen catabolic process / apoptotic cell clearance / supercoiled DNA binding / positive regulation of vascular endothelial cell proliferation / dendritic cell chemotaxis / DNA binding, bending / IRAK4 deficiency (TLR2/4) / positive regulation of DNA binding / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of wound healing / phosphatidylserine binding / chemoattractant activity / positive regulation of sprouting angiogenesis / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / TRAF6 mediated NF-kB activation / negative regulation of type II interferon production / DNA topological change / negative regulation of blood vessel endothelial cell migration / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / Advanced glycosylation endproduct receptor signaling / protein kinase activator activity / positive regulation of blood vessel endothelial cell migration / Pyroptosis / response to glucocorticoid / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / positive regulation of interleukin-12 production / positive regulation of autophagy / transcription repressor complex / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-8 production / positive regulation of JNK cascade / lipopolysaccharide binding / lung development / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / base-excision repair / double-strand break repair via nonhomologous end joining / positive regulation of interleukin-6 production / autophagy / neuron projection development / positive regulation of tumor necrosis factor production / transcription corepressor activity / integrin binding / heterochromatin formation / double-strand break repair / single-stranded DNA binding / double-stranded RNA binding / ER-Phagosome pathway / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / double-stranded DNA binding
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsJing, W. / Tochio, N. / Tate, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Redox-sensitive structural change in the A-domain of HMGB1 and its implication for the binding to cisplatin modified DNA.
Authors: Wang, J. / Tochio, N. / Takeuchi, A. / Uewaki, J. / Kobayashi, N. / Tate, S.
History
DepositionSep 12, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_software.name
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: High mobility group protein B1


Theoretical massNumber of molelcules
Total (without water)10,1191
Polymers10,1191
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)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein High mobility group protein B1 / High mobility group protein 1 / HMG-1


Mass: 10118.655 Da / Num. of mol.: 1 / Fragment: HMG box 1, UNP residues 1-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMGB1, HMG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09429
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY
1312D 1H-15N IPAP-HSQC
1422D 1H-15N IPAP-HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.6 mM [U-13C; U-15N] protein-1, 50 mM potassium phosphate-2, 10 % [U-2H] D2O-3, 150 mM potassium chloride-4, 90% H2O/10% D2O90% H2O/10% D2O
20.5-0.6 mM [U-13C; U-15N] protein-5, 5 % C12E5/n-hexanol-6, 10 % U-2H D2O-7, 150 mM potassium chloride-8, 50 mM potassium phosphate-9, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-13C; U-15N]0.5-0.61
50 mMpotassium phosphate-21
10 %D2O-3[U-2H]1
150 mMpotassium chloride-41
mMentity-5[U-13C; U-15N]0.5-0.62
5 %C12E5/n-hexanol-62
10 %D2O-7[U-2H]2
150 mMpotassium chloride-82
50 mMpotassium phosphate-92
Sample conditionsIonic strength: 200 / pH: 6.4 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MAGROKobayashi N.data analysis
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20 / Representative conformer: 1

+
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