[English] 日本語
Yorodumi
- PDB-1j5n: Solution Structure of the Non-Sequence-Specific HMGB protein NHP6... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j5n
TitleSolution Structure of the Non-Sequence-Specific HMGB protein NHP6A in complex with SRY DNA
Components
  • 5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C)-3'
  • 5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G)-3'
  • Nonhistone chromosomal protein 6A
KeywordsDNA BINDING PROTEIN/DNA / HMG-BOX / HMGB / PROTEIN-DNA COMPLEX / ALPHA HELIX / DOUBLE HELIX / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III / Apoptosis induced DNA fragmentation / Regulation of TLR by endogenous ligand / Mitochondrial transcription initiation / protein-DNA complex assembly / MutSalpha complex binding / Pyroptosis / RNA polymerase III preinitiation complex assembly / Mitochondrial protein degradation / DNA binding, bending ...maintenance of transcriptional fidelity during transcription elongation by RNA polymerase III / Apoptosis induced DNA fragmentation / Regulation of TLR by endogenous ligand / Mitochondrial transcription initiation / protein-DNA complex assembly / MutSalpha complex binding / Pyroptosis / RNA polymerase III preinitiation complex assembly / Mitochondrial protein degradation / DNA binding, bending / RNA polymerase II preinitiation complex assembly / nucleosome binding / Neutrophil degranulation / protein-DNA complex / chromosome / chromatin organization / nucleic acid binding / chromatin remodeling / DNA repair / nucleus
Similarity search - Function
: / 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
DNA / DNA (> 10) / Non-histone chromosomal protein 6A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsMasse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding
Authors: Masse, J.E. / Wong, B. / Yen, Y.-M. / Allain, F.H.-T. / Johnson, R.C. / Feigon, J.
History
DepositionMay 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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
B: 5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G)-3'
C: 5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C)-3'
A: Nonhistone chromosomal protein 6A


Theoretical massNumber of molelcules
Total (without water)20,0033
Polymers20,0033
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 / 100structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

-
Components

#1: DNA chain 5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G)-3'


Mass: 4696.042 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: unlabeled DNA made on a commercial synthesizer, 15N,13C-labeled DNA made enzymatically in vitro with Taq polymerase
#2: DNA chain 5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C)-3'


Mass: 4482.940 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: unlabeled DNA made on a commercial synthesizer, 15N,13C-labeled DNA made enzymatically in vitro with Taq polymerase
#3: Protein Nonhistone chromosomal protein 6A / NHP6A


Mass: 10824.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P11632

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1152D 13C-filtered NOESY Tmix=50
1252D 13C-filtered NOESY Tmix=100
1352D 13C-filtered NOESY Tmix=150
1452D 13C-filtered NOESY Tmix=200
1552D 13C-filtered NOESY Tmix=250
1652D 13C-filtered NOESY Tmix=300
1762D 13C-filtered NOESY Tmix=50
1862D 13C-filtered NOESY Tmix=100
1962D 13C-filtered NOESY Tmix=150
11062D 13C-filtered NOESY Tmix=200
11162D 13C-filtered NOESY Tmix=250
11262D 13C-filtered NOESY Tmix=300
11323D 15N-separated NOESY
11433D 13C-separated NOESY
11533D 13C double-half-filtered 13C-separated NOESY
11643D 13C double-half-filtered 13C-separated NOESY
11753D 13C double-half-filtered 13C-separated NOESY
11863D 13C double-half-filtered 13C-separated NOESY
21912D 11 echo NOESY
NMR detailsText: This structure calculated using standard 3D heteronuclear filtering and editing techniques with both labeled protein and labeled DNA.

-
Sample preparation

Details
Solution-IDContents
1protein and DNA unlabeled, 2mM sample 90% H2O, 10% D2O or 100% D2O
2Uniform labeling with 15N of protein, DNA unlabeled, 2mM 90% H2O, 10% D2O
3Uniform labeling with 15N,13C of protein, DNA unlabeled, 2mM 100% D2O
4Uniform labeling with 15N,13C of DNA (both strands), protein unlabeled, 2mM 100% D2O
5Uniform labeling with 15N,13C of G-rich DNA strand and protein, C-rich DNA strand unlabeled, 2mM 100% D2O
6Uniform labeling with 15N,13C of C-rich DNA strand and protein, G-rich DNA strand unlabeled, 2mM 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
12 mM NaPO4, 10 mM NaCl 5.8ambient 310 K
22 mM NaPO4, 10 mM NaCl 5.8ambient 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
Felix2000MSIprocessing
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 3035 restraints. 102 are from alpha-helical hydrogen bond restraints within the protein (2/h-bond). 76 are hydrogen bond restraints for Watson-Crick ...Details: The structures are based on a total of 3035 restraints. 102 are from alpha-helical hydrogen bond restraints within the protein (2/h-bond). 76 are hydrogen bond restraints for Watson-Crick base pairs in the DNA. The rest are NOE-derived. 2197 of the NOE restraints are protein-protein restraints, 578 are DNA-DNA restraints, and 82 are protein-DNA restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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