[English] 日本語
Yorodumi
- PDB-1jun: NMR STUDY OF C-JUN HOMODIMER -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jun
TitleNMR STUDY OF C-JUN HOMODIMER
ComponentsC-JUN HOMODIMER
KeywordsTRANSCRIPTION REGULATION / DNA-BINDING REGULATORY PROTEIN / ONCOGENE PROTEIN / TRANSCRIPTION ACTIVATION
Function / homology
Function and homology information


leading edge cell differentiation / cellular response to anisomycin / cAMP response element binding / transcription factor AP-1 complex / positive regulation of DNA-templated transcription initiation / integrated stress response signaling / release from viral latency / WNT5:FZD7-mediated leishmania damping / SMAD protein signal transduction / host-mediated activation of viral transcription ...leading edge cell differentiation / cellular response to anisomycin / cAMP response element binding / transcription factor AP-1 complex / positive regulation of DNA-templated transcription initiation / integrated stress response signaling / release from viral latency / WNT5:FZD7-mediated leishmania damping / SMAD protein signal transduction / host-mediated activation of viral transcription / response to steroid hormone / negative regulation of DNA binding / axon regeneration / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Activation of the AP-1 family of transcription factors / eyelid development in camera-type eye / R-SMAD binding / ubiquitin-like protein ligase binding / outflow tract morphogenesis / monocyte differentiation / general transcription initiation factor binding / positive regulation of epithelial cell migration / host-mediated suppression of viral transcription / positive regulation of vascular associated smooth muscle cell proliferation / JNK cascade / response to muscle stretch / positive regulation of endothelial cell proliferation / transcription repressor complex / GTPase activator activity / transforming growth factor beta receptor signaling pathway / cellular response to calcium ion / response to endoplasmic reticulum stress / liver development / Regulation of PTEN gene transcription / TP53 Regulates Transcription of DNA Repair Genes / FCERI mediated MAPK activation / microglial cell activation / euchromatin / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / Oxidative Stress Induced Senescence / transcription regulator complex / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / transcription cis-regulatory region binding / regulation of cell cycle / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper ...Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor Jun
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsJunius, F.K. / O'Donoghue, S.I. / Nilges, M. / King, G.F.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: High resolution NMR solution structure of the leucine zipper domain of the c-Jun homodimer.
Authors: Junius, F.K. / O'Donoghue, S.I. / Nilges, M. / Weiss, A.S. / King, G.F.
#1: Journal: To be Published
Title: Calculation of Symmetric Multimer Structures from NMR Data Using a Priori Knowledge of the Monomer Structure, Co-Monomer Restraints, and Interface Mapping: The Case of Leucine Zippers
Authors: O'Donoghue, S.I. / King, G.F. / Nilges, M.
#2: Journal: Thesis / Year: 1995
Title: Structural Studies of the Leucine Zipper Domain of the Oncoprotein C-Jun
Authors: Junius, F.K.
#3: Journal: Biochemistry / Year: 1995
Title: Nuclear Magnetic Resonance Characterization of the Jun Leucine Zipper Domain: Unusual Properties of Coiled-Coil Interfacial Polar Residues
Authors: Junius, F.K. / Mackay, J.P. / Bubb, W.A. / Jensen, S.A. / Weiss, A.S. / King, G.F.
#4: Journal: Eur.J.Biochem. / Year: 1993
Title: The Solution Structure of the Leucine Zipper Motif of the Jun Oncoprotein Homodimer
Authors: Junius, F.K. / Weiss, A.S. / King, G.F.
#5: Journal: Protein Eng. / Year: 1993
Title: Determination of the Structure of Symmetric Coiled-Coil Proteins from NMR Data: Application of the Leucine Zipper Proteins Jun and GCN4
Authors: O'Donoghue, S.I. / Junius, F.K. / King, G.F.
#6: Journal: Science / Year: 1989
Title: Preferential Heterodimer Formation by Isolated Leucine Zippers from Fos and Jun
Authors: O'Shea, E.K. / Rutkowski, R. / Stafford III, W.F. / Kim, P.S.
History
DepositionDec 19, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: 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
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
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-JUN HOMODIMER
B: C-JUN HOMODIMER


Theoretical massNumber of molelcules
Total (without water)9,7672
Polymers9,7672
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)7 / -
Representative

-
Components

#1: Protein/peptide C-JUN HOMODIMER / JUNLZ / JUNP1N


Mass: 4883.714 Da / Num. of mol.: 2 / Fragment: LEUCINE ZIPPER DOMAIN, RESIDUES 272 - 315 / Mutation: INS(272-275), INS(315)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P05412
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Sample conditionspH: 3.6 / Temperature: 310 K
Crystal grow
*PLUS
Method: other

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 7

+
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