[English] 日本語
Yorodumi
- PDB-1bhi: STRUCTURE OF TRANSACTIVATION DOMAIN OF CRE-BP1/ATF-2, NMR, 20 STR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bhi
TitleSTRUCTURE OF TRANSACTIVATION DOMAIN OF CRE-BP1/ATF-2, NMR, 20 STRUCTURES
ComponentsCRE-BP1
KeywordsDNA-BINDING REGULATORY PROTEIN / CRE BINDING PROTEIN / ATF-2 / TRANSCRIPTIONAL ACTIVATION DOMAIN / ZN FINGER
Function / homology
Function and homology information


abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / cellular response to anisomycin / positive regulation of transforming growth factor beta2 production ...abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / cellular response to anisomycin / positive regulation of transforming growth factor beta2 production / cAMP response element binding / cellular lipid metabolic process / leucine zipper domain binding / cAMP response element binding protein binding / positive regulation of mitochondrial membrane permeability involved in apoptotic process / histone H2B acetyltransferase activity / cellular response to leucine starvation / brainstem development / histone H4 acetyltransferase activity / NK T cell differentiation / vacuole organization / neurofilament cytoskeleton organization / apoptotic process involved in development / NGF-stimulated transcription / intrinsic apoptotic signaling pathway in response to hypoxia / mitotic intra-S DNA damage checkpoint signaling / motor neuron apoptotic process / response to osmotic stress / hepatocyte apoptotic process / outflow tract morphogenesis / Activation of the AP-1 family of transcription factors / p38MAPK cascade / Response of EIF2AK4 (GCN2) to amino acid deficiency / white fat cell differentiation / BMP signaling pathway / adipose tissue development / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / histone acetyltransferase activity / JNK cascade / transcription initiation-coupled chromatin remodeling / negative regulation of angiogenesis / liver development / Regulation of PTEN gene transcription / promoter-specific chromatin binding / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / mRNA transcription by RNA polymerase II / Heme signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Transcriptional activation of mitochondrial biogenesis / response to organic cyclic compound / cellular response to virus / protein import into nucleus / RNA polymerase II transcription regulator complex / positive regulation of DNA-binding transcription factor activity / Circadian Clock / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / site of double-strand break / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / Estrogen-dependent gene expression / mitochondrial outer membrane / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / DNA damage response / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / identical protein binding / cytoplasm
Similarity search - Function
Transcription factor cyclic AMP-dependent, CRE-BP1-type / bZIP transcription factor / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Cyclic AMP-dependent transcription factor ATF-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMULATED ANNEALING, ENERGY MINIMIZATION
AuthorsNagadoi, A. / Nakazawa, K. / Uda, H. / Maekawa, T. / Ishii, S. / Nishimura, Y.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain.
Authors: Nagadoi, A. / Nakazawa, K. / Uda, H. / Okuno, K. / Maekawa, T. / Ishii, S. / Nishimura, Y.
#1: Journal: Genes Dev. / Year: 1990
Title: Erratum. Transcription Factor ATF Cdna Clones: An Extensive Family of Leucine Zipper Proteins Able to Selectively Form DNA-Binding Heterodimers
Authors: Hai, T.W. / Liu, F. / Coukos, W.J. / Green, M.R.
#2: Journal: Genes Dev. / Year: 1989
Title: Transcription Factor ATF Cdna Clones: An Extensive Family of Leucine Zipper Proteins Able to Selectively Form DNA-Binding Heterodimers
Authors: Hai, T.W. / Liu, F. / Coukos, W.J. / Green, M.R.
#3: Journal: Embo J. / Year: 1989
Title: Leucine Zipper Structure of the Protein Cre-BP1 Binding to the Cyclic AMP Response Element in Brain
Authors: Maekawa, T. / Sakura, H. / Kanei-Ishii, C. / Sudo, T. / Yoshimura, T. / Fujisawa, J. / Yoshida, M. / Ishii, S.
History
DepositionJun 9, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRE-BP1


Theoretical massNumber of molelcules
Total (without water)4,3371
Polymers4,3371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100THE 20 FINAL STRUCTURES EXHIBITED NO DISTANCE RESTRAINT VIOLATIONS GREATER THAN 0.1 ANGSTROMS AND DIHEDRAL ANGLE VIOLATIONS GREATER THAN 6.0 DEGREES.
Representative

-
Components

#1: Protein/peptide CRE-BP1 / ATF-2


Mass: 4336.971 Da / Num. of mol.: 1
Fragment: ZINC FINGER-LIKE SUBDOMAIN OF THE TRANSACTIVATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDNA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P15336

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURES OF N- AND C-TERMINI OF THE PEPTIDE FRAGMENT (MET 1 - PRO 6 AND LYS 36 - GLY 38) WERE DISORDERED AMONG THE 20 STRUCTURES.

-
Sample preparation

Sample conditionspH: 6.3 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

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

-
Processing

NMR software
NameDeveloperClassification
EMBOSSNAKAI,KIDERA,NAKAMURArefinement
EMBOSSstructure solution
RefinementMethod: SIMULATED ANNEALING, ENERGY MINIMIZATION / Software ordinal: 1
NMR ensembleConformer selection criteria: THE 20 FINAL STRUCTURES EXHIBITED NO DISTANCE RESTRAINT VIOLATIONS GREATER THAN 0.1 ANGSTROMS AND DIHEDRAL ANGLE VIOLATIONS GREATER THAN 6.0 DEGREES.
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