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- PDB-1bhi: STRUCTURE OF TRANSACTIVATION DOMAIN OF CRE-BP1/ATF-2, NMR, 20 STR... -

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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 / positive regulation of transforming growth factor beta2 production / cellular response to anisomycin ...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 / positive regulation of transforming growth factor beta2 production / cellular response to anisomycin / cAMP response element binding / leucine zipper domain binding / cAMP response element binding protein binding / histone H2B acetyltransferase activity / positive regulation of mitochondrial membrane permeability involved in apoptotic process / brainstem development / cellular response to leucine starvation / NK T cell differentiation / histone H4 acetyltransferase activity / neurofilament cytoskeleton organization / vacuole 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 / Activation of the AP-1 family of transcription factors / p38MAPK cascade / outflow tract morphogenesis / white fat cell differentiation / peptidyl-threonine phosphorylation / Response of EIF2AK4 (GCN2) to amino acid deficiency / adipose tissue development / BMP signaling pathway / hematopoietic progenitor cell differentiation / histone acetyltransferase activity / : / cis-regulatory region sequence-specific DNA binding / JNK cascade / transcription initiation-coupled chromatin remodeling / negative regulation of angiogenesis / Regulation of PTEN gene transcription / RNA polymerase II transcription regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of DNA Repair Genes / promoter-specific chromatin binding / liver development / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / cellular response to virus / lipid metabolic process / RNA polymerase II transcription regulator complex / protein import into nucleus / sequence-specific double-stranded DNA binding / : / site of double-strand break / HATs acetylate histones / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial outer membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / 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 / Basic-leucine zipper domain superfamily / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...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 / Basic-leucine zipper domain superfamily / 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRE-BP1


Theoretical massNumber of molelcules
Total (without water)4,3371
Polymers4,3371
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 / 100THE 20 FINAL STRUCTURES EXHIBITED NO DISTANCE RESTRAINT VIOLATIONS GREATER THAN 0.1 ANGSTROMS AND DIHEDRAL ANGLE VIOLATIONS GREATER THAN 6.0 DEGREES.
Representative

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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

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Experimental details

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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.

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Sample preparation

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

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NMR measurement

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

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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

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