[English] 日本語
Yorodumi
- PDB-2agh: Structural basis for cooperative transcription factor binding to ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2agh
TitleStructural basis for cooperative transcription factor binding to the CBP coactivator
Components
  • Crebbp protein
  • Myb proto-oncogene protein
  • Zinc finger protein HRX
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


positive regulation of testosterone secretion / Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / myeloid cell development / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / positive regulation of hepatic stellate cell proliferation / Attenuation phase / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells ...positive regulation of testosterone secretion / Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / myeloid cell development / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / positive regulation of hepatic stellate cell proliferation / Attenuation phase / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / cAMP response element binding protein binding / Notch-HLH transcription pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / negative regulation of hematopoietic progenitor cell differentiation / positive regulation of hepatic stellate cell activation / skeletal muscle cell proliferation / positive regulation of cell adhesion molecule production / negative regulation of DNA methylation-dependent heterochromatin formation / positive regulation of transforming growth factor beta production / germ-line stem cell population maintenance / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-cysteine methyltransferase activity / Cytoprotection by HMOX1 / response to potassium ion / histone H3K4 trimethyltransferase activity / Estrogen-dependent gene expression / CD209 (DC-SIGN) signaling / embryonic digestive tract development / peptide lactyltransferase (CoA-dependent) activity / unmethylated CpG binding / Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / outer kinetochore / protein K48-linked deubiquitination / myeloid cell differentiation / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / negative regulation of interferon-beta production / histone H3K27 acetyltransferase activity / definitive hemopoiesis / MRF binding / cellular response to interleukin-6 / regulation of short-term neuronal synaptic plasticity / histone H3K4 methyltransferase activity / peroxisome proliferator activated receptor binding / anterior/posterior pattern specification / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / face morphogenesis / T-helper 2 cell differentiation / embryonic hemopoiesis / negative regulation of transcription by RNA polymerase I / cellular response to hepatocyte growth factor stimulus / stem cell division / WD40-repeat domain binding / acetyltransferase activity / Formation of WDR5-containing histone-modifying complexes / histone acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / positive regulation of dendritic spine development / histone methyltransferase complex / minor groove of adenine-thymine-rich DNA binding / TFIIB-class transcription factor binding / exploration behavior / positive regulation of collagen biosynthetic process / MLL1 complex / histone acetyltransferase complex / homeostasis of number of cells / positive regulation of glial cell proliferation / : / membrane depolarization / protein-lysine-acetyltransferase activity / cellular response to transforming growth factor beta stimulus / positive regulation of G1/S transition of mitotic cell cycle / long-term memory / histone acetyltransferase / negative regulation of fibroblast proliferation / positive regulation of double-strand break repair via homologous recombination / spleen development / negative regulation of megakaryocyte differentiation / cellular response to retinoic acid / energy homeostasis / behavioral response to cocaine / canonical NF-kappaB signal transduction / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / homeostasis of number of cells within a tissue / positive regulation of smooth muscle cell proliferation / cellular response to nutrient levels / B cell differentiation / Transferases; Transferring one-carbon groups; Methyltransferases / transcription initiation-coupled chromatin remodeling / response to ischemia / thymus development
Similarity search - Function
Coactivator CBP, KIX domain / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 ...Coactivator CBP, KIX domain / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Cysteine-rich motif following a subset of SET domains / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Post-SET domain / Post-SET domain profile. / Serum Albumin; Chain A, Domain 1 / Myb-type HTH DNA-binding domain profile. / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Myb domain / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Nuclear receptor coactivator, interlocking / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator Myb / Histone lysine acetyltransferase CREBBP / Histone-lysine N-methyltransferase 2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDe Guzman, R.N. / Goto, N.K. / Dyson, H.J. / Wright, P.E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis for Cooperative Transcription Factor Binding to the CBP Coactivator
Authors: De Guzman, R.N. / Goto, N.K. / Dyson, H.J. / Wright, P.E.
History
DepositionJul 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 7, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_ensemble / pdbx_nmr_refine / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_refine.method ..._pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_refine.method / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myb proto-oncogene protein
B: Crebbp protein
C: Zinc finger protein HRX


Theoretical massNumber of molelcules
Total (without water)16,6113
Polymers16,6113
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100lowest energy and lowest distance and angle violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Myb proto-oncogene protein / C-myb


Mass: 2947.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myb / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06876
#2: Protein Crebbp protein


Mass: 10353.856 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CBP, CREBBP / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45481
#3: Protein/peptide Zinc finger protein HRX / ALL-1 / Trithorax-like protein


Mass: 3309.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLL, ALL1, HRX, HTRX, TRX1 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03164

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N HSQC
1212D 13C HSQC
1312D 13C-{13C} SED
1412D 13C-{15N} SED
1513D HNCA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HBHA(CBCACO)NH
1913D C(CO)NH-TOCSY
11013D H(CCO)NH-TOCSY
11113D CCH-COSY
11213D CCH-TOCSY
11313D (H)CCH-TOCSY
11413D HACAHB-COSY
11513D HNHB
11613D HNHA
11713D 13C-EDITED NOESY
11813D 13C,15N-EDITED NOESY
11913D 12C-FILTERED/13C-EDITED NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.8 mM 15N,13C-labeled protein (e.g. CBP) + 3 fold excess of unlabeled binding partners (MYB + MLL), 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O
213C,15N-MYB + UNLABELED CBP & MYB, 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O
313C,15N-MLL + UNLABELED CBP & MLL, 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O
Sample conditionspH: 5.5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002
Bruker DRXBrukerDRX7503
Bruker DRXBrukerDRX6004

-
Processing

NMR software
NameDeveloperClassification
AmberDavid Case et al.refinement
DYANAGuntert, Braun and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: iNITIAL STRUCTURE CALCULATION USING TORSION ANGLE DYNAMICS IN DYANA FOLLOWED BY REFINEMENT IN AMBER USING SIMULATED ANNEALING AND ENERGY MINIMIZATION IN VACUO AND GENERALIZED BORN POTENTIAL
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy and lowest distance and angle violations
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