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- PDB-5u7g: Crystal Structure of the Catalytic Core of CBP -

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Basic information

Entry
Database: PDB / ID: 5u7g
TitleCrystal Structure of the Catalytic Core of CBP
ComponentsCREB-binding protein
KeywordsTRANSFERASE / Histone Acetyltransferase / Bromodomain / Zinc fingers / Transcriptional coactivator
Function / homology
Function and homology information


Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex ...Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / negative regulation of interferon-beta production / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / MRF binding / peroxisome proliferator activated receptor binding / face morphogenesis / negative regulation of transcription by RNA polymerase I / peptide-lysine-N-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / positive regulation of dendritic spine development / SMAD binding / behavioral response to cocaine / acetyltransferase activity / TFIIB-class transcription factor binding / positive regulation of double-strand break repair via homologous recombination / histone acetyltransferase complex / positive regulation of G1/S transition of mitotic cell cycle / long-term memory / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein destabilization / protein modification process / chromatin DNA binding / cellular response to virus / PML body / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / positive regulation of non-canonical NF-kappaB signal transduction / RNA polymerase II transcription regulator complex / cellular response to UV / disordered domain specific binding / rhythmic process / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / damaged DNA binding / molecular adaptor activity / transcription coactivator activity / nuclear body / protein domain specific binding / chromatin binding / protein-containing complex binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain ...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 / 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. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone lysine acetyltransferase CREBBP / Histone acetyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsPark, S. / Stanfield, R.L. / Martinez-Yamout, M.M. / Dyson, H.J. / Wilson, I.A. / Wright, P.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA096865 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)Y1-CO-1020 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)Y1-GM-1104 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Role of the CBP catalytic core in intramolecular SUMOylation and control of histone H3 acetylation.
Authors: Park, S. / Stanfield, R.L. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E.
History
DepositionDec 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,80110
Polymers145,2782
Non-polymers5238
Water81145
1
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9005
Polymers72,6391
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9005
Polymers72,6391
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)214.173, 87.170, 114.977
Angle α, β, γ (deg.)90.00, 109.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CREB-binding protein


Mass: 72638.820 Da / Num. of mol.: 2 / Fragment: UNP residues 1073-1550
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8QZV8, UniProt: P45481*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 77429 / % possible obs: 99.8 % / Redundancy: 5 % / CC1/2: 0.84 / Rmerge(I) obs: 0.112 / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BHW

4bhw


Resolution: 2.401→47.904 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2831 3886 5.02 %
Rwork0.254 --
obs0.2555 77429 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→47.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8852 0 8 45 8905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139140
X-RAY DIFFRACTIONf_angle_d1.06712348
X-RAY DIFFRACTIONf_dihedral_angle_d12.3415438
X-RAY DIFFRACTIONf_chiral_restr0.0571290
X-RAY DIFFRACTIONf_plane_restr0.0081600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4014-2.43070.39921190.37332350X-RAY DIFFRACTION90
2.4307-2.46140.36691310.34822600X-RAY DIFFRACTION98
2.4614-2.49380.38121420.33562567X-RAY DIFFRACTION98
2.4938-2.5280.35511570.33592614X-RAY DIFFRACTION100
2.528-2.56410.3581370.3322645X-RAY DIFFRACTION100
2.5641-2.60240.36881370.32252611X-RAY DIFFRACTION100
2.6024-2.6430.36241230.31732642X-RAY DIFFRACTION100
2.643-2.68640.32931250.3182632X-RAY DIFFRACTION100
2.6864-2.73270.33751300.3162653X-RAY DIFFRACTION100
2.7327-2.78240.37561360.32632634X-RAY DIFFRACTION100
2.7824-2.83590.35991290.32482627X-RAY DIFFRACTION100
2.8359-2.89380.33961490.32292643X-RAY DIFFRACTION100
2.8938-2.95670.31411460.30182602X-RAY DIFFRACTION99
2.9567-3.02540.3231490.3042619X-RAY DIFFRACTION100
3.0254-3.10110.3491430.30112634X-RAY DIFFRACTION100
3.1011-3.18490.32341500.29972605X-RAY DIFFRACTION100
3.1849-3.27860.34231270.30332657X-RAY DIFFRACTION100
3.2786-3.38440.29221440.29642631X-RAY DIFFRACTION100
3.3844-3.50530.30471300.26442669X-RAY DIFFRACTION100
3.5053-3.64560.31461490.25022618X-RAY DIFFRACTION100
3.6456-3.81150.27141500.23432634X-RAY DIFFRACTION100
3.8115-4.01230.26771220.2262658X-RAY DIFFRACTION100
4.0123-4.26360.22981370.20522663X-RAY DIFFRACTION100
4.2636-4.59250.20741430.19532654X-RAY DIFFRACTION100
4.5925-5.05420.22411360.1932665X-RAY DIFFRACTION100
5.0542-5.78450.22031430.20152663X-RAY DIFFRACTION100
5.7845-7.28380.27611640.22332647X-RAY DIFFRACTION99
7.2838-47.91310.22831380.21632706X-RAY DIFFRACTION98

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