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- PDB-4n3w: Crystal Structure of the Bromodomain-PHD Finger Module of Human T... -

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Basic information

Entry
Database: PDB / ID: 4n3w
TitleCrystal Structure of the Bromodomain-PHD Finger Module of Human Transcriptional Co-Activator CBP in complex with Acetylated Histone 4 Peptide (H4K20ac).
Components
  • CREB-binding protein
  • Histone H4 peptide
KeywordsTransferase/Nuclear Protein / histone binding / Transferase-Nuclear Protein complex
Function / homology
Function and homology information


Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / NFE2L2 regulating ER-stress associated genes / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / histone H3K18 acetyltransferase activity / peptide lactyltransferase (CoA-dependent) activity / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes ...Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / NFE2L2 regulating ER-stress associated genes / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / histone H3K18 acetyltransferase activity / peptide lactyltransferase (CoA-dependent) activity / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / regulation of smoothened signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulating MDR associated enzymes / MRF binding / embryonic digit morphogenesis / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / negative regulation of transcription by RNA polymerase I / RUNX3 regulates NOTCH signaling / Regulation of NFE2L2 gene expression / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of gene expression by Hypoxia-inducible Factor / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Nuclear events mediated by NFE2L2 / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / TRAF6 mediated IRF7 activation / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / Notch-HLH transcription pathway / acetyltransferase activity / Formation of paraxial mesoderm / stimulatory C-type lectin receptor signaling pathway / FOXO-mediated transcription of cell death genes / regulation of nucleotide-excision repair / positive regulation of transforming growth factor beta receptor signaling pathway / Zygotic genome activation (ZGA) / histone acetyltransferase activity / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / Attenuation phase / cAMP/PKA signal transduction / protein-lysine-acetyltransferase activity / histone acetyltransferase / cellular response to nutrient levels / canonical NF-kappaB signal transduction / positive regulation of double-strand break repair via homologous recombination / regulation of cellular response to heat / Regulation of lipid metabolism by PPARalpha / negative regulation of megakaryocyte differentiation / NPAS4 regulates expression of target genes / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / BMAL1:CLOCK,NPAS2 activates circadian expression / Transcriptional and post-translational regulation of MITF-M expression and activity / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / Activation of gene expression by SREBF (SREBP) / Packaging Of Telomere Ends / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / rhythmic process / CD209 (DC-SIGN) signaling / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Heme signaling / Defective pyroptosis / HDACs deacetylate histones / PPARA activates gene expression / Transcriptional regulation by small RNAs / Cytoprotection by HMOX1 / Transcriptional activation of mitochondrial biogenesis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / protein destabilization / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein localization to nucleus / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
Similarity search - Function
Histone acetyltransferase KAT11-type 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 / : ...Histone acetyltransferase KAT11-type 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 / : / 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. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Nuclear receptor coactivator, interlocking / Bromodomain-like / Histone Acetyltransferase; Chain A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Histone H4 / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPlotnikov, A.N. / Yang, S. / Zhou, M.-M.
CitationJournal: Structure / Year: 2014
Title: Structural Insights into Acetylated-Histone H4 Recognition by the Bromodomain-PHD Finger Module of Human Transcriptional Coactivator CBP.
Authors: Plotnikov, A.N. / Yang, S. / Zhou, T.J. / Rusinova, E. / Frasca, A. / Zhou, M.M.
History
DepositionOct 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
C: Histone H4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8774
Polymers29,7462
Non-polymers1312
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-3 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.460, 59.312, 53.444
Angle α, β, γ (deg.)90.00, 102.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CREB-binding protein


Mass: 27950.959 Da / Num. of mol.: 1 / Fragment: Bromodomain-PHD Finger Module, residues 1080-1316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793, histone acetyltransferase
#2: Protein/peptide Histone H4 peptide


Mass: 1795.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: biomolecule has been synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3,350, 0.2 M magnesium chloride, and 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 31, 2010
RadiationMonochromator: CHANNEL CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 12112 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.58 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.894 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.158 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28572 1119 5.1 %RANDOM
Rwork0.2333 ---
all0.256 22003 --
obs0.23612 22003 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0 Å22.36 Å2
2--0.6 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 2 127 1702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021614
X-RAY DIFFRACTIONr_bond_other_d0.0010.021515
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9752182
X-RAY DIFFRACTIONr_angle_other_deg0.95133511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2245185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24624.44481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80415286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5111510
X-RAY DIFFRACTIONr_chiral_restr0.1340.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 73 -
Rwork0.273 1431 -
obs--93.82 %

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