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- PDB-3dwy: Crystal Structure of the Bromodomain of Human CREBBP -

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Basic information

Entry
Database: PDB / ID: 3dwy
TitleCrystal Structure of the Bromodomain of Human CREBBP
ComponentsCREB-binding protein
KeywordsTRANSFERASE / bromodomain / CREB binding protein / structural genomics consortium / SGC / Activator / Disease mutation / Host-virus interaction / Metal-binding / Methylation / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / histone H3K27 acetyltransferase activity / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / MRF binding ...NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / histone H3K27 acetyltransferase activity / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / MRF binding / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / negative regulation of transcription by RNA polymerase I / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / peptide-lysine-N-acetyltransferase activity / NFE2L2 regulating anti-oxidant/detoxification enzymes / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / embryonic digit morphogenesis / homeostatic process / Notch-HLH transcription pathway / protein acetylation / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / Attenuation phase / regulation of cellular response to heat / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Formation of the beta-catenin:TCF transactivating complex / protein destabilization / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein localization to nucleus / transcription corepressor activity / cellular response to UV / rhythmic process / Circadian Clock / p53 binding / TRAF3-dependent IRF activation pathway / HATs acetylate histones / protein-containing complex assembly / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / response to hypoxia / nuclear body / chromatin binding / chromatin / regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / 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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Fedorov, O. / Karim, R. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wickstroem, M. / Bountra, C. ...Filippakopoulos, P. / Picaud, S. / Fedorov, O. / Karim, R. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wickstroem, M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionJul 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,6335
Polymers28,4472
Non-polymers1863
Water3,099172
1
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4104
Polymers14,2231
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CREB-binding protein


Theoretical massNumber of molelcules
Total (without water)14,2231
Polymers14,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.484, 121.484, 40.378
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASPASP2AA1086 - 11168 - 38
21LYSLYSASPASP2BB1086 - 11168 - 38
12PROPROLYSLYS4AA1117 - 113039 - 52
22PROPROLYSLYS4BB1117 - 113039 - 52
13ASNASNASNASN2AA1131 - 116853 - 90
23ASNASNASNASN2BB1131 - 116853 - 90
14ARGARGSERSER4AA1169 - 117291 - 94
24ARGARGSERSER4BB1169 - 117291 - 94
15ARGARGLEULEU6AA1173 - 119695 - 118
25ARGARGLEULEU6BB1173 - 119695 - 118

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Components

#1: Protein CREB-binding protein /


Mass: 14223.349 Da / Num. of mol.: 2 / Fragment: Bromo domain: residues 1084-1197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q92793, histone acetyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M KSCN, 25% PEG3350, 5% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.98→23.65 Å / Num. obs: 15467 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 11.6
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2 / Num. unique all: 2257 / Rsym value: 0.086 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.96 Å
Translation2.5 Å22.96 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble of 2NXB,2OO1,2OSS,2OUO,2RFJ,3DAI

2nxb

2oo1

2oss

2ouo

2rfj

3dai


Resolution: 1.98→23.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU B: 8.047 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 771 5 %RANDOM
Rwork0.159 ---
all0.162 15462 --
obs0.162 15460 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.41 Å2 / Biso mean: 30.488 Å2 / Biso min: 6.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å2-0.47 Å20 Å2
2---0.93 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.98→23.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 12 172 2041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221932
X-RAY DIFFRACTIONr_bond_other_d0.0010.021344
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9792624
X-RAY DIFFRACTIONr_angle_other_deg1.08733272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38124.37596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80215324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9941512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_nbd_refined0.1950.2394
X-RAY DIFFRACTIONr_nbd_other0.1870.21361
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2912
X-RAY DIFFRACTIONr_nbtor_other0.0870.2891
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.210
X-RAY DIFFRACTIONr_mcbond_it3.56531186
X-RAY DIFFRACTIONr_mcbond_other1.1433435
X-RAY DIFFRACTIONr_mcangle_it4.32251860
X-RAY DIFFRACTIONr_scbond_it6.8928882
X-RAY DIFFRACTIONr_scangle_it9.0311764
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A406TIGHT POSITIONAL0.180.05
B801MEDIUM POSITIONAL0.610.5
A309LOOSE POSITIONAL0.475
B406TIGHT THERMAL2.650.5
A801MEDIUM THERMAL2.92
B309LOOSE THERMAL2.8310
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 66 -
Rwork0.248 1079 -
all-1145 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4022-0.43080.40231.2811-0.0561.86170.03230.04230.2543-0.0795-0.01170.0882-0.1547-0.121-0.0206-0.11410.00880.0074-0.1197-0.001-0.069327.197612.206234.3427
24.1509-0.8157-0.48473.0678-0.26433.358-0.0432-0.1852-0.17640.122-0.1027-0.09660.33860.06620.1459-0.06350.03950.0347-0.05540.0171-0.05560.801216.689138.467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1084 - 11976 - 119
2X-RAY DIFFRACTION2BB1085 - 11967 - 118

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