3DWY

Crystal Structure of the Bromodomain of Human CREBBP

> Summary

Summary for 3DWY

DescriptorCREB-binding protein (E.C.2.3.1.48)
Functional Keywordsbromodomain, creb binding protein, structural genomics consortium, sgc, activator, disease mutation, host-virus interaction, metal-binding, methylation, nucleus, phosphoprotein, transcription, transcription regulation, transferase, zinc-finger
Biological sourceHomo sapiens (Human)
Cellular locationCytoplasm Q92793
Total number of polymer chains2
Total molecular weight28633.15
Authors
Primary citation
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.
Histone recognition and large-scale structural analysis of the human bromodomain family.
Cell(Cambridge,Mass.), 149:214-231, 2012
PubMed: 22464331
DOI: 10.1016/j.cell.2012.02.013
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.98 Å)
NMR Information
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.221302.5%8.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3dwy
no rotation
Molmil generated image of 3dwy
rotated about x axis by 90°
Molmil generated image of 3dwy
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 3dwy
no rotation
Molmil generated image of 3dwy
rotated about x axis by 90°
Molmil generated image of 3dwy
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (3dwy.pdb1.gz [22.88 KB])
Coordinate files for Biological unit (3dwy.pdb2.gz [21.73 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BCREB-binding proteinpolymer11914223.52
UniProt (Q92793)
Pfam (PF00439)
Pfam (PF06001)
Homo sapiens (Human)@PDBj
1,2-ETHANEDIOLnon-polymer62.13
waterwater18.0172

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight28446.9
Non-Polymers*Number of molecules3
Total molecular weight186.2
All*Total molecular weight28633.1
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.98 Å)

Cell axes121.484121.48440.378
Cell angles90.0090.00120.00
SpacegroupH 3
Resolution limits23.65 - 1.98
the highest resolution shell value2.031 - 1.980
R-factor0.162
R-work0.15900
the highest resolution shell value0.248
R-free0.21900
the highest resolution shell value0.394
RMSD bond length0.015
RMSD bond angle1.414

Data Collection Statistics

Resolution limits23.65 - 1.98
the highest resolution shell value -
Number of reflections15467
Rmerge_l_obs0.086
the highest resolution shell value0.624
Completeness99.9
Redundancy3.7
the highest resolution shell value3.6

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP7.5277

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0000123cellular_componenthistone acetyltransferase complex
A0016604cellular_componentnuclear body
A0000790cellular_componentnuclear chromatin
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0016407molecular_functionacetyltransferase activity
A0003682molecular_functionchromatin binding
A0000987molecular_functioncore promoter proximal region sequence-specific DNA binding
A0003684molecular_functiondamaged DNA binding
A0004402molecular_functionhistone acetyltransferase activity
A0043426molecular_functionMRF binding
A0002039molecular_functionp53 binding
A0034212molecular_functionpeptide N-acetyltransferase activity
A0001102molecular_functionRNA polymerase II activating transcription factor binding
A0001105molecular_functionRNA polymerase II transcription coactivator activity
A0001085molecular_functionRNA polymerase II transcription factor binding
A0004871molecular_functionsignal transducer activity
A0003713molecular_functiontranscription coactivator activity
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0008134molecular_functiontranscription factor binding
A0001078molecular_functiontranscriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
A0001191molecular_functiontranscriptional repressor activity, RNA polymerase II transcription factor binding
A0008270molecular_functionzinc ion binding
A1904837biological_processbeta-catenin-TCF complex assembly
A0044255biological_processcellular lipid metabolic process
A0034644biological_processcellular response to UV
A0042733biological_processembryonic digit morphogenesis
A0016573biological_processhistone acetylation
A0042592biological_processhomeostatic process
A0018076biological_processN-terminal peptidyl-lysine acetylation
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0007219biological_processNotch signaling pathway
A0045893biological_processpositive regulation of transcription, DNA-templated
A0032481biological_processpositive regulation of type I interferon production
A0006473biological_processprotein acetylation
A0006461biological_processprotein complex assembly
A0042981biological_processregulation of apoptotic process
A1900034biological_processregulation of cellular response to heat
A0008589biological_processregulation of smoothened signaling pathway
A0061418biological_processregulation of transcription from RNA polymerase II promoter in response to hypoxia
A0006355biological_processregulation of transcription, DNA-templated
A0001666biological_processresponse to hypoxia
A0048511biological_processrhythmic process
A0007165biological_processsignal transduction
A0002223biological_processstimulatory C-type lectin receptor signaling pathway
A0006367biological_processtranscription initiation from RNA polymerase II promoter
A0016032biological_processviral process
B0005737cellular_componentcytoplasm
B0000123cellular_componenthistone acetyltransferase complex
B0016604cellular_componentnuclear body
B0000790cellular_componentnuclear chromatin
B0005654cellular_componentnucleoplasm
B0005634cellular_componentnucleus
B0016407molecular_functionacetyltransferase activity
B0003682molecular_functionchromatin binding
B0000987molecular_functioncore promoter proximal region sequence-specific DNA binding
B0003684molecular_functiondamaged DNA binding
B0004402molecular_functionhistone acetyltransferase activity
B0043426molecular_functionMRF binding
B0002039molecular_functionp53 binding
B0034212molecular_functionpeptide N-acetyltransferase activity
B0001102molecular_functionRNA polymerase II activating transcription factor binding
B0001105molecular_functionRNA polymerase II transcription coactivator activity
B0001085molecular_functionRNA polymerase II transcription factor binding
B0004871molecular_functionsignal transducer activity
B0003713molecular_functiontranscription coactivator activity
B0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
B0008134molecular_functiontranscription factor binding
B0001078molecular_functiontranscriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
B0001191molecular_functiontranscriptional repressor activity, RNA polymerase II transcription factor binding
B0008270molecular_functionzinc ion binding
B1904837biological_processbeta-catenin-TCF complex assembly
B0044255biological_processcellular lipid metabolic process
B0034644biological_processcellular response to UV
B0042733biological_processembryonic digit morphogenesis
B0016573biological_processhistone acetylation
B0042592biological_processhomeostatic process
B0018076biological_processN-terminal peptidyl-lysine acetylation
B0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
B0007219biological_processNotch signaling pathway
B0045893biological_processpositive regulation of transcription, DNA-templated
B0032481biological_processpositive regulation of type I interferon production
B0006473biological_processprotein acetylation
B0006461biological_processprotein complex assembly
B0042981biological_processregulation of apoptotic process
B1900034biological_processregulation of cellular response to heat
B0008589biological_processregulation of smoothened signaling pathway
B0061418biological_processregulation of transcription from RNA polymerase II promoter in response to hypoxia
B0006355biological_processregulation of transcription, DNA-templated
B0001666biological_processresponse to hypoxia
B0048511biological_processrhythmic process
B0007165biological_processsignal transduction
B0002223biological_processstimulatory C-type lectin receptor signaling pathway
B0006367biological_processtranscription initiation from RNA polymerase II promoter
B0016032biological_processviral process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15BINDING SITE FOR RESIDUE EDO A 1
ChainResidue
ALEU1109
ALEU1166
AARG1173
BLEU1109
BPRO1110

AC22BINDING SITE FOR RESIDUE EDO A 2
ChainResidue
AASP1116
APRO1117

AC32BINDING SITE FOR RESIDUE EDO A 3
ChainResidue
ATRP1165
ATYR1175

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
EDO_3dwy_A_131,2-ETHANEDIOL binding site
ChainResidueligand
ALEU1109-PRO1110EDO: 1,2-ETHANEDIOL
AARG1173EDO: 1,2-ETHANEDIOL

EDO_3dwy_A_261,2-ETHANEDIOL binding site
ChainResidueligand
APRO1114-GLN1118EDO: 1,2-ETHANEDIOL
APHE1126EDO: 1,2-ETHANEDIOL

EDO_3dwy_A_341,2-ETHANEDIOL binding site
ChainResidueligand
ATRP1165EDO: 1,2-ETHANEDIOL
ALYS1170EDO: 1,2-ETHANEDIOL
ATYR1175EDO: 1,2-ETHANEDIOL
ASER1179EDO: 1,2-ETHANEDIOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS006332Bromodomain signature. [STANVFHG]-x(2)-[FAS]-x(4)-[DNSPAKT]-x(0,7)-[DENQTFG]-Y-[HFYLRKT]-x(2)
ChainResidueDetails
ANA*
BNA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb3dwy.ent.gz (47.66 KB)
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all (no-compress)pdb3dwy.ent (202.18 KB)
header onlypdb3dwy.ent.gz (6.65 KB)
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PDBx/mmCIF3dwy.cif.gz (61.22 KB)
PDBMLall3dwy.xml.gz (90.83 KB)
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no-atom3dwy-noatom.xml.gz (19.21 KB)
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ext-atom3dwy-extatom.xml.gz (48.89 KB)
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PDBMLplusall3dwy-plus.xml.gz (94.42 KB)
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no-atom3dwy-plus-noatom.xml.gz (22.8 KB)
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add only3dwy-add.xml.gz (3.59 KB)
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RDF3dwy.rdf.gz (34.16 KB)
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Structure factorsr3dwysf.ent.gz (249.87 KB)
Biological unit (PDB format)3dwy.pdb1.gz (22.88 KB) (A)
*author and software defined assembly, 1 molecule(s) (monomeric)
Display
3dwy.pdb2.gz (21.73 KB) (B)
*author and software defined assembly, 1 molecule(s) (monomeric)
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Validation reportsPDF3dwy​_validation.pdf.gz (270.54 KB)
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PDF-full3dwy​_full​_validation.pdf.gz (271.96 KB)
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XML3dwy​_validation.xml.gz (13.44 KB)
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PNG3dwy​_multipercentile​_validation.png.gz (149.48 KB)
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SVG3dwy​_multipercentile​_validation.svg.gz (931 B)
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Sequence (fasta)3dwy​_seq.txt
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