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- PDB-3gg3: Crystal Structure of the Bromodomain of Human PCAF -

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Basic information

Entry
Database: PDB / ID: 3gg3
TitleCrystal Structure of the Bromodomain of Human PCAF
ComponentsHistone acetyltransferase PCAF
KeywordsTRANSFERASE / PCAF / K(lysine) acetyltransferase 2B / KAT2B / GCN5 / GCN5L / P / P/CAF / CREBBP-associated factor / p300/CBP-associated factor / SGC / Structural Genomics Consortium / Acyltransferase / Bromodomain / Cell cycle / Host-virus interaction / Nucleus / Phosphoprotein / Transcription / Transcription regulation
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / Physiological factors / positive regulation of attachment of mitotic spindle microtubules to kinetochore / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor ...regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / Physiological factors / positive regulation of attachment of mitotic spindle microtubules to kinetochore / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / histone H3 acetyltransferase activity / positive regulation of fatty acid biosynthetic process / actomyosin / internal peptidyl-lysine acetylation / cyclin-dependent protein serine/threonine kinase inhibitor activity / ATAC complex / N-terminal peptidyl-lysine acetylation / I band / SAGA complex / cellular response to parathyroid hormone stimulus / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / limb development / RUNX3 regulates NOTCH signaling / A band / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / NOTCH3 Intracellular Domain Regulates Transcription / histone acetyltransferase binding / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / regulation of cell division / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / protein acetylation / regulation of RNA splicing / Formation of paraxial mesoderm / acetyltransferase activity / RNA Polymerase I Transcription Initiation / regulation of embryonic development / regulation of DNA repair / histone acetyltransferase activity / positive regulation of gluconeogenesis / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / positive regulation of glycolytic process / gluconeogenesis / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / positive regulation of neuron projection development / Metalloprotease DUBs / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / memory / kinetochore / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / vasodilation / histone deacetylase binding / cellular response to insulin stimulus / rhythmic process / cellular response to oxidative stress / heart development / HATs acetylate histones / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / cell cycle / negative regulation of cell population proliferation / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A ...PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsFilippakopoulos, P. / Keates, T. / Picaud, S. / Rehana, K. / Fedorov, O. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Keates, T. / Picaud, S. / Rehana, K. / Fedorov, O. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / 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
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: 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 1.4Sep 6, 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.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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

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Assembly

Deposited unit
A: Histone acetyltransferase PCAF
B: Histone acetyltransferase PCAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3803
Polymers28,3452
Non-polymers351
Water2,162120
1
A: Histone acetyltransferase PCAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2082
Polymers14,1721
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone acetyltransferase PCAF


Theoretical massNumber of molelcules
Total (without water)14,1721
Polymers14,1721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.226, 99.226, 101.137
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-103-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 726 - 828 / Label seq-ID: 14 - 116

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Histone acetyltransferase PCAF / Histone acetylase PCAF / P300/CBP-associated factor / P/CAF


Mass: 14172.371 Da / Num. of mol.: 2 / Fragment: UNP residues 715-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCAF / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q92831, histone acetyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.38 Å3/Da / Density % sol: 63.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 20% PEG10K, 4% Ethylene Glycol, 0.1M HEPES pH 8.2, 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: Jul 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.25→32.743 Å / Num. all: 17604 / Num. obs: 17604 / % possible obs: 100 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 12.5
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2 / Num. unique all: 2567 / Rsym value: 0.456 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.03 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.74 Å
Translation2.5 Å32.74 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: PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI

2nxb

2oo1

2oss

2ouo

2rfj

3dai


Resolution: 2.25→32.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.855 / SU B: 9.935 / SU ML: 0.129 / SU R Cruickshank DPI: 0.214 / SU Rfree: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 892 5.1 %RANDOM
Rwork0.207 ---
all0.209 17610 --
obs0.209 17594 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 83.81 Å2 / Biso mean: 31.265 Å2 / Biso min: 7.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 2.25→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 1 120 1849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221804
X-RAY DIFFRACTIONr_bond_other_d0.0010.021280
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9672436
X-RAY DIFFRACTIONr_angle_other_deg0.90333119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42524.14682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1615321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.367157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_mcbond_it3.90631081
X-RAY DIFFRACTIONr_mcbond_other1.253422
X-RAY DIFFRACTIONr_mcangle_it5.52151753
X-RAY DIFFRACTIONr_scbond_it9.3028723
X-RAY DIFFRACTIONr_scangle_it11.70911683
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1380 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.535
LOOSE THERMAL3.9510
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 70 -
Rwork0.384 1211 -
all-1281 -
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)
15.1168-1.09631.93746.39481.50654.51230.14150.1425-0.1049-0.1859-0.29690.11370.2148-0.11080.15540.0785-0.0421-0.04050.1848-0.03280.078420.517511.848515.019
22.0872-0.54692.80663.00870.51334.34470.2089-0.2373-0.03540.1715-0.45710.58060.2881-0.54980.24820.1818-0.0714-0.03790.3243-0.10490.201713.451212.726520.3887
32.51971.7492.23332.17022.29213.1030.3503-0.1608-0.11890.3228-0.2957-0.15360.2336-0.2236-0.05460.1909-0.1192-0.10680.20220.02150.133225.117211.510123.3669
44.1823-3.075-1.012712.7729-3.55212.020.1215-0.1826-0.1450.0318-0.11420.3798-0.10870.2168-0.00730.1313-0.104-0.14670.29230.12110.212230.421322.847918.0013
54.8994-1.2167-0.05494.98620.0223.6558-0.1956-0.0794-0.48670.99250.10620.16870.10420.12470.08940.27690.00320.0290.02460.03870.110233.910612.34844.7978
67.31954.0922-4.7856.6685-0.78023.9490.55950.08290.61210.4086-0.15960.3487-0.3145-0.1376-0.39980.3427-0.01470.01940.06230.08460.167538.100531.239133.7327
72.0230.3103-1.2964.34711.85342.8466-0.07090.1580.0180.2535-0.0630.70190.1148-0.1540.13390.0959-0.01550.01590.08220.01510.227429.623718.832338.4269
80.5289-0.40160.1747.70593.59261.93190.0520.1247-0.22550.4159-0.08440.36890.24080.04380.03230.1332-0.0511-0.09090.1341-0.00490.190934.01688.159734.5163
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A725 - 760
2X-RAY DIFFRACTION2A761 - 780
3X-RAY DIFFRACTION3A781 - 819
4X-RAY DIFFRACTION4A820 - 831
5X-RAY DIFFRACTION5B725 - 751
6X-RAY DIFFRACTION6B752 - 765
7X-RAY DIFFRACTION7B766 - 808
8X-RAY DIFFRACTION8B809 - 828

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