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- PDB-3d7c: Crystal structure of the bromodomain of human GCN5, the general c... -

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Basic information

Entry
Database: PDB / ID: 3d7c
TitleCrystal structure of the bromodomain of human GCN5, the general control of amino-acid synthesis protein 5-like 2
ComponentsGeneral control of amino acid synthesis protein 5-like 2
KeywordsTRANSCRIPTION / GCN5 / bromodomain / amino-acid synthesis / Structural Genomics Consortium / SGC / Host-virus interaction / Nucleus / Phosphoprotein / Transcription regulation / Transferase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / positive regulation of cell projection organization / : / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / positive regulation of cardiac muscle cell differentiation ...histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / positive regulation of cell projection organization / : / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / positive regulation of cardiac muscle cell differentiation / regulation of stem cell population maintenance / regulation of bone development / regulation of regulatory T cell differentiation / negative regulation of centriole replication / transcription factor TFTC complex / telencephalon development / histone H3 acetyltransferase activity / internal peptidyl-lysine acetylation / histone H3K18 acetyltransferase activity / ATAC complex / SAGA complex / Cardiogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / limb development / RUNX3 regulates NOTCH signaling / regulation of T cell activation / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / midbrain development / intracellular distribution of mitochondria / regulation of cell division / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / regulation of RNA splicing / Formation of paraxial mesoderm / RNA Polymerase I Transcription Initiation / regulation of embryonic development / histone acetyltransferase complex / long-term memory / regulation of DNA repair / negative regulation of gluconeogenesis / somitogenesis / histone acetyltransferase activity / positive regulation of gluconeogenesis / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to nutrient levels / cellular response to nerve growth factor stimulus / neural tube closure / gluconeogenesis / positive regulation of cytokine production / regulation of synaptic plasticity / multicellular organism growth / regulation of protein stability / B-WICH complex positively regulates rRNA expression / mitotic spindle / response to organic cyclic compound / 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 / histone deacetylase binding / cellular response to tumor necrosis factor / heart development / HATs acetylate histones / fibroblast proliferation / protein phosphatase binding / DNA-binding transcription factor binding / in utero embryonic development / transcription coactivator activity / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / cytoplasm
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 KAT2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsFilippakopoulos, P. / Eswaran, J. / Picaud, S. / Fedorov, O. / Murray, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.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
DepositionMay 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Aug 30, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General control of amino acid synthesis protein 5-like 2
B: General control of amino acid synthesis protein 5-like 2


Theoretical massNumber of molelcules
Total (without water)26,5752
Polymers26,5752
Non-polymers00
Water2,864159
1
A: General control of amino acid synthesis protein 5-like 2


Theoretical massNumber of molelcules
Total (without water)13,2871
Polymers13,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: General control of amino acid synthesis protein 5-like 2


Theoretical massNumber of molelcules
Total (without water)13,2871
Polymers13,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.428, 72.862, 75.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 730 - 835 / Label seq-ID: 5 - 110

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

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Components

#1: Protein General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / hsGCN5 / STAF97


Mass: 13287.313 Da / Num. of mol.: 2 / Fragment: Bromo domain: Residues 729-837
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCN5L2, GCN5, HGCN5 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q92830
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 25% PEG 3350, 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: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.06→45.41 Å / Num. all: 16156 / Num. obs: 16003 / % possible obs: 98.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 9.7
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2 / Rsym value: 0.736 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.98 Å
Translation2.5 Å38.98 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OSS

2oss


Resolution: 2.06→45.41 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.018 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25654 802 5 %RANDOM
Rwork0.17888 ---
obs0.18272 15959 98.78 %-
all-15959 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.483 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.06→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 0 159 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221817
X-RAY DIFFRACTIONr_bond_other_d0.0010.021283
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.982462
X-RAY DIFFRACTIONr_angle_other_deg1.05833109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34523.01283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11615312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0651513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.04631095
X-RAY DIFFRACTIONr_mcbond_other1.5073421
X-RAY DIFFRACTIONr_mcangle_it4.89651774
X-RAY DIFFRACTIONr_scbond_it7.828722
X-RAY DIFFRACTIONr_scangle_it9.88211688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1456 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.665
Bloose thermal4.2210
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 78 -
Rwork0.233 1077 -
obs--99.31 %
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)
12.5738-1.271-0.3571.64720.5981.1527-0.0387-0.0325-0.07990.0407-0.03120.0720.10120.01710.06990.02270.00320.01420.09520.00960.04059.83917.1011.956
22.2387-1.0331-0.4022.59830.75980.8067-0.0602-0.13870.00470.141-0.0112-0.00960.06790.03430.07140.0268-0.00070.0070.11380.01810.0286-0.10919.6669.45
31.3868-0.4283-0.15941.41230.77710.90440.05860.03810.0399-0.0761-0.0431-0.0838-0.1064-0.0011-0.01550.0420.0103-0.00090.08780.0040.06644.52927.095-1.169
43.53930.2622-0.73756.52852.8885.7094-0.10510.07970.2314-0.12660.1005-0.076-0.29230.31040.00470.0093-0.05340.0050.07810.02790.04652.1551.061-12.07
51.34621.05280.853.16710.63211.6444-0.06350.01390.1182-0.05680.08620.0711-0.08290.0155-0.02270.01860.0210.01430.05410.01020.0512-8.59243.203-10.288
64.20654.45371.736310.06173.8815.46010.14790.0957-0.0610.1895-0.0217-0.4283-0.08160.1835-0.12620.02820.0206-0.01920.117-0.00890.14315.19342.03-6.155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA727 - 7572 - 32
2X-RAY DIFFRACTION2AA758 - 79033 - 65
3X-RAY DIFFRACTION3AA791 - 83766 - 112
4X-RAY DIFFRACTION4BB730 - 7545 - 29
5X-RAY DIFFRACTION5BB755 - 81030 - 85
6X-RAY DIFFRACTION6BB811 - 83586 - 110

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