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- PDB-5trm: Crystal structure of human GCN5 histone acetyltransferase domain -

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Basic information

Entry
Database: PDB / ID: 5trm
TitleCrystal structure of human GCN5 histone acetyltransferase domain
ComponentsHistone acetyltransferase KAT2A
KeywordsTRANSFERASE / apo
Function / homology
Function and homology information


histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / positive regulation of cell projection organization / regulation of cartilage development / regulation of bone development / regulation of stem cell population maintenance / positive regulation of cardiac muscle cell differentiation / negative regulation of centriole replication ...histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / positive regulation of cell projection organization / regulation of cartilage development / regulation of bone development / regulation of stem cell population maintenance / positive regulation of cardiac muscle cell differentiation / negative regulation of centriole replication / regulation of regulatory T cell differentiation / transcription factor TFTC complex / telencephalon development / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / ATAC complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Cardiogenesis / limb development / NOTCH4 Intracellular Domain Regulates Transcription / regulation of T cell activation / SAGA complex / NOTCH3 Intracellular Domain Regulates Transcription / protein-lysine-acetyltransferase activity / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / midbrain development / Formation of paraxial mesoderm / histone acetyltransferase activity / intracellular distribution of mitochondria / regulation of RNA splicing / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of embryonic development / histone acetyltransferase complex / long-term memory / negative regulation of gluconeogenesis / somitogenesis / regulation of DNA repair / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of gluconeogenesis / positive regulation of cytokine production / gluconeogenesis / neural tube closure / cellular response to nerve growth factor stimulus / response to nutrient levels / : / regulation of protein stability / multicellular organism growth / regulation of synaptic plasticity / B-WICH complex positively regulates rRNA expression / Pre-NOTCH Transcription and Translation / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / mitotic spindle / cellular response to tumor necrosis factor / HATs acetylate histones / heart development / 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) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase ...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) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone acetyltransferase KAT2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGuo, Y.R. / Tao, Y.J.
CitationJournal: Nature / Year: 2017
Title: KAT2A coupled with the alpha-KGDH complex acts as a histone H3 succinyltransferase.
Authors: Wang, Y. / Guo, Y.R. / Liu, K. / Yin, Z. / Liu, R. / Xia, Y. / Tan, L. / Yang, P. / Lee, J.H. / Li, X.J. / Hawke, D. / Zheng, Y. / Qian, X. / Lyu, J. / He, J. / Xing, D. / Tao, Y.J. / Lu, Z.
History
DepositionOct 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT2A
W: Histone acetyltransferase KAT2A
V: Histone acetyltransferase KAT2A
U: Histone acetyltransferase KAT2A
T: Histone acetyltransferase KAT2A
S: Histone acetyltransferase KAT2A
R: Histone acetyltransferase KAT2A
Q: Histone acetyltransferase KAT2A
P: Histone acetyltransferase KAT2A
O: Histone acetyltransferase KAT2A
N: Histone acetyltransferase KAT2A
M: Histone acetyltransferase KAT2A
L: Histone acetyltransferase KAT2A
K: Histone acetyltransferase KAT2A
J: Histone acetyltransferase KAT2A
F: Histone acetyltransferase KAT2A
C: Histone acetyltransferase KAT2A
B: Histone acetyltransferase KAT2A
D: Histone acetyltransferase KAT2A
E: Histone acetyltransferase KAT2A
G: Histone acetyltransferase KAT2A
H: Histone acetyltransferase KAT2A
I: Histone acetyltransferase KAT2A
X: Histone acetyltransferase KAT2A


Theoretical massNumber of molelcules
Total (without water)465,76024
Polymers465,76024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.474, 173.474, 347.637
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ...
Histone acetyltransferase KAT2A / General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / HsGCN5 ...General control of amino acid synthesis protein 5-like 2 / Histone acetyltransferase GCN5 / HsGCN5 / Lysine acetyltransferase 2A / STAF97


Mass: 19406.660 Da / Num. of mol.: 24 / Fragment: catalytic domain, UNP residues 497-662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2A, GCN5, GCN5L2, HGCN5 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92830, histone acetyltransferase
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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.8M Sodium formate, 0.1M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 117491 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 43.66 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.051 / Rrim(I) all: 0.129 / Χ2: 1.048 / Net I/av σ(I): 15.05 / Net I/σ(I): 6.3 / Num. measured all: 726744
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.955.60.54358100.8450.2520.60.608100
2.95-35.60.44957940.890.2090.4970.617100
3-3.065.60.40257990.9170.1860.4440.625100
3.06-3.125.70.35158090.9270.1630.3880.631100
3.12-3.195.70.29358170.9470.1360.3240.649100
3.19-3.275.70.24158240.9620.1110.2660.67100
3.27-3.355.70.19758380.9770.090.2170.682100
3.35-3.445.80.16558080.9830.0760.1820.706100
3.44-3.545.80.15358550.9860.070.1680.715100
3.54-3.655.90.13558090.9890.0610.1490.743100
3.65-3.785.90.11258640.9920.0510.1230.803100
3.78-3.9460.10558640.9930.0460.1150.918100
3.94-4.116.10.10358520.9930.0450.1121.14499.9
4.11-4.336.20.10358690.9920.0440.1121.50699.9
4.33-4.66.30.09858910.9920.0420.1071.92599.9
4.6-4.966.50.10259210.9920.0430.1111.96799.8
4.96-5.466.80.10559180.9930.0420.1141.72699.5
5.46-6.247.20.09859390.9950.0380.1051.10899.4
6.24-7.867.70.07359790.9980.0270.0781.13198.6
7.86-507.70.04762310.9990.0180.0511.34497.9

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Processing

Software
NameVersionClassification
PHENIX1.10_2152refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1z4r

1z4r


Resolution: 2.9→48.179 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 5790 4.94 %
Rwork0.2151 111448 -
obs0.2181 117238 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.23 Å2 / Biso mean: 32.5282 Å2 / Biso min: 3.86 Å2
Refinement stepCycle: final / Resolution: 2.9→48.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31738 0 0 0 31738
Num. residues----3863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932577
X-RAY DIFFRACTIONf_angle_d0.86743919
X-RAY DIFFRACTIONf_chiral_restr0.0544700
X-RAY DIFFRACTIONf_plane_restr0.0055492
X-RAY DIFFRACTIONf_dihedral_angle_d17.07612071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9002-2.93310.35621890.275636683857100
2.9331-2.96760.35612000.274636543854100
2.9676-3.00380.32911970.265236803877100
3.0038-3.04180.34191800.265236743854100
3.0418-3.08190.28561960.255637013897100
3.0819-3.12410.32142000.261636453845100
3.1241-3.16870.32322070.256936793886100
3.1687-3.2160.32031810.249736883869100
3.216-3.26620.30951940.245336993893100
3.2662-3.31980.30851910.231836913882100
3.3198-3.3770.2931770.224537003877100
3.377-3.43840.28211860.220536833869100
3.4384-3.50450.32411860.229636953881100
3.5045-3.5760.2992010.236836873888100
3.576-3.65370.28942010.236136983899100
3.6537-3.73870.30331930.226537123905100
3.7387-3.83220.25631980.212237193917100
3.8322-3.93570.27282000.209136933893100
3.9357-4.05150.28151650.208337333898100
4.0515-4.18220.25742010.195136973898100
4.1822-4.33160.22981810.19237493930100
4.3316-4.50490.24642080.176237083916100
4.5049-4.70970.23371900.178237623952100
4.7097-4.95780.23161950.182437413936100
4.9578-5.26810.23931890.19537563945100
5.2681-5.67420.27221930.202737463939100
5.6742-6.24420.3051870.23493784397199
6.2442-7.14520.27352130.2153762397599
7.1452-8.99260.18112080.17373791399998
8.9926-48.18570.241830.20473853403694

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