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- PDB-1m1d: TETRAHYMENA GCN5 WITH BOUND BISUBSTRATE ANALOG INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1m1d
TitleTETRAHYMENA GCN5 WITH BOUND BISUBSTRATE ANALOG INHIBITOR
Components
  • HISTONE H3
  • TGCN5 HISTONE ACETYL TRANSFERASE
KeywordsTRANSFERASE / Histone Acetyltransferase / Gcn5-related N-acetyltransferase / inhibitor complex / transcription factor
Function / homology
Function and homology information


chromatin organization => GO:0006325 / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence ...chromatin organization => GO:0006325 / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / replication fork protection complex / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / Estrogen-dependent gene expression / histone acetyltransferase complex / intracellular copper ion homeostasis / 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 / CENP-A containing nucleosome / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / aerobic respiration / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Bromodomain, conserved site / Bromodomain signature. / Histone-fold / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Histone H3 / Histone H3 / Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPoux, A.N. / Cebrat, M. / Kim, C.M. / Cole, P.A. / Marmorstein, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of the GCN5 histone acetyltransferase bound to a bisubstrate inhibitor.
Authors: Poux, A.N. / Cebrat, M. / Kim, C.M. / Cole, P.A. / Marmorstein, R.
History
DepositionJun 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 600HETEROGEN INHIBITOR COMPOSED OF A HISTONE H3 FRAGMENT (RESIDUES 1-20) AND A COENZYME A MOLECULE ...HETEROGEN INHIBITOR COMPOSED OF A HISTONE H3 FRAGMENT (RESIDUES 1-20) AND A COENZYME A MOLECULE COVALENTLY BOUND THROUGH AN ISOPROPIONYL LINKER TO LYS14.
Remark 999SEQUENCE Residue 90 (Chain A) and residue 390 (Chain C) are both PHE. Author indicates that PHE is ...SEQUENCE Residue 90 (Chain A) and residue 390 (Chain C) are both PHE. Author indicates that PHE is present in many of the GCN5 homologues at that position. According to the author, residue 210 (Chain A) and residue 510 (Chain C) are both ARG and not ASN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TGCN5 HISTONE ACETYL TRANSFERASE
B: HISTONE H3
C: TGCN5 HISTONE ACETYL TRANSFERASE
D: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)44,9384
Polymers44,9384
Non-polymers00
Water1,928107
1
A: TGCN5 HISTONE ACETYL TRANSFERASE
B: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)22,4692
Polymers22,4692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-12 kcal/mol
Surface area8590 Å2
MethodPISA
2
C: TGCN5 HISTONE ACETYL TRANSFERASE
D: HISTONE H3


Theoretical massNumber of molelcules
Total (without water)22,4692
Polymers22,4692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-10 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.420, 67.830, 74.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TGCN5 HISTONE ACETYL TRANSFERASE / HAT A1


Mass: 19457.658 Da / Num. of mol.: 2 / Fragment: Catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Plasmid: PRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21
References: GenBank: 1245146, UniProt: Q27198*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide HISTONE H3


Mass: 3011.146 Da / Num. of mol.: 2
Fragment: 20 MER PEPTIDE (RESIDUES 1-20), Bisubstrate analog
Source method: obtained synthetically
Details: Inhibitor composed of a histone H3 fragment (residues 1-20) is chemically synthesized. The peptide's sequence occurs naturally in Saccharomyces cerevisiae (Baker's yeast).
References: UniProt: P02303, UniProt: P61830*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
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: 1.89 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Ammonium sulfate, sodium cacodylate, sodium chloride, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.36 mMprotein1drop
20.58 mMinhibitor1drop
32.0 Mammonium sulfate1reservoir
40.1 Msodium cacodylate1reservoirpH6.6
50.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0082 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 22, 2001
RadiationMonochromator: Rosenbaum-Rock / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0082 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 27647 / Num. obs: 26519 / % possible obs: 96.1 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.2→2.28 Å / % possible all: 97.7
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 37.3 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 97.7 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QSN

1qsn


Resolution: 2.2→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 1615 RANDOM
Rwork0.213 --
all0.271 17294 -
obs0.26 16027 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.169 Å20 Å20 Å2
2--2.417 Å20 Å2
3---1.752 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 0 107 2965
Refinement
*PLUS
Lowest resolution: 37.3 Å / % reflection Rfree: 10 % / Rfactor all: 0.271 / Rfactor obs: 0.26 / Rfactor Rfree: 0.2652 / Rfactor Rwork: 0.2134
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0095
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.75

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