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- PDB-3q33: Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for ... -

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Basic information

Entry
Database: PDB / ID: 3q33
TitleStructure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation
Components
  • HISTONE H3
  • Histone acetyltransferase RTT109
  • Vacuolar protein sorting-associated protein 75Vacuole
KeywordsTRANSFERASE / CHAPERONE/GENE REGULATION / Rtt109:Vps75=2:2 stoichiometry complex / histone acetyltransferase / with Acetyl Coenzyme A (ACoA) bound / autoacetylation on Rtt109 Lys290 / nuclear / TRANSFERASE-CHAPERONE-TRANSCRIPTION REGULATOR complex / TRANSFERASE-CHAPERONE complex / CHAPERONE-GENE REGULATION complex
Function / homology
Function and homology information


: / : / : / : / histone H3K23 acetyltransferase activity / : / histone H3K56 acetyltransferase activity / : / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly ...: / : / : / : / histone H3K23 acetyltransferase activity / : / histone H3K56 acetyltransferase activity / : / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / : / sexual sporulation resulting in formation of a cellular spore / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / acetyltransferase activator activity / peptidyl-lysine acetylation / replication-born double-strand break repair via sister chromatid exchange / histone H3 acetyltransferase activity / retrotransposon silencing / : / replication fork protection complex / histone H3K27 acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / positive regulation of transcription by RNA polymerase I / protein acetylation / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / CENP-A containing nucleosome / histone acetyltransferase / nucleosome assembly / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / protein transport / chromatin organization / histone binding / regulation of gene expression / protein heterodimerization activity / DNA damage response / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Histone acetyltransferase Rtt109 / Rtt109-type histone acetyltransferase (HAT) domain profile. / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Histone H3 signature 1. / Histone H3 signature 2. ...Histone acetyltransferase Rtt109 / Rtt109-type histone acetyltransferase (HAT) domain profile. / Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP) / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
ACETYL COENZYME *A / Vacuolar protein sorting-associated protein 75 / Histone H3 / Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTang, Y. / Yuan, H. / Meeth, K. / Marmorstein, R.
Citation
Journal: Structure / Year: 2011
Title: Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation.
Authors: Tang, Y. / Holbert, M.A. / Delgoshaie, N. / Wurtele, H. / Guillemette, B. / Meeth, K. / Yuan, H. / Drogaris, P. / Lee, E.H. / Durette, C. / Thibault, P. / Verreault, A. / Cole, P.A. / Marmorstein, R.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP.
Authors: Tang, Y. / Holbert, M.A. / Wurtele, H. / Meeth, K. / Rocha, W. / Gharib, M. / Jiang, E. / Thibault, P. / Verreault, A. / Verrault, A. / Cole, P.A. / Marmorstein, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure of Vps75 and implications for histone chaperone function.
Authors: Tang, Y. / Meeth, K. / Jiang, E. / Luo, C. / Marmorstein, R.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase RTT109
B: Vacuolar protein sorting-associated protein 75
D: HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0065
Polymers79,1343
Non-polymers8722
Water41423
1
A: Histone acetyltransferase RTT109
B: Vacuolar protein sorting-associated protein 75
D: HISTONE H3
hetero molecules

A: Histone acetyltransferase RTT109
B: Vacuolar protein sorting-associated protein 75
D: HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,01210
Polymers158,2696
Non-polymers1,7434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)97.543, 119.570, 80.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Histone acetyltransferase RTT109 / Regulator of Ty1 transposition protein 109


Mass: 50348.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BamHI/XhoI insert
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: KIM2, L1377, REM50, RTT109, SCY_3578, YLL002W / Plasmid: 6His-TEV-pCDF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q07794, histone acetyltransferase
#2: Protein Vacuolar protein sorting-associated protein 75 / Vacuole


Mass: 27292.619 Da / Num. of mol.: 1 / Fragment: unp residues 1-232
Source method: isolated from a genetically manipulated source
Details: BamHI/XhoI insert
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: N0890, VPS75, YNL246W / Plasmid: GST-TEV-pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: P53853

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Protein/peptide , 1 types, 1 molecules D

#3: Protein/peptide HISTONE H3 /


Mass: 1492.727 Da / Num. of mol.: 1 / Fragment: unp residues 1-14 / Source method: obtained synthetically / Source: (synth.) synthetic (others) / References: UniProt: P61830

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Non-polymers , 3 types, 25 molecules

#4: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 10.0% (v/v) PEG 8000 8% (v/v) ethylene glycol 100 mM Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.988
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2008 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 23924 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 80.7 Å2 / Rsym value: 0.047 / Net I/σ(I): 26.1
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.363 / % possible all: 78.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
PHENIXphenix.refine: 1.6.4_486refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3D35 3DM7

3d35
PDB Unreleased entry

3dm7


Resolution: 2.8→45.16 Å / Isotropic thermal model: ISOTROPIC / Phase error: 28.43 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.255 1166 5.1 %
Rwork0.195 --
obs0.195 22879 100 %
all-25210 -
Displacement parametersBiso min: 28.43 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 55 23 5077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095170
X-RAY DIFFRACTIONf_angle_d1.1546984
X-RAY DIFFRACTIONf_mcbond_it
X-RAY DIFFRACTIONf_mcangle_it
X-RAY DIFFRACTIONf_scbond_it
X-RAY DIFFRACTIONf_scangle_it
LS refinement shellResolution: 2.8→2.9275 Å /
RfactorNum. reflection
Rfree0.3532 119
Rwork0.2983 2251
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)
10.63291.2179-2.01910.6236-1.5913.22660.24860.39730.30860.2953-0.01620.161-0.309-0.6945-0.17660.12050.0808-0.00850.2565-0.02960.3898-20.371519.0239-0.1635
20.27250.48490.1831.45-1.3193.4421-0.0898-0.03250.0060.63240.5953-0.4723-1.4994-0.2407-0.38551.03640.14660.10560.5735-0.10950.7009-19.81829.584733.4727
31.9783-0.04-2.28491.6758-1.95333.4298-0.07680.46160.0269-0.2153-0.1838-0.04190.413-0.49470.18630.31060.0364-0.04160.3604-0.03830.2442-12.306714.4705-11.8491
41.54551.04980.66071.02980.56740.42950.11380.6598-0.31880.0886-0.2133-1.5073-0.01570.37770.05090.2612-0.0195-0.02910.50520.19180.8834.486220.2526-3.2103
51.40570.9563-1.69361.3979-0.94242.62980.08330.44690.2520.2694-0.08470.14510.1485-0.4815-0.00120.04440.0350.06790.2601-0.05110.2946-24.134111.00554.4664
61.437-0.61660.68010.2536-0.04381.0628-0.2934-0.2211-0.10140.43890.13630.0792-0.0160.06480.12380.69590.1440.23290.28470.08340.2586-13.3738-1.821839.7311
70.5671-0.28230.19750.1722-0.14172.6205-0.16-0.0399-0.26950.0908-0.04870.060.5211-0.10650.22670.5433-0.0450.26040.3331-0.01740.5208-24.2898-5.210627.5923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:127)A1 - 127
2X-RAY DIFFRACTION2(chain A and resid 128:176)A128 - 176
3X-RAY DIFFRACTION3(chain A and resid 177:269)A177 - 269
4X-RAY DIFFRACTION4(chain A and resid 270:321)A270 - 321
5X-RAY DIFFRACTION5(chain A and resid 322:404)A322 - 404
6X-RAY DIFFRACTION6(chain B and resid 9:114)B9 - 114
7X-RAY DIFFRACTION7(chain B and resid 115:226)B115 - 226

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