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- PDB-3q35: Structure of the Rtt109-AcCoA/Vps75 complex and implications for ... -

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Basic information

Entry
Database: PDB / ID: 3q35
TitleStructure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation
Components
  • Histone acetyltransferase
  • Vacuolar protein sorting-associated protein 75
KeywordsTRANSFERASE/CHAPERONE / Rtt109:Vps75=2:2 stoichiometry complex / Acetyl Coenzyme A (ACoA) bound / autoacetylation at Rtt109 Lys290 / nuclear / TRANSFERASE-CHAPERONE complex
Function / homology
Function and homology information


H3 histone acetyltransferase complex / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / acetyltransferase activator activity / replication-born double-strand break repair via sister chromatid exchange / transposable element silencing / histone H3 acetyltransferase activity / protein-lysine-acetyltransferase activity / cellular response to stress / histone H4K16 acetyltransferase activity ...H3 histone acetyltransferase complex / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / acetyltransferase activator activity / replication-born double-strand break repair via sister chromatid exchange / transposable element silencing / histone H3 acetyltransferase activity / protein-lysine-acetyltransferase activity / cellular response to stress / 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 / protein modification process / double-strand break repair via nonhomologous end joining / protein transport / nucleosome assembly / regulation of gene expression / histone binding / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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
Similarity search - Domain/homology
ACETYL COENZYME *A / Vacuolar protein sorting-associated protein 75 / Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 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
B: Vacuolar protein sorting-associated protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5134
Polymers77,6422
Non-polymers8722
Water19811
1
A: Histone acetyltransferase
B: Vacuolar protein sorting-associated protein 75
hetero molecules

A: Histone acetyltransferase
B: Vacuolar protein sorting-associated protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,0268
Polymers155,2834
Non-polymers1,7434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area12770 Å2
ΔGint-55 kcal/mol
Surface area56300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.0850, 119.0010, 80.2920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Histone acetyltransferase / 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, 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


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
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


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


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10.0% (v/v) PEG8000; 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 Å
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: 3.3→50 Å / Num. all: 15348 / Num. obs: 15302 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rsym value: 0.083 / Net I/σ(I): 16.5
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.427 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
AMoREphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3Q33

3q33


Resolution: 3.3→48.01 Å / SU ML: 0.35 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 735 5.02 %
Rwork0.2071 --
obs0.2091 14631 99.37 %
all-15348 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.394 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-34.3659 Å2-0 Å2-0 Å2
2---16.2766 Å20 Å2
3----18.0893 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 55 11 5040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115147
X-RAY DIFFRACTIONf_angle_d1.3096956
X-RAY DIFFRACTIONf_dihedral_angle_d23.6343147
X-RAY DIFFRACTIONf_chiral_restr0.082754
X-RAY DIFFRACTIONf_plane_restr0.006878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.55490.30681590.26482627X-RAY DIFFRACTION97
3.5549-3.91250.27821510.23412746X-RAY DIFFRACTION100
3.9125-4.47830.26621480.20452780X-RAY DIFFRACTION100
4.4783-5.64080.20221360.18242796X-RAY DIFFRACTION100
5.6408-48.01540.23291410.19692947X-RAY DIFFRACTION100
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)
12.89940.6941-2.26312.9023-2.88125.70880.0820.27570.33390.32260.01940.22-0.507-0.571500.55430.11120.02890.7729-0.05920.7171-20.349519.2253-0.2737
2-0.1667-0.2583-0.080.66530.09920.1246-0.45670.42850.49850.60940.4744-0.5945-2.2884-0.0147-01.88370.1193-0.12151.1268-0.03641.2291-19.681129.766433.4424
32.8244-0.0248-1.55722.9139-2.87955.7841-0.16890.2549-0.1312-0.5014-0.1639-0.03850.3752-0.3466-00.63240.0101-0.04960.7289-0.06060.7544-12.183214.5456-11.8322
42.10190.03410.25470.82961.57052.0249-0.0063-0.13710.00210.221-0.1336-1.3763-0.49550.6995-01.0241-0.1145-0.09560.92730.15551.22664.469420.2964-3.0528
52.69511.0564-2.76722.4702-1.06313.83540.150.12480.11290.4233-0.11030.51290.0626-0.4783-00.59840.03290.03580.8642-0.08070.8408-24.123611.26774.4478
61.8128-1.08680.71710.506-0.12531.5707-0.1954-0.3415-0.28820.47440.15530.02950.1222-0.04501.17270.03010.15090.84010.07570.8713-13.3569-1.652739.7258
73.18340.84991.5623.07912.02675.9945-0.01310.1238-0.1807-0.1581-0.10840.34370.3463-0.2293-00.928-0.02350.25880.7305-0.00380.8884-24.3354-4.973627.6755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:127)
2X-RAY DIFFRACTION2(chain A and resid 128:176)
3X-RAY DIFFRACTION3(chain A and resid 177:269)
4X-RAY DIFFRACTION4(chain A and resid 270:321)
5X-RAY DIFFRACTION5(chain A and resid 322:404)
6X-RAY DIFFRACTION6(chain B and resid 9:114)
7X-RAY DIFFRACTION7(chain B and resid 115:226)

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