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- PDB-3q66: Structure of the Vps75-Rtt109 histone chaperone-lysine acetyltran... -

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Basic information

Entry
Database: PDB / ID: 3q66
TitleStructure of the Vps75-Rtt109 histone chaperone-lysine acetyltransferase complex (Full-length proteins in space group P6122)
Components
  • Histone acetyltransferase RTT109
  • Vacuolar protein sorting-associated protein 75
KeywordsCHAPERONE/TRANSFERASE / histone chaperone / lysine acetyltransferase / CHAPERONE-TRANSFERASE complex
Function / homology
Function and homology information


histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / histone H3K14 acetyltransferase activity / histone H3K9 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / transposable element silencing / histone H3 acetyltransferase activity / replication-born double-strand break repair via sister chromatid exchange ...histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / histone H3K14 acetyltransferase activity / histone H3K9 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / transposable element silencing / histone H3 acetyltransferase activity / replication-born double-strand break repair via sister chromatid exchange / acetyltransferase activator activity / histone H3K27 acetyltransferase activity / protein-lysine-acetyltransferase activity / cellular response to stress / histone acetyltransferase / protein modification process / double-strand break repair via nonhomologous end joining / nucleosome assembly / protein transport / 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
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: 2.705 Å
AuthorsSu, D. / Thompson, J.R. / Mer, G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure and histone binding properties of the Vps75-Rtt109 chaperone-lysine acetyltransferase complex.
Authors: Su, D. / Hu, Q. / Zhou, H. / Thompson, J.R. / Xu, R.M. / Zhang, Z. / Mer, G.
History
DepositionDec 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 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
Revision 1.4Oct 9, 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: Vacuolar protein sorting-associated protein 75
C: Histone acetyltransferase RTT109
B: Vacuolar protein sorting-associated protein 75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3115
Polymers112,1193
Non-polymers1922
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-70 kcal/mol
Surface area43690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.385, 99.385, 479.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-294-

HOH

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Components

#1: Protein Vacuolar protein sorting-associated protein 75


Mass: 30656.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: N0890, VPS75, YNL246W / Plasmid: pCOLA Duet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P53853
#2: Protein Histone acetyltransferase RTT109 / Regulator of Ty1 transposition protein 109


Mass: 50806.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: KIM2, L1377, REM50, RTT109, YLL002W / Plasmid: GST-based pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q07794, histone acetyltransferase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dihydrate, 2 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 37636 / % possible obs: 99.4 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 34.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 17.5 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 5.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3CZ7 2ZD7

3cz7

2zd7


Resolution: 2.705→40.505 Å / SU ML: 0.4 / σ(F): 0.12 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 503 1.34 %RANDOM
Rwork0.2061 ---
obs0.2066 37636 94.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.248 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8139 Å2-0 Å2-0 Å2
2--1.8139 Å20 Å2
3----3.6277 Å2
Refinement stepCycle: LAST / Resolution: 2.705→40.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7262 0 10 118 7390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117477
X-RAY DIFFRACTIONf_angle_d1.19610100
X-RAY DIFFRACTIONf_dihedral_angle_d15.5062845
X-RAY DIFFRACTIONf_chiral_restr0.0621075
X-RAY DIFFRACTIONf_plane_restr0.0061298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7053-2.97750.31771120.25528708X-RAY DIFFRACTION91
2.9775-3.40810.30771190.23079035X-RAY DIFFRACTION94
3.4081-4.29310.22021330.17459391X-RAY DIFFRACTION96
4.2931-40.50950.22281390.19959999X-RAY DIFFRACTION97
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)
13.44490.352-0.52780.9468-0.17974.363-0.49640.2472-0.26910.01290.3898-0.1289-0.7683-0.95610.04040.55040.1008-0.06080.8747-0.14750.4777-35.235755.6117-29.3472
20.4971-0.36310.03840.52580.06861.1746-0.1688-0.18920.4441-0.0418-0.03360.06990.1594-0.66080.19520.144-0.0768-0.03550.6979-0.02020.2725-31.035837.2497-3.9674
32.5128-0.59240.8237-0.03250.1471-0.4499-0.34520.2460.27820.04090.11280.13650.07310.0570.16790.1171-0.1227-0.05640.15210.09020.2165-30.477840.107423.9848
42.7639-1.34341.07141.734-2.70937.5503-0.01190.8965-0.39350.10160.09390.2506-0.70560.9538-0.05430.2692-0.0351-0.05240.58210.02010.3228-37.891832.32267.8257
52.0195-0.0106-0.33630.27240.29140.1778-0.11870.1801-0.02470.07240.1370.00510.0052-0.2995-0.06870.2918-0.0375-0.01910.3421-0.0210.2742-41.309436.546919.3608
66.2818-1.73191.46292.5540.5445.73130.3297-0.7147-0.4043-0.72710.38120.1587-0.87090.4051-0.40230.564-0.0506-0.020.36490.01840.3061-47.025947.77050.2827
70.40940.3086-0.14810.19480.52331.6108-0.3923-0.1030.67250.16310.1026-0.1450.0221-0.15770.17280.1037-0.0912-0.00590.36490.05540.2814-51.731345.238328.3604
84.69822.075-0.08092.491-1.84763.61520.27530.3967-0.54980.3118-0.45041.3102-0.61670.35990.08650.43880.011-0.05380.37650.04620.6843-53.58356.292327.3711
92.2913-0.70650.15111.25550.27540.2294-0.00781.0147-0.03910.03950.1040.25450.01620.2055-0.04970.225-0.02550.0120.46140.04160.3063-47.31648.945918.0762
10-0.0984-0.12040.63210.33970.09011.0453-0.33420.31870.3694-0.01290.1243-0.19270.02080.1580.16560.1481-0.02740.00920.39650.11340.3347-26.159443.909617.9231
111.83842.9292-1.63675.4106-1.10794.0531.6411-0.5822-0.54860.1482-1.22220.2404-0.16610.6697-0.04290.22160.0935-0.01490.5761-0.06980.7378-14.994851.629624.5378
128.2668-0.4447-9.6130.12590.58361.9861-0.70290.62921.16830.29640.86620.0670.5561-0.2437-0.21060.99890.28790.00841.75880.11580.9885-5.665169.30845.0274
130.9281-0.3622-0.15830.3954-1.5408-0.1090.0943-0.1568-0.01950.4741-0.1063-0.0175-0.18570.142-0.00390.4921-0.1460.00180.4029-0.09360.3076-24.598971.73139.8866
142.3406-1.6369-1.18485.9442-0.27474.7482-0.210.7659-0.00751.1855-1.0844-0.4212-0.15270.29831.07620.3165-0.1712-0.0270.60750.30990.2527-4.128473.712.9634
150.36470.287-1.13090.4498-0.59173.6584-0.060.9185-0.74070.1883-1.0326-0.5062-0.09081.18590.78641.0643-0.6177-0.12051.68980.12121.45192.057576.746218.0028
160.12160.58570.66871.3103-0.57232.2723-0.24390.10040.01580.09550.07780.35870.05380.23350.11890.3607-0.0642-0.00360.25530.06470.3309-26.676469.989930.0759
172.46051.0628-0.47030.2565-0.01190.48360.2370.2541-0.09370.19370.1237-0.0229-0.5633-0.1066-0.17610.4638-0.1748-0.01780.43470.05070.3013-7.654275.728225.9374
180.15640.11410.0218-0.19350.1149-0.1152-0.08440.0635-0.06090.33370.17580.1137-0.3518-0.0225-0.10890.51340.06310.07880.30230.10090.4278-37.813275.868328.6959
19-0.05120.154-0.60110.5999-0.10990.04820.2974-0.1598-0.03690.3009-0.33020.0332-0.08230.13870.03730.387-0.18580.00430.34330.06260.2656-16.255371.031932.5053
209.2138-3.2967-4.24847.4716-2.47622.0392-1.26980.9264-1.99210.2821-0.16360.5958-0.25430.55270.60660.38090.00920.00020.84230.56130.68770.077244.202425.578
211.27421.3775-0.23261.093-0.36330.99590.10520.3877-0.10320.0744-0.11-0.1989-0.14880.36350.04620.25470.0015-0.05710.41130.03680.2446-9.634337.940826.6291
222.0625.664-2.82356.8354-4.21895.23241.37331.966-0.19441.0045-0.1992-0.5449-0.5259-1.0916-0.65970.3876-0.0809-0.10.64280.10770.3566-1.540651.034834.9694
230.4729-0.688-0.08962.3668-1.2780.65360.31860.1281-0.09070.3406-0.32130.3195-0.11330.2328-0.02760.4495-0.18250.020.27840.04650.2967-14.934275.019526.0881
240.81691.14270.6586-0.5564-1.47630.30280.5583-0.03430.08350.4954-0.05410.2575-0.52190.0275-0.41760.4935-0.05760.06520.12890.03160.367-28.833284.901723.9918
250.43620.64611.36830.85971.69648.4979-1.0023-0.09510.3994-0.4182-0.68452.3352-2.21670.00151.35040.8066-0.0187-0.06210.2979-0.00280.7788-25.739897.637515.145
261.23530.4763-1.34910.6907-0.75811.9890.07020.04970.20390.092-0.17350.0534-0.09490.09470.0520.4841-0.0687-0.10070.29140.08570.2554-13.066987.609716.658
271.86440.1931-0.12092.3541-0.80951.32550.40210.09750.0199-0.4384-0.2240.4229-0.10270.1665-0.10180.51680.0663-0.10460.36370.11260.3912-17.782678.45175.3195
281.266-0.3878-0.39711.3247-2.24331.33350.1952-0.0269-0.03620.2647-0.03540.1744-0.14090.0475-0.0790.4421-0.1327-0.0470.29620.04390.2918-19.796577.720427.5964
295.6362-1.44792.3741.53130.19521.3362-0.16830.4787-0.37010.15370.09890.38390.10870.24150.08810.3291-0.0732-0.02610.16910.07010.2098-32.364361.117225.0386
301.5653-0.6733-0.07712.8622-1.80110.51770.3183-0.2578-0.2940.06940.08150.0252-0.2063-0.0587-0.31880.2815-0.01830.04690.26180.01180.2673-34.51361.934337.2843
312.26091.90971.75342.3520.34642.746-0.36480.21180.37770.78061.20330.55040.02270.9185-0.54551.15580.36090.02580.9063-0.31040.9184-37.089290.112948.2387
325.51790.819-1.72831.48261.1921.8801-0.05160.8255-0.7719-0.5056-0.7440.0527-1.9694-0.81020.60670.89780.0721-0.14070.7203-0.1970.3883-24.087785.027157.3638
331.84041.50690.53373.4293-1.23714.2481-0.33130.5805-0.5386-0.00830.2331-0.9168-0.2320.13720.12280.25920.0539-0.00940.4935-0.03620.4186-17.168429.442921.6289
34-0.1722-0.61440.3620.0025-0.64623.633-0.4049-0.19560.2935-0.0098-0.3225-0.04590.0290.50620.6130.3254-0.02380.05540.68090.02740.474-21.328137.413-4.7148
351.1415-0.0851-1.00820.9268-0.63680.99180.06040.49-0.0374-0.6032-0.5654-0.06250.1225-0.87620.28090.3650.1223-0.0970.51850.07410.2091-25.18254.7177-21.891
362.04151.39750.6992.92721.37680.68-0.4272-0.74490.1965-0.9436-0.05390.1003-0.3441-0.04970.37020.75460.3033-0.10060.6391-0.20610.5719-17.154367.2434-10.7896
371.83221.38740.5091.79630.6461-0.2602-0.0897-0.158-0.2182-0.4137-0.1853-0.1463-0.0666-0.13610.24770.40730.160.04340.40880.07230.3051-11.44752.6039-16.6679
381.6602-0.92660.07494.17241.7464.0807-1.3016-1.425-0.5265-0.24290.28950.8309-0.34830.09640.75561.07020.0731-0.03891.83790.32521.3581-5.675946.77817.5518
391.43692.3079-0.12743.0043-1.17141.22890.5315-0.28510.2729-0.0785-0.8474-0.4369-0.04410.75320.26470.22860.14580.21860.43130.18330.5881-0.814963.764-16.1802
404.16370.01851.66610.03710.15125.2953-0.2687-1.1141-0.38740.8849-0.04590.0421-1.7460.70610.40410.826-0.1096-0.09930.9790.17710.50665.879374.2931-8.8068
41-0.08970.56070.10740.8125-0.47991.2622-0.2029-0.30260.09460.1023-0.2655-0.1644-0.008-0.18540.33650.25320.0085-0.0380.38-0.02490.3878-3.649662.6666-7.7758
421.70590.05641.16322.9009-0.94950.6039-0.2513-1.81730.2696-0.2170.011-0.3360.1225-0.82120.17650.22540.0784-0.04560.6882-0.14430.2678-21.348655.3114-9.6533
431.48850.6633-1.96920.8221-0.30773.3329-0.4314-0.21530.2163-0.0519-0.4388-0.2391-0.20620.68220.3160.6760.40640.00230.9841-0.39680.7624-35.325365.6432-14.4005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:20)
2X-RAY DIFFRACTION2(chain A and resid 21:42)
3X-RAY DIFFRACTION3(chain A and resid 43:86)
4X-RAY DIFFRACTION4(chain A and resid 87:95)
5X-RAY DIFFRACTION5(chain A and resid 96:125)
6X-RAY DIFFRACTION6(chain A and resid 126:140)
7X-RAY DIFFRACTION7(chain A and resid 141:163)
8X-RAY DIFFRACTION8(chain A and resid 164:177)
9X-RAY DIFFRACTION9(chain A and resid 178:197)
10X-RAY DIFFRACTION10(chain A and resid 198:223)
11X-RAY DIFFRACTION11(chain A and resid 224:231)
12X-RAY DIFFRACTION12(chain A and resid 247:253)
13X-RAY DIFFRACTION13(chain B and resid -5:29)
14X-RAY DIFFRACTION14(chain B and resid 30:38)
15X-RAY DIFFRACTION15(chain B and resid 39:43)
16X-RAY DIFFRACTION16(chain B and resid 44:67)
17X-RAY DIFFRACTION17(chain B and resid 68:84)
18X-RAY DIFFRACTION18(chain B and resid 85:98)
19X-RAY DIFFRACTION19(chain B and resid 99:130)
20X-RAY DIFFRACTION20(chain B and resid 131:136)
21X-RAY DIFFRACTION21(chain B and resid 137:166)
22X-RAY DIFFRACTION22(chain B and resid 167:174)
23X-RAY DIFFRACTION23(chain B and resid 175:199)
24X-RAY DIFFRACTION24(chain B and resid 200:246)
25X-RAY DIFFRACTION25(chain B and resid 247:257)
26X-RAY DIFFRACTION26(chain B and resid 258:284)
27X-RAY DIFFRACTION27(chain B and resid 285:319)
28X-RAY DIFFRACTION28(chain B and resid 320:352)
29X-RAY DIFFRACTION29(chain B and resid 353:374)
30X-RAY DIFFRACTION30(chain B and resid 375:402)
31X-RAY DIFFRACTION31(chain B and resid 403:407)
32X-RAY DIFFRACTION32(chain B and resid 408:426)
33X-RAY DIFFRACTION33(chain C and resid 9:22)
34X-RAY DIFFRACTION34(chain C and resid 23:44)
35X-RAY DIFFRACTION35(chain C and resid 45:62)
36X-RAY DIFFRACTION36(chain C and resid 63:77)
37X-RAY DIFFRACTION37(chain C and resid 78:128)
38X-RAY DIFFRACTION38(chain C and resid 129:137)
39X-RAY DIFFRACTION39(chain C and resid 138:161)
40X-RAY DIFFRACTION40(chain C and resid 162:172)
41X-RAY DIFFRACTION41(chain C and resid 173:196)
42X-RAY DIFFRACTION42(chain C and resid 197:216)
43X-RAY DIFFRACTION43(chain C and resid 217:225)

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