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- PDB-3m99: Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module -

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Basic information

Entry
Database: PDB / ID: 3m99
TitleStructure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module
Components
  • (SAGA-associated factor ...) x 2
  • Protein SUS1
  • Ubiquitin carboxyl-terminal hydrolase 8
KeywordsTRANSCRIPTION / Zinc Finger / Activator / Chromatin regulator / Metal-binding / Nucleus / Transcription regulation / Zinc-finger / mRNA transport / ubiquitination / deubiquitination / Nuclear pore complex / Protein modification
Function / homology
Function and homology information


RITS complex assembly / DUBm complex / : / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex ...RITS complex assembly / DUBm complex / : / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus / enzyme activator activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / nuclear pore / RNA splicing / transcription elongation by RNA polymerase II / P-body / regulation of protein localization / protein transport / chromatin organization / protein-containing complex assembly / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / transcription coactivator activity / molecular adaptor activity / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of transcription by RNA polymerase II / proteolysis / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / ENY2/SUS1 / SAGA complex, Sgf11 subunit / SAGA-associated factor 73, zinc finger domain / Sgf11 (transcriptional regulation protein) / Zinc finger domain / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 ...Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / ENY2/SUS1 / SAGA complex, Sgf11 subunit / SAGA-associated factor 73, zinc finger domain / Sgf11 (transcriptional regulation protein) / Zinc finger domain / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAGA-associated factor 73 / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Helix Hairpins - #210 / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Classic Zinc Finger / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Serum Albumin; Chain A, Domain 1 / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Double Stranded RNA Binding Domain / Papain-like cysteine peptidase superfamily / Helix Hairpins / Zinc finger, RING/FYVE/PHD-type / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 8 / SAGA-associated factor 73 / SAGA-associated factor 11 / Transcription and mRNA export factor SUS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 2.7 Å
AuthorsKohler, A. / Zimmerman, E. / Schneider, M. / Hurt, E. / Zheng, N.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module.
Authors: Kohler, A. / Zimmerman, E. / Schneider, M. / Hurt, E. / Zheng, N.
History
DepositionMar 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 8
B: SAGA-associated factor 11
C: Protein SUS1
D: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,08011
Polymers87,6224
Non-polymers4587
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16840 Å2
ΔGint-159 kcal/mol
Surface area31770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.424, 103.519, 70.350
Angle α, β, γ (deg.)90.000, 108.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Ubiquitin carboxyl-terminal hydrolase 8 / Ubiquitin thioesterase 8 / Ubiquitin-specific-processing protease 8 / Deubiquitinating enzyme 8


Mass: 53692.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBP8, YM9959.05, YMR223W / Production host: Escherichia coli (E. coli) / References: UniProt: P50102, EC: 3.1.2.15
#3: Protein Protein SUS1


Mass: 11094.497 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUS1, YBR111W-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WNK7

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SAGA-associated factor ... , 2 types, 2 molecules BD

#2: Protein SAGA-associated factor 11 / 11 kDa SAGA-associated factor


Mass: 11297.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SGF11, YPL047W / Production host: Escherichia coli (E. coli) / References: UniProt: Q03067
#4: Protein SAGA-associated factor 73 / 73 kDa SAGA-associated factor / SAGA histone acetyltransferase complex 73 kDa subunit


Mass: 11538.081 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES: 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SGF73, SGF73 (AA 1-104), YGL066W / Production host: Escherichia coli (E. coli) / References: UniProt: P53165

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Non-polymers , 2 types, 48 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.2M ammonium citrate, 18% PEG 3,350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 22908 / Num. obs: 22908 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 50 Å2 / Rsym value: 0.092 / Net I/σ(I): 35.3
Reflection shellHighest resolution: 2.7 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1569 / Rsym value: 0.304 / % possible all: 64.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHENIXphasing
RefinementMethod to determine structure: SAD, molecular replacement
Starting model: PDB entry 2HD5

2hd5


Resolution: 2.7→48.116 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.49 / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3 2073 4.92 %
Rwork0.234 --
obs0.237 22908 88.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.968 Å2 / ksol: 0.292 e/Å3
Displacement parametersBiso max: 196.44 Å2 / Biso mean: 75.484 Å2 / Biso min: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-27.635 Å20 Å2-13.829 Å2
2---6.489 Å20 Å2
3----21.146 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5509 0 7 41 5557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095615
X-RAY DIFFRACTIONf_angle_d1.0647561
X-RAY DIFFRACTIONf_chiral_restr0.074845
X-RAY DIFFRACTIONf_plane_restr0.003969
X-RAY DIFFRACTIONf_dihedral_angle_d19.2792072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.7630.358610.3331476153749
2.763-2.8320.428920.3061913200562
2.832-2.9080.3621160.3232146226272
2.908-2.9940.4011240.3162416254081
2.994-3.0910.371540.3012641279588
3.091-3.2010.3351450.2762822296793
3.201-3.3290.3571390.2762876301596
3.329-3.4810.3471690.2782902307197
3.481-3.6640.3061300.2452943307398
3.664-3.8940.3511430.2333011315499
3.894-4.1940.2661800.2152957313799
4.194-4.6160.2611710.1812968313999
4.616-5.2830.2761680.1822982315099
5.283-6.6530.2991270.21330183145100
6.653-48.1240.2191540.1852989314399
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)
10.65560.1427-0.20791.4371-0.81942.42920.0391-0.13790.07930.2441-0.1087-0.1729-0.21860.159800.39090.041-0.0150.4346-0.02390.511519.9648-17.37351.6486
21.34440.72910.43020.26730.42890.4196-0.22040.5394-0.6063-0.68620.31410.47070.1748-0.055600.9290.05750.05130.5785-0.03190.669617.5987-21.384422.4964
30.47910.0275-0.18480.5066-0.14320.43510.01340.4486-0.0981-0.4618-0.00440.32150.1538-0.3206-00.6681-0.0215-0.1050.730.05370.6546-3.7435-25.314524.69
4-0.7894-0.09590.9642-0.52410.2565-0.04520.00250.18030.0169-0.60910.11260.4660.1522-0.4719-00.6353-0.0301-0.16240.72370.06770.6707-6.2655-20.757720.1249
51.40920.95070.55221.1860.48160.7922-0.04910.04280.2392-0.186-0.06320.2757-0.3583-0.349-00.52470.1031-0.03790.52220.01450.49731.3606-8.560734.2219
6-0.05020.0339-0.0962-0.0221-0.01510.0168-0.1089-0.5435-0.0455-0.44120.38420.769-0.4112-0.196300.31670.1640.12850.82840.0830.6832-10.3328-26.755966.6069
70.5038-0.23980.5597-0.0617-0.25930.9033-0.32550.87690.46960.10820.41070.0695-0.2342-0.006600.72150.1271-0.02930.4883-0.04810.580712.792-9.514358.3635
80.2489-0.03710.05260.0807-0.05640.01140.3434-0.0880.1984-0.8969-0.15660.6693-0.548-0.140701.0687-0.031-0.13260.6057-0.0360.79311.99269.542340.6752
90.12070.0745-0.070.0813-0.12870.1467-0.29551.14490.35240.42490.0710.4907-0.460.667301.207-0.1813-0.15540.7052-0.03770.948528.7036.868822.506
100.07080.1007-0.07810.1753-0.06220.341-0.5020.53790.05270.02280.6939-0.0390.4610.3534-00.82180.07430.13350.57980.00080.633525.64415.505817.062
11-0.0252-0.0664-0.01570.00980.0015-0.0121-0.10490.33180.336-0.29320.2226-0.7455-0.12360.1848-01.0875-0.1225-0.0351.0617-0.18940.637528.88180.00549.736
12-0.0119-0.0157-0.02870.00710.01310.00170.4757-0.60640.4276-0.3950.16280.11340.6093-0.525600.5855-0.06740.11611.26010.08510.9208-4.9355-36.693770.3356
130.0723-0.05480.02340.0661-0.00760.00520.25860.1242-0.4887-0.0380.0136-0.4683-0.078-0.7056-00.5725-0.02450.1050.7889-0.0340.5995-3.9844-34.768157.0238
140.1689-0.0748-0.10280.117-0.02030.107-0.29650.57080.3005-0.554-0.12110.7726-0.1164-1.0956-00.34540.1276-0.08180.70520.01010.6507-4.6621-17.204651.5682
150.13610.00830.03690.13220.0089-0.00170.3110.18760.66230.10880.23530.2034-0.47270.9448-00.91790.10870.03690.6377-0.12720.6716.16-5.865763.4812
16-0.0831-0.01820.2990.075-0.02810.01570.122-0.91140.61950.6946-0.32231.5436-0.571-0.8300.40710.14940.17350.9876-0.03570.7999-10.8103-18.626759.8406
170.0131-0.00640.01580.0394-0.0301-0.0073-0.45750.268-0.38050.11240.00640.2508-0.0926-0.0701-01.541-0.1878-0.0711.15320.06411.0723-16.4049-38.236263.9515
180.0520.09710.1556-0.0155-0.08680.14420.2799-0.0758-0.4451-0.50110.24730.60660.45110.0091-01.1797-0.15190.17271.30930.14881.2586-8.9574-44.114967.6492
19-0.0387-0.24940.22790.5426-0.22751.0121-0.06350.0276-0.0461-0.03740.0299-0.1593-0.08150.042900.56020.03750.00390.4520.00350.530718.5294-25.092746.3008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:225)A2 - 225
2X-RAY DIFFRACTION2(chain A and resid 226:272)A226 - 272
3X-RAY DIFFRACTION3(chain A and resid 273:322)A273 - 322
4X-RAY DIFFRACTION4(chain A and resid 323:372)A323 - 372
5X-RAY DIFFRACTION5(chain A and resid 373:471)A373 - 471
6X-RAY DIFFRACTION6(chain B and resid 7:19)B7 - 19
7X-RAY DIFFRACTION7(chain B and resid 20:46)B20 - 46
8X-RAY DIFFRACTION8(chain B and resid 47:65)B47 - 65
9X-RAY DIFFRACTION9(chain B and resid 66:76)B66 - 76
10X-RAY DIFFRACTION10(chain B and resid 77:90)B77 - 90
11X-RAY DIFFRACTION11(chain B and resid 91:95)B91 - 95
12X-RAY DIFFRACTION12(chain C and resid 6:14)C6 - 14
13X-RAY DIFFRACTION13(chain C and resid 15:27)C15 - 27
14X-RAY DIFFRACTION14(chain C and resid 28:41)C28 - 41
15X-RAY DIFFRACTION15(chain C and resid 42:64)C42 - 64
16X-RAY DIFFRACTION16(chain C and resid 65:86)C65 - 86
17X-RAY DIFFRACTION17(chain C and resid 87:96)C87 - 96
18X-RAY DIFFRACTION18(chain D and resid 7:30)D7 - 30
19X-RAY DIFFRACTION19(chain D and resid 31:98)D31 - 98

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