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- PDB-4fk5: Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module -

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Basic information

Entry
Database: PDB / ID: 4fk5
TitleStructure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module
Components
  • (SAGA-associated factor ...) x 2
  • Protein SUS1
  • Ubiquitin carboxyl-terminal hydrolase 8
KeywordsHYDROLASE / Multi-protein complex / Deubiquitination / Transcription / Nucleosome
Function / homology
Function and homology information


RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / SLIK (SAGA-like) complex / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus ...RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / nuclear mRNA surveillance / SLIK (SAGA-like) complex / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / regulation of protein localization to chromatin / SAGA complex / poly(A)+ mRNA export from nucleus / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / Ub-specific processing proteases / nuclear pore / mRNA export from nucleus / RNA splicing / transcription elongation by RNA polymerase II / P-body / enzyme activator activity / protein transport / regulation of protein localization / chromatin organization / protein-containing complex assembly / molecular adaptor activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / transcription coactivator 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-associated factor 73, zinc finger domain / Zinc finger domain / SAGA complex, Sgf11 subunit / Sgf11 (transcriptional regulation protein) / Transcription factor, enhancer of yellow 2 / SAGA-associated factor 73 / Transcription factor EnY2 superfamily ...Yeast SAGA-associated factor 11, N-terminal domain / SAGA-associated factor 11 N-terminal domain / ENY2/SUS1 / SAGA-associated factor 73, zinc finger domain / Zinc finger domain / SAGA complex, Sgf11 subunit / Sgf11 (transcriptional regulation protein) / Transcription factor, enhancer of yellow 2 / SAGA-associated factor 73 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / 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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Cathepsin B; Chain A / 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 complex subunit SGF73 / SAGA complex subunit SGF11 / SAGA complex subunit SUS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.032 Å
AuthorsSamara, N.L. / Ringel, A.E. / Wolberger, C.
CitationJournal: Structure / Year: 2012
Title: A Role for Intersubunit Interactions in Maintaining SAGA Deubiquitinating Module Structure and Activity.
Authors: Samara, N.L. / Ringel, A.E. / Wolberger, C.
History
DepositionJun 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,04715
Polymers87,2774
Non-polymers77011
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17590 Å2
ΔGint-96 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.528, 104.775, 107.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 54060.656 Da / Num. of mol.: 1 / Mutation: S144N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: UBP8, YM9959.05, YMR223W / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: P50102, ubiquitinyl hydrolase 1
#2: 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)
Strain: ATCC 204508 / S288c / Gene: SUS1, YBR111W-A / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q6WNK7

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

#3: 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)
Strain: ATCC 204508 / S288c / Gene: SGF11, YPL047W / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q03067
#4: Protein SAGA-associated factor 73 / 73 kDa SAGA-associated factor / SAGA histone acetyltransferase complex 73 kDa subunit


Mass: 10824.273 Da / Num. of mol.: 1 / Fragment: UNP Residues 1-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SGF73, YGL066W / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: P53165

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Non-polymers , 4 types, 407 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: sodium citrate pH 5.2, 16% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.032→74.868 Å / Num. all: 61150 / Num. obs: 60890 / % possible obs: 99.5 %
Reflection shellResolution: 2.032→2.07 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 4.64 / Rsym value: 0.865 / % possible all: 100

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Processing

Software
NameVersionClassification
Locallymodified Blu-Ice GUI interface to EPICS controldata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.032→74.868 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.636 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21203 3085 5.1 %RANDOM
Rwork0.17481 ---
obs0.17669 57655 99.33 %-
all-61049 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---1.3 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.032→74.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5681 0 24 396 6101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025839
X-RAY DIFFRACTIONr_bond_other_d0.0010.023975
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.9547876
X-RAY DIFFRACTIONr_angle_other_deg0.85239761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9515715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71925.39282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.726151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.491524
X-RAY DIFFRACTIONr_chiral_restr0.110.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021108
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.032→2.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 210 -
Rwork0.206 3842 -
obs--96.27 %
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)
10.28050.20230.16520.73590.16620.10950.01130.03860.00850.0842-0.03880.08350.02380.03230.02750.0614-0.00890.00650.08860.01640.064410.548624.112322.1598
20.84190.7696-0.75341.14-0.5280.9887-0.07990.0358-0.1075-0.05190.1008-0.2510.11930.11-0.02090.04530.02760.00350.0754-0.02850.168136.844627.521622.4844
30.47710.4211-0.06741.1873-0.00150.01590.00950.0689-0.16050.2059-0.019-0.11740.0187-0.01540.00950.073-0.0076-0.01330.0630.0190.109211.594910.080227.3361
40.24890.22280.00430.5780.17530.1005-0.0353-0.02220.03640.07450.0207-0.030.0392-0.01380.01460.0913-0.0042-0.04070.0875-0.02260.115421.397136.594229.977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 471
2X-RAY DIFFRACTION1A501 - 508
3X-RAY DIFFRACTION1A601 - 842
4X-RAY DIFFRACTION2B5 - 96
5X-RAY DIFFRACTION2B101 - 143
6X-RAY DIFFRACTION3C4 - 95
7X-RAY DIFFRACTION3C101 - 102
8X-RAY DIFFRACTION3C201 - 254
9X-RAY DIFFRACTION4E5 - 95
10X-RAY DIFFRACTION4E101
11X-RAY DIFFRACTION4E201 - 257

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