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- PDB-4fip: Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf... -

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Basic information

Entry
Database: PDB / ID: 4fip
TitleStructure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module
Components
  • (SAGA-associated factor ...) x 2
  • Protein SUS1
  • Ubiquitin carboxyl-terminal hydrolase 8
KeywordsHYDROLASE / Domain-swapping / Deubiquitination / Transcription / Nucleosomes
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. / 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 / 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: 2.686 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 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)169,46522
Polymers168,5498
Non-polymers91614
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33790 Å2
ΔGint-189 kcal/mol
Surface area59200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.973, 79.975, 274.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a domain swapped dimer of a tetrameric complex.

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Components

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Protein , 2 types, 4 molecules AEBF

#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.: 2 / 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.: 2
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, 4 molecules CGDH

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


Mass: 8295.177 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-72
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 / 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.: 2 / 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 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: P53165

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Non-polymers , 2 types, 106 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG3350, 0.18-0.22 M Tri-ammonium citrate, 8-14% glycerol, 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: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.686→50 Å / Num. all: 47615 / Num. obs: 43495 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.151 / Rsym value: 0.151 / Net I/σ(I): 12.227
Reflection shellResolution: 2.686→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.345 / Rsym value: 0.637 / % possible all: 84.9

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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
Starting model: PDB entry 3MHS

3mhs


Resolution: 2.686→47.18 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 26.775 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26361 2192 5.1 %RANDOM
Rwork0.18329 ---
all0.18717 47615 --
obs0.18717 41136 90.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.481 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å20 Å20 Å2
2---0.2 Å20 Å2
3----2.95 Å2
Refinement stepCycle: LAST / Resolution: 2.686→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10616 0 14 92 10722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0210819
X-RAY DIFFRACTIONr_bond_other_d0.0010.027303
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.95314593
X-RAY DIFFRACTIONr_angle_other_deg0.963317960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63351311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89125.601516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5281534
X-RAY DIFFRACTIONr_chiral_restr0.0840.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022039
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: 2.686→2.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 135 -
Rwork0.249 2334 -
obs--75.25 %
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)
10.1635-0.1457-0.00950.36280.48711.06620.0212-0.0088-0.03280.0266-0.01690.05210.0666-0.0557-0.00430.064-0.03490.00440.02440.0110.04613.8448-28.8311-31.9181
21.85050.9172-0.95644.69260.39191.4798-0.1002-0.29180.03270.11990.1668-0.4719-0.18070.4826-0.06660.1001-0.0601-0.0380.158-0.02440.0629.66264.802510.4497
34.68135.5152.75136.61773.53193.47-0.08660.0317-0.10170.01050.1306-0.1337-0.01840.4391-0.0440.13950.0471-0.00490.1163-0.02780.110423.0366-4.05399.6396
41.03860.43220.15141.53060.92121.3343-0.1213-0.02880.1415-0.04510.15450.0899-0.22790.0051-0.03330.0960.02540.00650.03450.00880.044711.91747.39620.808
50.1071-0.02290.05680.3044-0.0190.0643-0.0080.03990.0497-0.0657-0.01910.0524-0.06490.0790.02710.1289-0.1056-0.02160.11260.01950.036521.7434-7.8632-43.032
61.56350.88080.39516.7314-0.38171.74190.11960.2577-0.1372-0.5438-0.1657-0.65590.33930.4160.04610.11490.08190.0580.1782-0.01190.075828.2856-46.4007-82.4966
70.5877-2.1517-0.969414.99387.35973.9871-0.05670.22010.1186-0.30.2662-0.6860.01130.2844-0.20950.2147-0.03120.08560.27230.03060.088827.4877-36.1955-83.1554
80.83520.10930.02272.4920.64910.76050.06770.1725-0.1302-0.28980.02580.2176-0.0209-0.1455-0.09350.09830.0035-0.08560.07470.00950.10139.8399-38.6875-76.8711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 471
2X-RAY DIFFRACTION1A501 - 506
3X-RAY DIFFRACTION1A601 - 634
4X-RAY DIFFRACTION2B6 - 95
5X-RAY DIFFRACTION2B101 - 103
6X-RAY DIFFRACTION3C5 - 45
7X-RAY DIFFRACTION3C101
8X-RAY DIFFRACTION4D5 - 95
9X-RAY DIFFRACTION4D101
10X-RAY DIFFRACTION4D201 - 211
11X-RAY DIFFRACTION5E1 - 471
12X-RAY DIFFRACTION5E501 - 506
13X-RAY DIFFRACTION5E601 - 634
14X-RAY DIFFRACTION6F6 - 95
15X-RAY DIFFRACTION6F101 - 105
16X-RAY DIFFRACTION7G3 - 45
17X-RAY DIFFRACTION7G101
18X-RAY DIFFRACTION8H6 - 96
19X-RAY DIFFRACTION8H101
20X-RAY DIFFRACTION8H201 - 203

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