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- PDB-4wa6: Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angst... -

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Basic information

Entry
Database: PDB / ID: 4wa6
TitleStructure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution
Components
  • (SAGA-associated factor ...) x 2
  • Transcription and mRNA export factor SUS1
  • Ubiquitin carboxyl-terminal hydrolase 8
Keywordshydrolase/transcription / Multi-Protein Complex / Hydrolase-transcription complex
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. / 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 / Cathepsin B; Chain A / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Papain-like cysteine peptidase superfamily / Zinc finger, RING/FYVE/PHD-type / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SAGA-associated factor 11 / Ubiquitin carboxyl-terminal hydrolase 8 / SAGA-associated factor 73 / Transcription and mRNA export factor SUS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsWolberger, C. / Yan, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-095822 United States
CitationJournal: To Be Published
Title: Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution
Authors: Wolberger, C. / Yan, M.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: atom_site_anisotrop / entity_src_gen ...atom_site_anisotrop / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 2.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.3Dec 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Transcription and mRNA export factor SUS1
C: SAGA-associated factor 11
E: SAGA-associated factor 73
D: Ubiquitin carboxyl-terminal hydrolase 8
F: Transcription and mRNA export factor SUS1
G: SAGA-associated factor 11
H: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,48323
Polymers174,5028
Non-polymers98115
Water2,504139
1
A: Ubiquitin carboxyl-terminal hydrolase 8
B: Transcription and mRNA export factor SUS1
C: SAGA-associated factor 11
E: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,77412
Polymers87,2514
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16940 Å2
ΔGint-168 kcal/mol
Surface area32100 Å2
MethodPISA
2
D: Ubiquitin carboxyl-terminal hydrolase 8
F: Transcription and mRNA export factor SUS1
G: SAGA-associated factor 11
H: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,70911
Polymers87,2514
Non-polymers4587
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-130 kcal/mol
Surface area29910 Å2
MethodPISA
3
A: Ubiquitin carboxyl-terminal hydrolase 8
B: Transcription and mRNA export factor SUS1
C: SAGA-associated factor 11
E: SAGA-associated factor 73
hetero molecules

D: Ubiquitin carboxyl-terminal hydrolase 8
F: Transcription and mRNA export factor SUS1
G: SAGA-associated factor 11
H: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,48323
Polymers174,5028
Non-polymers98115
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area34940 Å2
ΔGint-313 kcal/mol
Surface area59620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.076, 68.004, 137.858
Angle α, β, γ (deg.)90.00, 106.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBF

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


Mass: 54033.633 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: UBP8, YMR223W, YM9959.05 / Production host: Escherichia coli (E. coli) / References: UniProt: P50102, ubiquitinyl hydrolase 1
#2: Protein Transcription and mRNA export factor 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6WNK7

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SAGA-associated factor ... , 2 types, 4 molecules CGEH

#3: Protein SAGA-associated factor 11


Mass: 11297.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: SGF11, SCY_5678 / Production host: Escherichia coli (E. coli) / References: UniProt: A6ZWK1
#4: Protein SAGA-associated factor 73 / 73 kDa SAGA-associated factor / SAGA histone acetyltransferase complex 73 kDa subunit


Mass: 10825.258 Da / Num. of mol.: 2 / Mutation: N59D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SGF73, YGL066W / Production host: Escherichia coli (E. coli) / References: UniProt: P53165

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Non-polymers , 2 types, 154 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.034 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2013
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.034 Å / Relative weight: 1
ReflectionResolution: 2.36→47.41 Å / Num. obs: 59279 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 23

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
Blu-Icedata collection
Cootmodel building
HKL-2000data scaling
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→47.41 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 18.851 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 2993 5 %RANDOM
Rwork0.18307 ---
obs0.18615 56297 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.681 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.89 Å2
2--2.75 Å20 Å2
3----2.47 Å2
Refinement stepCycle: 1 / Resolution: 2.36→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10935 0 15 139 11089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911231
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210731
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.95715108
X-RAY DIFFRACTIONr_angle_other_deg0.8313.00324724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58751357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62925.367531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.522152100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8311542
X-RAY DIFFRACTIONr_chiral_restr0.0910.21697
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022539
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.361→2.422 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 219 -
Rwork0.274 4070 -
obs--99.03 %
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)
10.5335-0.2031-0.45040.5282-0.0861.7073-0.019-0.0505-0.02550.0099-0.0068-0.06380.14820.16770.02590.18640.016-0.11370.0715-0.07170.18421.99143.924136.272
20.9936-0.0056-0.63682.872-0.59471.8880.18180.07050.07950.16680.04370.00860.0734-0.2527-0.22550.1360.0122-0.05690.1201-0.04190.110512.80456.883113.49
30.53220.0256-0.27050.751-0.7551.04150.05580.1299-0.1138-0.1246-0.06180.13770.2589-0.07560.0060.4248-0.0706-0.08180.1241-0.12920.303114.41833.068128.939
40.5354-0.0502-0.62061.3541-0.43421.11950.0936-0.16540.03480.088-0.0366-0.1544-0.02550.3861-0.05690.20660.0204-0.08570.2089-0.07820.184829.37152.106122.978
51.10730.1155-0.10131.01810.04470.9057-0.04420.16680.13820.0499-0.0078-0.2464-0.1567-0.06020.0520.0743-0.0153-0.08350.04780.03710.1555-2.3747.2770.316
60.4372-1.3796-0.034.44970.44922.51160.04130.02020.0773-0.0736-0.1215-0.11610.15510.30440.08020.0301-0.060.050.4255-0.1490.383112.95130.69657.168
70.3173-0.1360.26920.0917-0.15211.1619-0.01310.2320.2050.0456-0.0726-0.2013-0.23780.15330.08570.3076-0.13040.00930.2944-0.00770.62216.96650.90866.288
81.133-0.5683-0.27130.63740.17220.52760.07050.40050.0557-0.1294-0.1616-0.0185-0.0258-0.21150.09110.1281-0.028-0.08090.22250.00630.1133-5.3439.68956.767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 471
2X-RAY DIFFRACTION1A501 - 506
3X-RAY DIFFRACTION1A601 - 649
4X-RAY DIFFRACTION2B1 - 96
5X-RAY DIFFRACTION2B101 - 108
6X-RAY DIFFRACTION3C5 - 94
7X-RAY DIFFRACTION3C101
8X-RAY DIFFRACTION3C201 - 203
9X-RAY DIFFRACTION4E2 - 95
10X-RAY DIFFRACTION4E101
11X-RAY DIFFRACTION4E201 - 208
12X-RAY DIFFRACTION5D1 - 471
13X-RAY DIFFRACTION5D501 - 505
14X-RAY DIFFRACTION5D601 - 649
15X-RAY DIFFRACTION6F3 - 95
16X-RAY DIFFRACTION6F101 - 106
17X-RAY DIFFRACTION7G1 - 94
18X-RAY DIFFRACTION7G101
19X-RAY DIFFRACTION7G201 - 203
20X-RAY DIFFRACTION8H4 - 96
21X-RAY DIFFRACTION8H101
22X-RAY DIFFRACTION8H201 - 213

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