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- PDB-4w4u: Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstr... -

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Basic information

Entry
Database: PDB / ID: 4w4u
TitleStructure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution
Components
  • (SAGA-associated factor ...) x 2
  • Transcription and mRNA export factor SUS1
  • Ubiquitin carboxyl-terminal hydrolase
Keywordstranscription/hydrolase / Multi-Protein Complex / Hydrolase-transcription complex / transcription-hydrolase complex
Function / homology
Function and homology information


RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / DNA binding, bending / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination ...RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / transcription export complex 2 / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / DNA binding, bending / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / nuclear pore / mRNA export from nucleus / transcription elongation by RNA polymerase II / P-body / enzyme activator activity / protein transport / chromatin organization / protein-containing complex assembly / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / transcription coactivator activity / chromatin remodeling / regulation of transcription by RNA polymerase II / structural molecule activity / 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
SAGA-associated factor 11 / Ubiquitin carboxyl-terminal hydrolase / Transcription and mRNA export factor SUS1 / SAGA complex subunit SGF73
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: J.Mol.Biol. / Year: 2015
Title: Uncovering the role of Sgf73 in maintaining SAGA deubiquitinating module structure and activity.
Authors: Yan, M. / Wolberger, C.
History
DepositionAug 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: atom_site_anisotrop / citation ...atom_site_anisotrop / citation / 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 / _citation.journal_id_CSD / _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 2.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: Transcription and mRNA export factor SUS1
C: SAGA-associated factor 11
E: SAGA-associated factor 73
D: Ubiquitin carboxyl-terminal hydrolase
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)175,16621
Polymers174,3168
Non-polymers85013
Water95553
1
A: Ubiquitin carboxyl-terminal hydrolase
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)87,61611
Polymers87,1584
Non-polymers4587
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15820 Å2
ΔGint-126 kcal/mol
Surface area31140 Å2
MethodPISA
2
D: Ubiquitin carboxyl-terminal hydrolase
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)87,55010
Polymers87,1584
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14820 Å2
ΔGint-120 kcal/mol
Surface area28800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.739, 67.273, 137.145
Angle α, β, γ (deg.)90.00, 106.84, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22F
13C
23G
14E
24H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASNASNAA1 - 4716 - 476
21METMETASNASNDE1 - 4716 - 476
12METMETTHRTHRBB3 - 953 - 95
22METMETTHRTHRFF3 - 953 - 95
13THRTHRARGARGCC5 - 465 - 46
23THRTHRARGARGGG5 - 465 - 46
14GLYGLYLEULEUED4 - 944 - 94
24GLYGLYLEULEUHH4 - 944 - 94

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules ADBF

#1: Protein Ubiquitin carboxyl-terminal hydrolase


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: CEN.PK113-7D / Gene: CENPK1137D_262 / Production host: Escherichia coli (E. coli) / References: UniProt: N1P0J5, 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: CEN.PK113-7D / Gene: SUS1, CENPK1137D_4659 / Production host: Escherichia coli (E. coli) / References: UniProt: N1P8F5

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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: CEN.PK113-7D / Gene: SGF11, CENPK1137D_1654 / Production host: Escherichia coli (E. coli) / References: UniProt: N1NXA6
#4: Protein SAGA-associated factor 73 / 73 kDa SAGA-associated factor / SAGA histone acetyltransferase complex 73 kDa subunit


Mass: 10732.178 Da / Num. of mol.: 2 / Mutation: Y57A
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, 66 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
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: May 18, 2013
RadiationMonochromator: Double crystal cryo-cooled Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.034 Å / Relative weight: 1
ReflectionResolution: 2.8→47.02 Å / Num. obs: 34989 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 23.2

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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
Starting model: 3MHS

3mhs


Resolution: 2.8→47.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 32.348 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24067 1755 5 %RANDOM
Rwork0.182 ---
obs0.18496 33234 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.258 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å22.64 Å2
2---3.58 Å20 Å2
3---3.49 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10484 0 13 53 10550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910774
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210328
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.95914507
X-RAY DIFFRACTIONr_angle_other_deg0.933.00323809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02951306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20225.478502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87152016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5311536
X-RAY DIFFRACTIONr_chiral_restr0.0740.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212008
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022414
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A241830.09
12D241830.09
21B52980.11
22F52980.11
31C21600.13
32G21600.13
41E38650.07
42H38650.07
LS refinement shellResolution: 2.799→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 119 -
Rwork0.266 2376 -
obs--98 %
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)
10.6427-0.0858-0.5560.48630.1192.3422-0.04040.15060.0368-0.04810.06460.14130.214-0.1247-0.02420.3657-0.0945-0.10530.37550.13270.089-21.212672.1727-4.3314
20.41490.9072-0.22292.50220.46372.4966-0.014-0.0090.0076-0.17880.1739-0.01990.14940.2967-0.160.29110.0023-0.02960.42340.07640.0361-12.094784.993818.3382
30.4647-0.3246-0.46880.32980.5741.3441-0.0447-0.2245-0.00720.09830.0615-0.04230.32030.2827-0.01680.59760.0958-0.04360.42050.13030.0618-12.403367.347212.6939
40.5261-0.1537-0.71161.82560.76871.2834-0.12390.11940.0136-0.07090.15490.1990.0934-0.2496-0.0310.2591-0.0459-0.06580.39350.13450.0794-28.707680.0638.9507
51.0323-0.1508-0.04850.80860.21511.1347-0.03430.03210.1866-0.1088-0.02260.1198-0.2170.04290.05680.20670.0136-0.07250.1434-0.03270.07933.266175.156161.1028
60.34730.4259-0.07323.0492-0.6012.2672-0.0006-0.05070.1315-0.1408-0.07480.090.1754-0.08050.07540.07870.024-0.0020.1606-0.01920.0883-12.269659.055674.3233
71.39391.4946-0.34532.405-1.20161.0598-0.1926-0.14050.0609-0.16580.247-0.03510.0497-0.3712-0.05450.24430.0302-0.01770.222-0.06350.2078-12.943468.058877.0965
80.61280.59180.04581.3543-0.26211.0937-0.0324-0.17180.11330.01440.09770.12230.07470.2939-0.06540.19190.0686-0.05760.3172-0.05710.03776.082168.444574.7345
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-IDSelection details
1X-RAY DIFFRACTION1A1 - 471
2X-RAY DIFFRACTION1A501 - 506
3X-RAY DIFFRACTION1A601 - 608
4X-RAY DIFFRACTION2B1 - 96
5X-RAY DIFFRACTION2B101 - 105
6X-RAY DIFFRACTION3C5 - 63
7X-RAY DIFFRACTION4E2 - 95
8X-RAY DIFFRACTION4E101
9X-RAY DIFFRACTION4E201 - 203
10X-RAY DIFFRACTION5D1 - 471
11X-RAY DIFFRACTION5D501 - 505
12X-RAY DIFFRACTION5D601 - 625
13X-RAY DIFFRACTION6F3 - 96
14X-RAY DIFFRACTION6F101 - 104
15X-RAY DIFFRACTION7G1 - 47
16X-RAY DIFFRACTION7G101 - 102
17X-RAY DIFFRACTION8H4 - 96
18X-RAY DIFFRACTION8H101
19X-RAY DIFFRACTION8H201 - 206'?

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