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- PDB-2lo3: Solution structure of Sgf73(59-102) zinc finger domain -

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Basic information

Entry
Database: PDB / ID: 2lo3
TitleSolution structure of Sgf73(59-102) zinc finger domain
ComponentsSAGA-associated factor 73
KeywordsTRANSCRIPTION / ZINC-FINGER / DEUBIQUITINATION / TRANSCRIPTION FACTOR / SAGA COMPLEX
Function / homology
Function and homology information


RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / enzyme activator activity / mRNA export from nucleus / chromatin organization ...RITS complex assembly / DUBm complex / regulation of nucleocytoplasmic transport / SLIK (SAGA-like) complex / regulation of protein localization to chromatin / SAGA complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / enzyme activator activity / mRNA export from nucleus / chromatin organization / protein-containing complex assembly / chromatin remodeling / regulation of transcription by RNA polymerase II / structural molecule activity / nucleus / cytosol
Similarity search - Function
SAGA-associated factor 73, zinc finger domain / Zinc finger domain / SAGA-associated factor 73 / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Classic Zinc Finger / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SAGA-associated factor 73
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 19
AuthorsGao, X. / Koehler, C. / Bonnet, J. / Devys, D. / Kieffer, B.
CitationJournal: To be Published
Title: Insights into the role of SGF11 and SGF73 for the interaction between SAGA and nucleosomes
Authors: Koehler, C. / Gao, X. / Bonnet, J. / Devys, D. / Kieffer, B.
History
DepositionJan 10, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: SAGA-associated factor 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8582
Polymers4,7921
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide SAGA-associated factor 73 / 73 kDa SAGA-associated factor / SAGA histone acetyltransferase complex 73 kDa subunit


Mass: 4792.471 Da / Num. of mol.: 1 / Fragment: UNP residues 59-102
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) / Strain (production host): BL21(DE3) / References: UniProt: P53165
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: First CCHH zinc finger domain of SAGA-associated factor 73
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H NOESY
1312D 1H-1H TOCSY
1432D 1H-1H TOCSY
1532D 1H-1H COSY
1632D 1H-1H TOCSY
1722D 1H-13C HSQC aliphatic
1823D CBCA(CO)NH
1923D HNCO
11023D HNCA
11123D HN(CA)CB
11223D (H)CCH-TOCSY
11323D HN(CA)CO
11423D HN(CO)CA
11522D 1H-1H NOESY
11622D 1H-15N HSQC R1 edited
11722D 1H-15N HSQC R2 edited
11822D 1H-15N heteronuclear NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-98% 15N] sgf73, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 mM TCEP, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-98% 15N] sgf73, 20 mM sodium phosphate, 75 mM sodium chloride, 1 mM DTT, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
30.2 mM [U-98% 15N] sgf73, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 mM TCEP, 100 % D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMsgf73-1[U-98% 15N]1
50 mMsodium phosphate-21
100 mMsodium chloride-31
0.05 mMTCEP-41
10 %D2O-51
1 mMsgf73-6[U-99% 13C; U-98% 15N]2
20 mMsodium phosphate-72
75 mMsodium chloride-82
1 mMDTT-92
10 %D2O-102
0.2 mMsgf73-11[U-98% 15N]3
50 mMsodium phosphate-123
100 mMsodium chloride-133
0.05 mMTCEP-143
100 %D2O-153
Sample conditionsIonic strength: 0.175 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE9503

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
SparkyGoddarddata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: RECOORD scripts
NMR constraintsNOE constraints total: 752 / NOE intraresidue total count: 459 / NOE long range total count: 98 / NOE medium range total count: 48 / NOE sequential total count: 147 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 36 / Protein psi angle constraints total count: 36
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.11 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.2 ° / Maximum upper distance constraint violation: 0.34 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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