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- PDB-2kkr: Solution structure of SCA7 zinc finger domain from human ataxin-7... -

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Basic information

Entry
Database: PDB / ID: 2kkr
TitleSolution structure of SCA7 zinc finger domain from human ataxin-7 protein
ComponentsAtaxin-7
KeywordsTRANSCRIPTION / PROTEIN BINDING / Structural Genomics / Structural Proteomics in Europe / Zinc Finger / SPINE
Function / homology
Function and homology information


transcription factor TFTC complex / negative regulation of microtubule depolymerization / SAGA complex / nucleus organization / regulation of RNA splicing / regulation of DNA repair / visual perception / nuclear matrix / microtubule cytoskeleton organization / microtubule cytoskeleton ...transcription factor TFTC complex / negative regulation of microtubule depolymerization / SAGA complex / nucleus organization / regulation of RNA splicing / regulation of DNA repair / visual perception / nuclear matrix / microtubule cytoskeleton organization / microtubule cytoskeleton / HATs acetylate histones / Ub-specific processing proteases / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #670 / SCA7 domain / SCA7, zinc-binding domain / SCA7 domain profile. / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWang, Y. / Atkinson, A.R. / Bonnet, J. / Romier, C. / Kieffer, B. / Structural Proteomics in Europe (SPINE)
CitationJournal: To be Published
Title: Histone deubiquitination by SAGA is modulated by an atypical zinc finger domain of Ataxin-7
Authors: Bonnet, J. / Wang, Y. / Atkinson, A. / Koffler, J. / Romier, C. / Hamiche, A. / Tora, L. / Devys, D. / Kieffer, B.
History
DepositionJun 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: 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_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ataxin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8322
Polymers8,7661
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 64structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ataxin-7 / Spinocerebellar ataxia type 7 protein


Mass: 8766.183 Da / Num. of mol.: 1 / Fragment: residues 339-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATXN7, SCA7 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15265
#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: Solution structure of human ataxin-7(339-397) SCA7 domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CA)CB
1413D HN(CO)CA
1513D HN(COCA)CB
1613D (H)CCH-TOCSY
1722D 1H-1H NOESY
1822D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 0.3 mM [U-99% 13C; U-99% 15N] ATXN7, 90% H2O/10% D2O90% H2O/10% D2O
250 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 0.6 mM ATXN7, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
200 mMsodium chloride-21
2 mMDTT-31
0.3 mMentity_1-4[U-99% 13C; U-99% 15N]1
50 mMsodium phosphate-52
200 mMsodium chloride-62
2 mMDTT-72
0.6 mMentity_1-82
Sample conditionsIonic strength: 0.3 / pH: 7.1 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE9502

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: In explicit water using RECOORD protocol
NMR constraintsNOE constraints total: 1589 / NOE intraresidue total count: 387 / NOE long range total count: 352 / NOE medium range total count: 376 / NOE sequential total count: 474 / Protein phi angle constraints total count: 29 / Protein psi angle constraints total count: 27
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 64 / Conformers submitted total number: 20

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