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- PDB-2kdp: Solution Structure of the SAP30 zinc finger motif -

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Basic information

Entry
Database: PDB / ID: 2kdp
TitleSolution Structure of the SAP30 zinc finger motif
ComponentsHistone deacetylase complex subunit SAP30
KeywordsTRANSCRIPTION / sap30 / sin3 / zinc finger motif / nucleic acid interaction / Nucleus / Repressor / Transcription regulation
Function / homology
Function and homology information


skeletal muscle cell differentiation / histone deacetylase complex / transcription coregulator activity / HDACs deacetylate histones / NoRC negatively regulates rRNA expression / transcription corepressor activity / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding
Similarity search - Function
His-Me finger endonuclease fold - #30 / Histone deacetylase complex subunit SAP30 zinc-finger / SAP30 zinc-finger / Histone deacetylase complex subunit SAP30/SAP30-like / Histone deacetylase complex subunit SAP30, Sin3 binding domain / SAP30, C-terminal domain superfamily / Sin3 binding region of histone deacetylase complex subunit SAP30 / His-Me finger endonuclease fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone deacetylase complex subunit SAP30
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 1
AuthorsHe, Y. / Imhoff, R. / Sahu, A. / Radhakrishnan, I.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Solution structure of a novel zinc finger motif in the SAP30 polypeptide of the Sin3 corepressor complex and its potential role in nucleic acid recognition
Authors: He, Y. / Imhoff, R. / Sahu, A. / Radhakrishnan, I.
History
DepositionJan 14, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 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_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase complex subunit SAP30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1922
Polymers8,1261
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)47 / 3000structures with acceptable covalent geometry and in good agreement with experimental data
RepresentativeModel #1closest to the average

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Components

#1: Protein Histone deacetylase complex subunit SAP30 / Sin3-associated polypeptide / 30 kDa / Sin3 corepressor complex subunit SAP30


Mass: 8126.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAP30 / Production host: Escherichia coli (E. coli) / References: UniProt: O75446
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D H(CCO)NH
1723D (H)CCH-TOCSY
1823D (H)CCH-COSY
1913D 1H-15N NOESY
11023D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.56 mM [U-95% 13C; U-95% 15N] SAP30 ZnF, 20 mM [U-13C; U-15N] TRIS, 20 mM [U-13C] acetic acid, 2 mM [U-2H] DTT, 0.2 % Sodium Azide, 0.56 mM zinc chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.56 mM [U-95% 13C; U-95% 15N] SAP30 ZnF, 20 mM [U-13C; U-15N] TRIS, 20 mM [U-13C] acetic acid, 2 mM [U-2H] DTT, 0.2 % Sodium Azide, 0.56 mM zinc chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.56 mMSAP30 ZnF[U-95% 13C; U-95% 15N]1
20 mMTRIS[U-13C; U-15N]1
20 mMacetic acid[U-13C]1
2 mMDTT[U-2H]1
0.2 %Sodium Azide1
0.56 mMzinc chloride1
0.56 mMSAP30 ZnF[U-95% 13C; U-95% 15N]2
20 mMTRIS[U-13C; U-15N]2
20 mMacetic acid[U-13C]2
2 mMDTT[U-2H]2
0.2 %Sodium Azide2
0.56 mMzinc chloride2
Sample conditionsIonic strength: 0.04 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
FelixAccelrys Software Inc.data analysis
FelixAccelrys Software Inc.peak picking
FelixAccelrys Software Inc.processing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorefinement
ISD1.1Rieping, Habeck, and Lamazhapovarefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Structures were determined using a combination of replica-exchange Monte Carlo and bayesian inference using the Inferential Structure Determination program (ISD). NOE assignments were made using Aria and CNS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry and in good agreement with experimental data
Conformers calculated total number: 3000 / Conformers submitted total number: 47

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