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- PDB-2n1u: Structure of SAP30L corepressor protein -

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Basic information

Entry
Database: PDB / ID: 2n1u
TitleStructure of SAP30L corepressor protein
ComponentsHistone deacetylase complex subunit SAP30L
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


non-sequence-specific DNA binding, bending / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding / histone deacetylase complex / nucleosome binding / HDACs deacetylate histones / transcription coregulator activity / NoRC negatively regulates rRNA expression / histone binding ...non-sequence-specific DNA binding, bending / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding / histone deacetylase complex / nucleosome binding / HDACs deacetylate histones / transcription coregulator activity / NoRC negatively regulates rRNA expression / histone binding / regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm
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 SAP30L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTossavainen, H. / Permi, P.
CitationJournal: Protein Sci. / Year: 2016
Title: Redox-dependent disulfide bond formation in SAP30L corepressor protein: Implications for structure and function.
Authors: Laitaoja, M. / Tossavainen, H. / Pihlajamaa, T. / Valjakka, J. / Viiri, K. / Lohi, O. / Permi, P. / Janis, J.
History
DepositionApr 23, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
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 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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_ref_seq_dif.details / _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: Histone deacetylase complex subunit SAP30L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1862
Polymers8,1201
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone deacetylase complex subunit SAP30L / HCV non-structural protein 4A-transactivated protein 2 / Sin3 corepressor complex subunit SAP30L / ...HCV non-structural protein 4A-transactivated protein 2 / Sin3 corepressor complex subunit SAP30L / Sin3-associated protein p30-like


Mass: 8120.453 Da / Num. of mol.: 1 / Fragment: UNP residues 25-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAP30L, NS4ATP2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HAJ7
#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
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D HN(COCA)CB
1513D HNCA
1613D HN(CO)CA
1713D C(CO)NH
1813D H(CCO)NH
1913D (H)CCH-COSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
1121(HB)CB(CGCD)HD
1131(HB)CB(CGCDCE)HE

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] protein, 0.5 mM ZINC ION, 20 mM BIS-TRIS, 30 mM sodium chloride, 0.04% sodium azide, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein-1[U-13C; U-15N]1
0.5 mMZINC ION-21
20 mMBIS-TRIS-31
30 mMsodium chloride-41
0.04 %sodium azide-51
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJAgilentcollection
VnmrJAgilentprocessing
SparkyGoddarddata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanminimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 15

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