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- PDB-2cs8: Solution structure of tandem repeat of the fifth and sixth zinc-f... -

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Basic information

Entry
Database: PDB / ID: 2cs8
TitleSolution structure of tandem repeat of the fifth and sixth zinc-finger C2HC domains from human ST18
ComponentsKIAA0535 protein
KeywordsTRANSCRIPTION / ST18 / zinc-finger / C2HC / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / chromatin => GO:0000785 / interleukin-1-mediated signaling pathway / interleukin-6-mediated signaling pathway / tumor necrosis factor-mediated signaling pathway / protein-DNA complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II ...positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / chromatin => GO:0000785 / interleukin-1-mediated signaling pathway / interleukin-6-mediated signaling pathway / tumor necrosis factor-mediated signaling pathway / protein-DNA complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Dihydrolipoamide Transferase - #30 / Myelin transcription factor 1 / Myelin transcription factor 1 / Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Dihydrolipoamide Transferase / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Suppression of tumorigenicity 18 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSuetake, T. / Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of tandem repeat of the fifth and sixth zinc-finger C2HC domains from human ST18
Authors: Suetake, T. / Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KIAA0535 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2203
Polymers11,0901
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violation, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein KIAA0535 protein / ST18 / suppression of tumorigenicity 18 / breast carcinoma / zinc-finger protein


Mass: 11089.596 Da / Num. of mol.: 1 / Fragment: the fifth and sixth C2HC domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: KAZUSA cDNA hg03847 / Plasmid: P040921-02 / References: UniProt: O60284
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.21mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d10-DTT; 0.02% NaN3; 0.01mM ZnCl2
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.0 / 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
NameVersionDeveloperClassification
VNMR6.1CVARIANcollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.927Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violation, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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