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- PDB-2ebt: Solution structure of three tandem repeats of zf-C2H2 domains fro... -

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Basic information

Entry
Database: PDB / ID: 2ebt
TitleSolution structure of three tandem repeats of zf-C2H2 domains from human Kruppel-like factor 5
ComponentsKrueppel-like factor 5
KeywordsTRANSCRIPTION / C2H2-type zinc-finger / metal bind / transcription factor / kruppel-like factor / GC-box promoter elements / 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 transcription by transcription factor localization / satellite cell activation involved in skeletal muscle regeneration / cell-cell signaling via exosome / myotube differentiation involved in skeletal muscle regeneration / skeletal muscle satellite cell differentiation / regulation of microvillus assembly / microvillus assembly / cellular response to peptide / chromatin => GO:0000785 / intestinal epithelial cell development ...positive regulation of transcription by transcription factor localization / satellite cell activation involved in skeletal muscle regeneration / cell-cell signaling via exosome / myotube differentiation involved in skeletal muscle regeneration / skeletal muscle satellite cell differentiation / regulation of microvillus assembly / microvillus assembly / cellular response to peptide / chromatin => GO:0000785 / intestinal epithelial cell development / MRF binding / cellular response to organic cyclic compound / positive regulation of fat cell differentiation / cellular response to leukemia inhibitory factor / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / transcription regulator complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Krueppel-like factor 5 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Krueppel-like factor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of three tandem repeats of zf-C2H2 domains from human Kruppel-like factor 5
Authors: Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionFeb 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Krueppel-like factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8464
Polymers11,6501
Non-polymers1963
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 lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Krueppel-like factor 5 / Intestinal-enriched krueppel-like factor / Colon krueppel-like factor / Transcription factor BTEB2 ...Intestinal-enriched krueppel-like factor / Colon krueppel-like factor / Transcription factor BTEB2 / Basic transcription element-binding protein 2 / BTE-binding protein 2 / GC box-binding protein 2


Mass: 11650.169 Da / Num. of mol.: 1 / Fragment: zf-C2H2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P060116-02 / References: UniProt: Q13887
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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: 0.59mM uniformly 13C/15N-labelled protein, 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3, 50uM ZnCl2, 1mM IDA, 10% D2O, 90% H2O
Solvent system: 10% D2O, 90% H2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA9001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9822Kobayashi, 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 lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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