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- PDB-2epp: Solution structure of the first C2H2 type zinc finger domain of Z... -

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Basic information

Entry
Database: PDB / ID: 2epp
TitleSolution structure of the first C2H2 type zinc finger domain of Zinc finger protein 278
ComponentsPOZ-, AT hook-, and zinc finger-containing protein 1
KeywordsTRANSCRIPTION / C2H2 / zinc finger domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of immune system process / negative regulation of endothelial cell migration / T cell differentiation / regulation of cytokine production / male germ cell nucleus / DNA-binding transcription repressor activity, RNA polymerase II-specific / male gonad development / spermatogenesis / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription ...regulation of immune system process / negative regulation of endothelial cell migration / T cell differentiation / regulation of cytokine production / male germ cell nucleus / DNA-binding transcription repressor activity, RNA polymerase II-specific / male gonad development / spermatogenesis / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / ubiquitin protein ligase binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Putative zinc-finger between two C2H2 zinc-fingers on Patz / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger ...Putative zinc-finger between two C2H2 zinc-fingers on Patz / HMG-I/HMG-Y, DNA-binding, conserved site / HMG-I and HMG-Y DNA-binding domain (A+T-hook). / C2H2-type zinc finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
POZ-, AT hook-, and zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dyanamics, simulated annealing
AuthorsTanabe, W. / Suzuki, S. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the first C2H2 type zinc finger domain of Zinc finger protein 278
Authors: Tanabe, W. / Suzuki, S. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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: POZ-, AT hook-, and zinc finger-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8002
Polymers6,7351
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)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein POZ-, AT hook-, and zinc finger-containing protein 1 / Zinc finger protein 278 / Zinc finger sarcoma gene protein / BTB-POZ domain zinc finger ...Zinc finger protein 278 / Zinc finger sarcoma gene protein / BTB-POZ domain zinc finger transcription factor / Protein kinase A RI-subunit alpha- associated protein / Zinc finger and BTB domain-containing protein 19


Mass: 6734.532 Da / Num. of mol.: 1 / Fragment: zinc finger domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PATZ1, PATZ, RIAZ, ZBTB19, ZNF278, ZSG / Plasmid: P061204-01 / References: UniProt: Q9HBE1
#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
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.89mM 13C-15N PROTEIN, 20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O, 0.05mM ZnCl2, 1mM IDA
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20060702Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.982Kobayashi,N.data analysis
CYANA2.1Guntert,P.structure solution
CYANA2.1Guntert,P.refinement
RefinementMethod: torsion angle dyanamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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