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- PDB-2ruz: Solution structures of the DNA-binding domain (ZF11) of immune-re... -

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Basic information

Entry
Database: PDB / ID: 2ruz
TitleSolution structures of the DNA-binding domain (ZF11) of immune-related zinc-finger protein ZFAT
ComponentsZinc finger protein ZFAT
KeywordsTRANSCRIPTION / ZFAT / zinc finger
Function / homology
Function and homology information


hematopoietic progenitor cell differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / zinc ion binding / nucleus / cytosol
Similarity search - Function
: / C2H2-type zinc-finger domain / 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
Zinc finger protein ZFAT
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsTochio, N. / Umehara, T. / Kigawa, T. / Yokoyama, S.
CitationJournal: J.Struct.Funct.Genom. / Year: 2015
Title: Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT
Authors: Tochio, N. / Umehara, T. / Nakabayashi, K. / Yoneyama, M. / Tsuda, K. / Shirouzu, M. / Koshiba, S. / Watanabe, S. / Kigawa, T. / Sasazuki, T. / Shirasawa, S. / Yokoyama, S.
History
DepositionJan 26, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2May 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_nmr_spectrometer / 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_nmr_spectrometer.model / _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

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein ZFAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0792
Polymers4,0141
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Zinc finger protein ZFAT / Zinc finger gene in AITD susceptibility region / Zinc finger protein 406


Mass: 4013.512 Da / Num. of mol.: 1 / Fragment: UNP residues 796-826
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZFAT, KIAA1485, ZFAT1, ZNF406 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9P243
#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 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 1.16 mM [U-13C; U-15N] protein-1, 20 mM [U-2H] TRIS-2, 100 mM sodium chloride-3, 1 mM [U-2H] DTT-4, 0.02 % sodium azide-5, 50 uM zinc chloride-6, 90 % H2O-7, 10 % [U-2H] D2O-8, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.16 mMprotein-1[U-13C; U-15N]1
20 mMTRIS-2[U-2H]1
100 mMsodium chloride-31
1 mMDTT-4[U-2H]1
0.02 %sodium azide-51
50 uMzinc chloride-61
90 %H2O-71
10 %D2O-8[U-2H]1
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: 1 atm / Temperature: 296 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
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
KUJIRAN. Kobayashidata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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