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- PDB-2mkd: Human JAZ ZF3 Residues 168-227 -

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Basic information

Entry
Database: PDB / ID: 2mkd
TitleHuman JAZ ZF3 Residues 168-227
ComponentsZinc finger protein 346
KeywordsDNA BINDING PROTEIN / Zinc finger / dsRNA-binding
Function / homology
Function and homology information


miRNA binding / double-stranded RNA binding / nucleolus / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Zinc-finger of C2H2 type / Classic Zinc Finger / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 superfamily / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger protein 346
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWright, P. / Dyson, J. / Burge, R. / Martinez-Yamout, M.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and Nucleic Acids.
Authors: Burge, R.G. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
History
DepositionFeb 5, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein 346
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0962
Polymers7,0301
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 favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Zinc finger protein 346


Mass: 7030.144 Da / Num. of mol.: 1 / Fragment: UNP residues 168-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF346, JAZ / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UL40
#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
1213D 1H-15N NOESY
1313D HNCA
1413D HNCO
1513D HN(CA)CB
1613D 1H-15N TOCSY
1713D 1H-13C NOESY
1813D (H)CCH-COSY
1913D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 200-300 mM [U-95% 13C; U-95% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: entity_1-1 / Isotopic labeling: [U-95% 13C; U-95% 15N] / Conc. range: 200-300
Sample conditionsIonic strength: 55 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRViewJohnson, One Moon Scientificchemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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