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Basic information

Entry
Database: PDB / ID: 2mkn
TitleStructural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and dsRNA
Components
  • RNA (5'-R(*GP*CP*CP*GP*UP*GP*GP*UP*CP*UP*GP*GP*UP*GP*GP*CP*CP*GP*G)-3')
  • RNA (5'-R(P*CP*CP*GP*GP*CP*CP*AP*CP*CP*AP*GP*AP*CP*CP*AP*CP*GP*GP*C)-3')
  • Zinc finger protein 346
KeywordsRNA BINDING PROTEIN/RNA / Zinc finger / dsRNA-binding / RNA BINDING PROTEIN-RNA complex
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
RNA / RNA (> 10) / Zinc finger protein 346
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
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 10, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Apr 27, 2016Group: Structure summary
Revision 1.3May 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_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_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 346
B: RNA (5'-R(*GP*CP*CP*GP*UP*GP*GP*UP*CP*UP*GP*GP*UP*GP*GP*CP*CP*GP*G)-3')
C: RNA (5'-R(P*CP*CP*GP*GP*CP*CP*AP*CP*CP*AP*GP*AP*CP*CP*AP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3034
Polymers19,2383
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)1 / 100
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 181-224
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: RNA chain RNA (5'-R(*GP*CP*CP*GP*UP*GP*GP*UP*CP*UP*GP*GP*UP*GP*GP*CP*CP*GP*G)-3')


Mass: 6157.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*CP*CP*GP*GP*CP*CP*AP*CP*CP*AP*GP*AP*CP*CP*AP*CP*GP*GP*C)-3')


Mass: 6049.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Compound detailsTHE HADDOCK STARTING RNA STRUCTURE IS AN IDEALIZED A-FORM HELIX AND WAS GENERATED FROM THE MAKE-NA SERVER.

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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
HADDOCKAlexandre Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: HADDOCK MODEL OF JAZ ZINC FINGER 3 COMPLEXED WITH DSRNA.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 1

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