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- PDB-1zu1: Solution Structure of the N-terminal Zinc Fingers of the Xenopus ... -

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Basic information

Entry
Database: PDB / ID: 1zu1
TitleSolution Structure of the N-terminal Zinc Fingers of the Xenopus laevis double stranded RNA binding protein ZFa
ComponentsRNA binding protein ZFa
KeywordsRNA BINDING PROTEIN / zinc finger protein / helix-loop-helix / helix-turn-helix
Function / homology
Function and homology information


double-stranded RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
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 speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / simulated annealing
AuthorsMoller, H.M. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Solution structure of the N-terminal zinc fingers of the Xenopus laevis double-stranded RNA-binding protein ZFa
Authors: Moller, H.M. / Martinez-Yamout, M.A. / Dyson, H.J. / Wright, P.E.
History
DepositionMay 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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_conn_angle / pdbx_struct_oper_list / 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_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_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: RNA binding protein ZFa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2033
Polymers14,0721
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein RNA binding protein ZFa / dsRBP-ZFa


Mass: 14071.909 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8AVN9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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
1233D 13C-separated NOESY
131HNHA
1433D HACAHB-COSY
15313C [13CO] and 13C [15N] spin-echo difference CT HSQC
NMR detailsText: The protein consists of two domains that tumble more or less independently. The linker connecting both domains is completely disorderd.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM dsRBP-ZFa2-128 U-15N, 25mM Tris-Buffer, 100mM NaCl, 2mM DTT, pH=6.9, 95% H2O, 5% D2O95% H2O/5% D2O
21mM dsRBP-ZFa2-128 U-15N,13C, 25mM Tris-Buffer, 100mM NaCl, 2mM DTT, pH=6.9, 95% H2O, 5% D2O95% H2O/5% D2O
31mM dsRBP-ZFa2-128 U-15N,13C, 25mM Tris-Buffer, 100mM NaCl, 2mM DTT, pH=6.9, 100% D2O100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker DMXBrukerDMX7502
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1-3.5Brukercollection
NMRPipe2.3F.Delaglio,S.Grzesiek,G.W.Vuister,Z.Guang,J.Pfeifer,A.Baxprocessing
NMRView5.0.4B.A.Johnson,R.A.Blevinsdata analysis
CYANA1.0.5P.Guntert,C.Mumenthaler,K.Wuthrichstructure solution
Amber8D.A.Case,T.Cheatham,T.Darden,H.Gohlke,R.Luo,K.M.J.Merz,A.Onufriev,C.Simmerling,B.Wang,R.Woods.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1142 unique NOE restraints, 216 dihedral angle restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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