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- PDB-2hgh: Transcription Factor IIIA zinc fingers 4-6 bound to 5S rRNA 55mer... -

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Basic information

Entry
Database: PDB / ID: 2hgh
TitleTranscription Factor IIIA zinc fingers 4-6 bound to 5S rRNA 55mer (NMR structure)
Components
  • 55-MER
  • Transcription factor IIIA
KeywordsTRANSCRIPTION/RNA / zinc finger / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


ribosomal large subunit biogenesis / DNA binding / RNA binding / nucleus / metal ion binding
Similarity search - Function
Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Transcription factor IIIA
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics, generalized Born solvation model
AuthorsLee, B.M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Induced Fit and 'Lock and Key' Recognition of 5 S RNA by Zinc Fingers of Transcription Factor IIIA
Authors: Lee, B.M. / Xu, J. / Clarkson, B.K. / Martinez-Yamout, M.A. / Dyson, J.H. / Case, D.A. / Gottesfeld, J.M. / Wright, P.E.
History
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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_conn_angle / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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
B: 55-MER
A: Transcription factor IIIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1225
Polymers27,9262
Non-polymers1963
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 55-MER


Mass: 17626.416 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was synthesized by in vitro transcription from linearized pUC18 plasmid containing the 55mer sequence and the primer binding site for T7 RNA polymerase
#2: Protein Transcription factor IIIA / Factor A / TFIIIA / S-TFIIIA/O-TFIIIA


Mass: 10299.835 Da / Num. of mol.: 1 / Fragment: zinc fingers 4-6 (residues 127-212)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03001
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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 NOESY
1213D 15N-separated NOESY
1323D 13C-separated NOESY
1433D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N, 90% H2O, 10% D2O90% H2O/10% D2O
2U-13C;U-15N, D2OD2O
3U-2H;U-13C;U-15N, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM / pH: 6.5 / Pressure: 1 atm / Temperature: 291 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 DRXBrukerDRX8002
Bruker DMXBrukerDMX7503
Bruker DRXBrukerDRX6004
Bruker AMXBrukerAMX5005

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglioprocessing
NMRView5.4Johnsondata analysis
DYANA1.5Guntertstructure solution
Amber8Caserefinement
RefinementMethod: torsion angle dynamics, molecular dynamics, generalized Born solvation model
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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