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- PDB-1qfq: Bacteriophage Lambda N-protein-NutboxB-RNA Complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1qfq
TitleBacteriophage Lambda N-protein-NutboxB-RNA Complex
Components
  • 15-mer nutRboxB RNA hairpin
  • 36-mer N-terminal peptide of the N protein
KeywordsTRANSCRIPTION/RNA / BACTERIOPHAGE LAMBDA / ANTITERMINATION / PEPTIDE-RNA-COMPLEX / N-NUT / GNRA TETRALOOP / BENT-ALPHA-HELIX / PEPTIDE-RNA-RECOGNITION / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme binding / RNA polymerase binding / transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / RNA stem-loop binding / single-stranded RNA binding / regulation of transcription by RNA polymerase II / DNA binding / RNA binding
Similarity search - Function
Antitermination protein N, arginine-rich motif / 36-mer N-terminal peptide of the N protein (N36)
Similarity search - Domain/homology
RNA / RNA (> 10) / Antitermination protein N
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodSOLUTION NMR / molecular dynamics
AuthorsSchaerpf, M. / Sticht, H. / Roesch, P.
CitationJournal: Eur.J.Biochem. / Year: 2000
Title: Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex
Authors: Schaerpf, M. / Sticht, H. / Schweimer, K. / Boehm, M. / Hoffmann, S. / Roesch, P.
History
DepositionApr 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 15-mer nutRboxB RNA hairpin
B: 36-mer N-terminal peptide of the N protein


Theoretical massNumber of molelcules
Total (without water)8,8622
Polymers8,8622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)29 / 100LOWEST ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
RepresentativeModel #1

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Components

#1: RNA chain 15-mer nutRboxB RNA hairpin


Mass: 4853.994 Da / Num. of mol.: 1 / Fragment: BACTERIOPHAGE LAMBDA NUT boxB-RNA / Source method: obtained synthetically
Details: SEQUENCE FROM BACTERIOPHAGE LAMBDA. RNA WAS UNIFORMLY LABELLED WITH (13)C AND (15)N
#2: Protein/peptide 36-mer N-terminal peptide of the N protein / N36


Mass: 4007.587 Da / Num. of mol.: 1 / Fragment: N-TERMINAL BINDING-DOMAIN, RESIDUES 2-36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Production host: Escherichia coli (E. coli) / References: UniProt: P03045

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111(1)H-(31)P-COSY
121(1)H-(13)C-CT- HSQC
131(1)H-(15)N-HSQC
141(1)H-(1)H-COSY
151(1)H-(1)H-TOCSY
161(1)H-(1)H-NOESY WITH 75 AND 150 MS MIXING TIME
171'(13)C-ED.-NOESY
181(1)H-(15)N-(1)H-NOESY-HSQC
191(1)H-(15)N-(1)H-TOCSY-HSQC
1101HNHA
1111(13)C-NOESY-HSQC
1121(H)CCH-TOCSY
1131(H)CCH-COSY
1141CCH-COSY

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Sample preparation

DetailsContents: 10% H2O/90% D2O
Sample conditionsIonic strength: 0 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NDEEstructure solution
Xndeestructure solution
X-PLORstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 100 / Conformers submitted total number: 29

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