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- PDB-2kvq: Solution structure of NusE:NusG-CTD complex -

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Basic information

Entry
Database: PDB / ID: 2kvq
TitleSolution structure of NusE:NusG-CTD complex
Components
  • NusE
  • Transcription antitermination protein nusG
KeywordsTRANSCRIPTION / NusE:NusG complex
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / transcription antitermination factor activity, RNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation ...transcription elongation-coupled chromatin remodeling / transcription antitermination factor activity, RNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / structural constituent of ribosome / cytosol / cytoplasm
Similarity search - Function
: / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / Ribosomal protein S10 / SH3 type barrels. - #30 / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. ...: / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / Ribosomal protein S10 / SH3 type barrels. - #30 / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / SH3 type barrels. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S10 / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Roll / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS10 / Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBurmann, B.M. / Schweimer, K. / Roesch, P.
CitationJournal: Science / Year: 2010
Title: A NusE:NusG complex links transcription and translation.
Authors: Burmann, B.M. / Schweimer, K. / Luo, X. / Wahl, M.C. / Stitt, B.L. / Gottesman, M.E. / Rosch, P.
History
DepositionMar 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: 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
E: NusE
G: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)16,5642
Polymers16,5642
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)18 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NusE


Mass: 9608.144 Da / Num. of mol.: 1 / Fragment: UNp residues 1-45,68-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A7R5
#2: Protein Transcription antitermination protein nusG


Mass: 6955.832 Da / Num. of mol.: 1 / Fragment: UNP residues 123-181, KOW domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nusG, b3982, JW3945 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AFG0
Sequence detailsRESIDUES 46-67 OF CHAIN E ARE REPLACED WITH A SINGLE SER.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D 13C filtered(F1)-13C edited NOESY
1632D 1H-15N HSQC
1732D 1H-13C HSQC
1833D 1H-13C NOESY
1933D 1H-15N NOESY
11033D 13C filtered(F1)-133D 13C filtered(F1)-13C edited NOESY
11123D HNCA
11223D HN(CA)CB
11333D (H)CCH-TOCSY
11413D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1300 uM [U-100% 13C; U-100% 15N] 15N, 13C -NusG-CTD-1, 300 uM NusE-2, 300 uM NusB-3, 90% H2O/10% D2O90% H2O/10% D2O
2300 uM [U-100% 13C; U-100% 15N; U-80% 2H] 15N, 13C, 2H-NusE-4, 300 uM NusB-5, 300 uM NusG-CTD-6, 90% H2O/10% D2O90% H2O/10% D2O
30.3 mM NusG-CTD-7, 0.3 mM [U-100% 13C; U-100% 15N] 15N, 13C NusE-8, 0.3 mM NusB-9, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uM15N, 13C -NusG-CTD-1[U-100% 13C; U-100% 15N]1
300 uMNusE-21
300 uMNusB-31
300 uM15N, 13C, 2H-NusE-4[U-100% 13C; U-100% 15N; U-80% 2H]2
300 uMNusB-52
300 uMNusG-CTD-62
0.3 mMNusG-CTD-73
0.3 mM15N, 13C NusE-8[U-100% 13C; U-100% 15N]3
0.3 mMNusB-93
Sample conditionsIonic strength: 50 / pH: 7.5 / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure was calculated using rigid body docking with experimental derived intermolecular distance restraints. The structures of unbound NusG-CTD (pdb 2JVV) and unbound NusE:NusB (pdb 3D3B) were used.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 18

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