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- PDB-2a8v: RHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2a8v
TitleRHO TRANSCRIPTION TERMINATION FACTOR/RNA COMPLEX
Components
  • 5'-R(P*CP*CP*C)-3'
  • 5'-R(P*CP*CP*CP*CP*CP*C)-3'
  • RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR
KeywordsPROTEIN/RNA / RHO / OB FOLD / SINGLE-STRANDED NUCLEIC ACID BINDING DOMAIN / PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


ATP-dependent activity, acting on RNA / DNA-templated transcription termination / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Transcription termination factor Rho / Rho termination factor, N-terminal / Rho termination factor, RNA-binding domain / Transcription termination factor Rho, ATP binding domain / Rho termination factor, RNA-binding domain / Rho termination factor, N-terminal domain / Rho RNA-binding domain profile. / Rho termination factor, N-terminal domain / Rho termination factor, N-terminal domain superfamily / Cold shock domain / Cold shock protein domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
RNA / Transcription termination factor Rho / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBogden, C.E. / Fass, D. / Bergman, N. / Nichols, M.D. / Berger, J.M.
CitationJournal: Mol.Cell / Year: 1999
Title: The structural basis for terminator recognition by the Rho transcription termination factor.
Authors: Bogden, C.E. / Fass, D. / Bergman, N. / Nichols, M.D. / Berger, J.M.
History
DepositionNov 8, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: 5'-R(P*CP*CP*C)-3'
E: 5'-R(P*CP*CP*CP*CP*CP*C)-3'
A: RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR
B: RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR
C: RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR


Theoretical massNumber of molelcules
Total (without water)42,3115
Polymers42,3115
Non-polymers00
Water1,45981
1
D: 5'-R(P*CP*CP*C)-3'
A: RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR


Theoretical massNumber of molelcules
Total (without water)14,0892
Polymers14,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-R(P*CP*CP*CP*CP*CP*C)-3'
B: RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR


Theoretical massNumber of molelcules
Total (without water)15,0042
Polymers15,0042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR


Theoretical massNumber of molelcules
Total (without water)13,2181
Polymers13,2181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.783, 31.308, 105.751
Angle α, β, γ (deg.)90.00, 122.98, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9853, -0.01163, -0.17042), (0.00073, 0.99796, -0.06391), (0.17081, 0.06285, 0.9833)9.95693, 1.32919, 58.18643
2given(0.98096, -0.153, 0.11959), (0.16053, 0.98544, -0.05604), (-0.10928, 0.07417, 0.99124)68.2959, 25.45975, 29.209

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Components

#1: RNA chain 5'-R(P*CP*CP*C)-3'


Mass: 870.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5A / Plasmid: PET24B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: RNA chain 5'-R(P*CP*CP*CP*CP*CP*C)-3'


Mass: 1786.133 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein RNA BINDING DOMAIN OF RHO TRANSCRIPTION TERMINATION FACTOR / RHO


Mass: 13218.041 Da / Num. of mol.: 3 / Fragment: N-TERMINAL RNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
References: UniProt: P03002, UniProt: P0AG30*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temperature: 30 ℃ / Method: vapor diffusion, hanging drop / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210-20 %MPD1reservoir
350-100 mMammonium acetate1reservoir
4100 mMTris1reservoirpH8.5
54 mM1reservoirCuCl2
62 mMerbium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9779
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.4→14 Å / Num. obs: 14393 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.074 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.283 / % possible all: 99.6
Reflection
*PLUS
Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.283

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A8V

1a8v


Resolution: 2.4→14 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.297 728 5 %RANDOM
Rwork0.2455 ---
obs0.2455 14393 98.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å2-6.51 Å2
2--0.484 Å20 Å2
3---1.957 Å2
Refinement stepCycle: LAST / Resolution: 2.4→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 182 0 81 3050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.14
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.14
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22

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