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- PDB-2ht1: The closed ring structure of the Rho transcription termination fa... -

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Basic information

Entry
Database: PDB / ID: 2ht1
TitleThe closed ring structure of the Rho transcription termination factor in complex with nucleic acid in the motor domains
Components
  • 5'-R(*UP*C)-3'
  • 5'-R(*UP*CP*UP*CP*U)-3'
  • Transcription termination factor rho
KeywordsHYDROLASE/RNA / ATPase / Translocase / HYDROLASE-RNA COMPLEX
Function / homology
Function and homology information


ATP-dependent activity, acting on RNA / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
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 ...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) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsSkordalakes, E. / Berger, J.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural Insights into RNA-Dependent Ring Closure and ATPase Activation by the Rho Termination Factor.
Authors: Skordalakes, E. / Berger, J.M.
History
DepositionJul 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _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
J: 5'-R(*UP*C)-3'
K: 5'-R(*UP*C)-3'
M: 5'-R(*UP*CP*UP*CP*U)-3'
A: Transcription termination factor rho
B: Transcription termination factor rho
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7987
Polymers99,6065
Non-polymers1922
Water00
1
J: 5'-R(*UP*C)-3'
K: 5'-R(*UP*C)-3'
M: 5'-R(*UP*CP*UP*CP*U)-3'
A: Transcription termination factor rho
B: Transcription termination factor rho
hetero molecules

J: 5'-R(*UP*C)-3'
K: 5'-R(*UP*C)-3'
M: 5'-R(*UP*CP*UP*CP*U)-3'
A: Transcription termination factor rho
B: Transcription termination factor rho
hetero molecules

J: 5'-R(*UP*C)-3'
K: 5'-R(*UP*C)-3'
M: 5'-R(*UP*CP*UP*CP*U)-3'
A: Transcription termination factor rho
B: Transcription termination factor rho
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,39321
Polymers298,81715
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)257.686, 257.686, 257.686
Angle α, β, γ (deg.)90, 90, 90
Int Tables number211
Space group name H-MI432

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Components

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


Mass: 566.390 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain 5'-R(*UP*CP*UP*CP*U)-3'


Mass: 1483.904 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Transcription termination factor rho / ATP-dependent helicase rho


Mass: 48494.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rho, nitA, psuA, rnsC, sbaA, tsu / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: P0AG30, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 3.87 Å3/Da / Density % sol: 68.19 %
Crystal growTemperature: 291 K / Method: microbatch under paraffine oil / pH: 6.5
Details: 50 mM Na cacodylate, 10 mM MgOAc, 1.8 M LiSO4, 2% benzamidine, 10 mM spermine-HCl, pH 6.5, Microbatch under paraffine oil, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1Na cacodylate11
2MgOAc11
3LiSO411
4benzamidine11
5spermine-HCl11
6HOH11
7Na cacodylate12
8MgOAc12
9LiSO412
10HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 15818 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.5→3.68 Å / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PVO

1pvo


Resolution: 3.51→20 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.829 / SU B: 88.349 / SU ML: 0.636 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.7 / ESU R: 6.352 / ESU R Free: 0.711 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3281 854 5.1 %RANDOM
Rwork0.29446 ---
all0.2857 ---
obs0.28707 15818 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 118.555 Å2
Refinement stepCycle: LAST / Resolution: 3.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 171 10 0 5223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225314
X-RAY DIFFRACTIONr_angle_refined_deg0.952.0227198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.855646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5423.707232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81915946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8121548
X-RAY DIFFRACTIONr_chiral_restr0.0620.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023909
X-RAY DIFFRACTIONr_nbd_refined0.1950.22258
X-RAY DIFFRACTIONr_nbtor_refined0.30.23551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.28
LS refinement shellResolution: 3.508→3.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 78 -
Rwork0.289 1030 -
obs--84.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1208-0.68040.55321.32211.07992.478-0.01130.0710.0506-0.0637-0.0118-0.0919-0.0756-0.07640.02310.0047-0.0571-0.13010.20480.1297-0.0046-87.0793-58.2794-28.1602
23.48912.3544-1.14332.5662-0.52620.43620.5318-0.4865-0.3245-0.6509-0.50720.2640.015-0.1175-0.02450.1336-0.0298-0.1041-0.0387-0.16560.0085-57.3636-87.0814-28.7144
31.9852-0.62760.71082.1125-1.27411.41210.11-0.24820.2494-0.04990.09120.1265-0.26-0.0479-0.20120.0178-0.0042-0.014-0.0306-0.0238-0.0882-68.9467-35.2005-22.5688
43.1937-0.3235-0.58812.34030.76171.95370.15040.04140.0528-0.0846-0.23080.07040.00920.14270.0803-0.1268-0.0909-0.0257-0.0865-0.0061-0.2747-48.8683-61.871-15.5945
50.453-5.668-6.242670.920778.110786.0295-1.57994.60786.42090.86975.18487.08830.59150.9651-3.60490.03730.0560.02720.03050.0243-0.0023-54.2916-81.5164-39.3781
63.2792-21.7126-5.7896170.059934.688710.7279-1.6508-5.6009-11.269-0.77255.3083-0.4851-8.8194-5.6297-3.6575-0.00220.00040.00370.00470.01480.006-78.1834-62.3065-36.3318
72.90451.0341-0.425512.2685-5.40742.38372.46290.5925-1.0149-0.7664-0.295-0.3332-2.22411.5693-2.16790.0553-0.0831-0.23670.03580.13320.108-41.3355-40.6018-9.8317
8372.6966394.8006-281.7197563.8183-531.7294586.7729-1.1173-9.86571.13223.2547-3.7313-0.6415-2.22430.81734.84860.0303-0.3161-0.04540.20580.0999-0.0197-56.6041-38.5245-11.4331
9539.729233.0591-218.6282249.6626-244.7094304.63370.12861.96545.2368-2.5508-1.2579-3.8205-0.45051.71551.1294-0.05450.01450.04510.0580.16170.1639-32.3238-58.8079-15.4784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AD31 - 11853 - 140
2X-RAY DIFFRACTION2BE31 - 11853 - 140
3X-RAY DIFFRACTION3AD119 - 354141 - 376
4X-RAY DIFFRACTION4BE119 - 354141 - 376
5X-RAY DIFFRACTION5JA1 - 21 - 2
6X-RAY DIFFRACTION6KB1 - 21 - 2
7X-RAY DIFFRACTION7MC1 - 51 - 5
8X-RAY DIFFRACTION8AF600
9X-RAY DIFFRACTION9BG601

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