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- PDB-5jji: Rho transcription termination factor bound to rU7 and 6 ADP-BeF3 ... -

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Basic information

Entry
Database: PDB / ID: 5jji
TitleRho transcription termination factor bound to rU7 and 6 ADP-BeF3 molecules
Components
  • Transcription termination factor Rho
  • rU12: 5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)- 3'
KeywordsTRANSCRIPTION/RNA / protein-RNA complex / TRANSCRIPTION-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 / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA / RNA (> 10) / Transcription termination factor Rho / Transcription termination factor Rho
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.601 Å
AuthorsThomsen, N.D. / Lawson, M.R. / Witkowsky, L.B. / Qu, S. / Berger, J.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071747 United States
G. Harold and Leila Y. Mathers Foundation United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.
Authors: Thomsen, N.D. / Lawson, M.R. / Witkowsky, L.B. / Qu, S. / Berger, J.M.
History
DepositionApr 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription termination factor Rho
B: Transcription termination factor Rho
C: Transcription termination factor Rho
D: Transcription termination factor Rho
E: Transcription termination factor Rho
F: Transcription termination factor Rho
G: rU12: 5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)- 3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,54926
Polymers291,3267
Non-polymers3,22319
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27910 Å2
ΔGint-128 kcal/mol
Surface area93100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.997, 198.567, 111.448
Angle α, β, γ (deg.)90.000, 104.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 7 molecules ABCDEFG

#1: Protein
Transcription termination factor Rho / ATP-dependent helicase Rho


Mass: 47949.500 Da / Num. of mol.: 6 / Fragment: rho / Mutation: N-terminal MGH insertion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: rho, Z5293, ECs4716 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P0AG32, UniProt: P0AG30*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: RNA chain rU12: 5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)- 3'


Mass: 3629.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 271 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5 / Details: 200 mM KOAc, 40% MPD, 0.5% ethyl acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.601→47.425 Å / Num. obs: 88380 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14
Reflection shellResolution: 2.601→2.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.8 / % possible all: 99.1

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Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.63 / FOM acentric: 0.63 / FOM centric: 0.66 / Reflection: 88394 / Reflection acentric: 86734 / Reflection centric: 1660
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-47.4250.950.950.938083618190
4.6-7.40.90.910.781175311452301
3.7-4.60.890.90.831489214591301
3.3-3.70.780.780.741499114729262
2.8-3.30.490.490.522667026285385
2.6-2.80.190.190.241628016059221

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.1.4phasing
RESOLVE2.14phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.601→47.425 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 4429 5.01 %Random
Rwork0.2188 ---
obs0.2202 88380 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.2 Å2 / Biso mean: 67.3841 Å2 / Biso min: 17.78 Å2
Refinement stepCycle: final / Resolution: 2.601→47.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19164 141 200 252 19757
Biso mean--52.58 45.35 -
Num. residues----2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619838
X-RAY DIFFRACTIONf_angle_d0.57526740
X-RAY DIFFRACTIONf_chiral_restr0.043057
X-RAY DIFFRACTIONf_plane_restr0.0043416
X-RAY DIFFRACTIONf_dihedral_angle_d18.74112200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.601-2.63010.37961520.3472523267590
2.6301-2.66110.42751300.342628392969100
2.6611-2.69350.35761370.326127942931100
2.6935-2.72760.3531460.30827792925100
2.7276-2.76350.33341640.307128503014100
2.7635-2.80130.29251360.293827782914100
2.8013-2.84140.32721490.280328142963100
2.8414-2.88380.26481630.27927962959100
2.8838-2.92880.32951370.27727852922100
2.9288-2.97680.26671450.283828172962100
2.9768-3.02810.31681510.278127972948100
3.0281-3.08320.30731460.269428152961100
3.0832-3.14250.29961460.270528522998100
3.1425-3.20660.29791470.26627702917100
3.2066-3.27630.27751520.241128462998100
3.2763-3.35250.28991480.245527852933100
3.3525-3.43630.26061520.229428122964100
3.4363-3.52920.23781470.220427742921100
3.5292-3.6330.27771580.215428202978100
3.633-3.75030.22111450.20927982943100
3.7503-3.88420.22971510.198828112962100
3.8842-4.03970.2051460.183528312977100
4.0397-4.22340.21681450.174227882933100
4.2234-4.44590.17521640.173328012965100
4.4459-4.72420.22741330.164828172950100
4.7242-5.08860.20831550.16842810296599
5.0886-5.60.22591460.2022815296199
5.6-6.40860.22771420.21772820296299
6.4086-8.06770.20871510.20532805295699
8.0677-47.43290.18641450.16832809295498
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)
10.0059-0.0221-0.03180.11840.03750.04020.2111.1407-0.3282-1.2559-0.0456-0.111-0.01310.22750.00091.213-0.0341-0.03431.35820.09621.255844.419318.6362-19.6618
20.19990.1484-0.08380.2509-0.22080.3550.06980.28510.7292-0.5673-0.0044-0.5985-0.22860.2073-0.00010.67-0.0654-0.09210.53680.20431.133746.56920.843-1.0613
30.98840.0413-0.3151.63760.40760.8155-0.22570.08840.65480.04660.01940.1617-0.3345-0.1771-0.0060.55550.0438-0.08410.31990.02350.675317.332110.71729.9446
40.3486-0.0580.03530.02440.01490.0743-0.1599-0.099-1.111-0.101-0.1723-0.01241.2154-0.28290.00271.22820.3001-0.07141.7403-0.58121.278744.3358-43.2641-19.6297
50.45120.1903-0.02480.2398-0.27961.07920.24751.004-0.0643-0.5145-0.2845-0.18720.41990.47220.2565-0.00630.41380.7731.2883-0.1702-0.455645.4385-24.3246-14.294
61.7233-0.01290.1121.4408-0.33911.15470.09840.43320.1007-0.1401-0.06660.16-0.0082-0.07710.00020.29420.0261-0.0030.3105-0.03130.203716.186-18.9189-0.1086
70.1058-0.07280.02840.14230.09740.30470.0462-0.5829-0.80190.3978-0.485-0.34940.46290.5306-0.00510.82130.03330.02130.65970.3031.234143.0875-68.167333.1494
80.45060.3108-0.3210.3413-0.09960.37090.17580.0884-0.9981-0.2307-0.2772-0.34470.66890.5738-0.02460.55480.1742-0.09970.469-0.09310.932443.7713-58.645918.6205
91.3733-0.15270.12621.01290.09662.16810.1814-0.0162-0.54990.01980.03870.22760.2567-0.22080.0210.3153-0.0537-0.03390.17270.03940.356314.6476-42.634520.6712
100.00470.01670.0130.04150.04210.04780.1699-0.67080.00821.23340.14980.09350.24850.22540.00011.24840.2168-0.02791.6103-0.05780.795143.1388-40.360280.9514
110.65420.1727-0.04040.53760.13910.36850.0843-0.5387-0.73410.43370.2874-0.53720.29290.6530.01180.56610.1432-0.0591.01360.02570.650842.6083-46.266661.7443
121.0350.04950.2771.79890.25571.7510.0342-0.8023-0.22240.19110.16120.28180.1398-0.52360.04430.389-0.07210.08330.70.18440.318113.4286-36.449651.6358
130.0182-0.00620.0190.0076-0.00660.01350.3346-0.28450.50850.64630.1011-0.2098-0.62550.26010.00021.1198-0.2879-0.06011.4623-0.26621.683241.915917.076878.8959
140.08210.03460.0420.34810.1540.06070.0763-0.92230.4460.2488-0.3791-1.05330.03610.5147-0.00140.824-0.0444-0.10311.6764-0.04981.013341.0603-4.566474.2421
150.3049-0.00110.07682.8052-0.50230.9733-0.1272-0.82690.4617-0.02560.07950.6328-0.2589-0.4637-0.0390.56230.11490.03491.1814-0.25330.615712.3042-6.583362.3337
160.00720.03130.00150.0383-0.0290.0169-0.25090.45070.1614-0.48340.0469-0.2907-0.21660.2225-01.5745-0.2599-0.33511.7578-0.00481.408744.631243.857129.6853
170.09050.135-0.05950.1571-0.09940.0487-0.0229-0.54990.20380.0762-0.3281-0.48610.02510.4051-0.00011.3453-0.1025-0.23821.1686-0.2111.434742.696730.84946.9522
180.78620.6895-0.39481.2713-1.03122.1384-0.1347-0.14750.44330.0386-0.03260.1183-0.0808-0.1851-0.00890.93320.137-0.16760.6538-0.36860.977614.547417.634640.645
19-0.00170.0089-0.0040.8514-0.59830.4285-0.13150.01410.273-0.27720.32480.3697-0.799-0.49750.04390.49070.00150.06020.3739-0.01560.297225.9836-13.332330.5228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:54 )A1 - 54
2X-RAY DIFFRACTION2( CHAIN A AND RESID 55:130 )A55 - 130
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 131:414 OR RESID 415:416 ) )A131 - 414
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 131:414 OR RESID 415:416 ) )A415 - 416
5X-RAY DIFFRACTION4( CHAIN B AND RESID 1:52 )B1 - 52
6X-RAY DIFFRACTION5( CHAIN B AND RESID 53:129 )B53 - 129
7X-RAY DIFFRACTION6( CHAIN B AND ( RESID 130:417 OR RESID 501:503 ) )B130 - 417
8X-RAY DIFFRACTION6( CHAIN B AND ( RESID 130:417 OR RESID 501:503 ) )B501 - 503
9X-RAY DIFFRACTION7( CHAIN C AND RESID 1:61 )C1 - 61
10X-RAY DIFFRACTION8( CHAIN C AND RESID 62:130 )C62 - 130
11X-RAY DIFFRACTION9( CHAIN C AND ( RESID 131:417 OR RESID 1000:1002 ) )C131 - 417
12X-RAY DIFFRACTION9( CHAIN C AND ( RESID 131:417 OR RESID 1000:1002 ) )C1000 - 1002
13X-RAY DIFFRACTION10( CHAIN D AND RESID 1:54 )D1 - 54
14X-RAY DIFFRACTION11( CHAIN D AND RESID 55:132 )D55 - 132
15X-RAY DIFFRACTION12( CHAIN D AND ( RESID 133:414 OR RESID 415:416 ) )D133 - 414
16X-RAY DIFFRACTION12( CHAIN D AND ( RESID 133:414 OR RESID 415:416 ) )D415 - 416
17X-RAY DIFFRACTION13( CHAIN E AND RESID 2:54 )E2 - 54
18X-RAY DIFFRACTION14( CHAIN E AND RESID 55:136 )E55 - 136
19X-RAY DIFFRACTION15( CHAIN E AND ( RESID 137:414 OR RESID 415:416 ) )E137 - 414
20X-RAY DIFFRACTION15( CHAIN E AND ( RESID 137:414 OR RESID 415:416 ) )E415 - 416
21X-RAY DIFFRACTION16( CHAIN F AND RESID 1:54 )F1 - 54
22X-RAY DIFFRACTION17( CHAIN F AND RESID 55:135 )F55 - 135
23X-RAY DIFFRACTION18( CHAIN F AND ( RESID 136:414 OR RESID 415:416 ) )F136 - 414
24X-RAY DIFFRACTION18( CHAIN F AND ( RESID 136:414 OR RESID 415:416 ) )F415 - 416
25X-RAY DIFFRACTION19( CHAIN G AND RESID 1:7 )G1 - 7

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