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- PDB-5jjl: Rho transcription termination factor bound to rU8 and 5 ADP-BeF3 ... -

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Basic information

Entry
Database: PDB / ID: 5jjl
TitleRho transcription termination factor bound to rU8 and 5 ADP-BeF3 molecules
Components
  • Transcription termination factor Rho
  • rU12: RNA (5'-R(P*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 / hydrolase activity / RNA binding / ATP binding / membrane / identical protein binding / 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 / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.5Sep 27, 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 / 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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,91422
Polymers291,3267
Non-polymers2,58815
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26370 Å2
ΔGint-98 kcal/mol
Surface area92450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.091, 199.071, 111.666
Angle α, β, γ (deg.)90.000, 105.022, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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 / 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: RNA (5'-R(P*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 , 4 types, 31 molecules

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


Mass: 427.201 Da / Num. of mol.: 5 / 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.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: BeF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
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: May 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 3.2→49.52 Å / Num. obs: 46060 / % possible obs: 96.12 % / Biso Wilson estimate: 63.31 Å2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JJI

5jji


Resolution: 3.2→49.52 Å / SU ML: 0.410615569722 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.7612787883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 2310 5.01519756839 %
Rwork0.232 43750 -
obs0.234 46060 96.1205367391 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.3330848993 Å2
Refinement stepCycle: LAST / Resolution: 3.2→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18888 165 160 16 19229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062515017640219504
X-RAY DIFFRACTIONf_angle_d0.57346508041626316
X-RAY DIFFRACTIONf_chiral_restr0.03976390524553028
X-RAY DIFFRACTIONf_plane_restr0.003098246677023363
X-RAY DIFFRACTIONf_dihedral_angle_d23.96311032647533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.201-3.27060.3520257643241480.3269906712332731X-RAY DIFFRACTION95.5526053767
3.2706-3.34670.315374535721460.3044658948492695X-RAY DIFFRACTION96.9955616251
3.3467-3.43030.3229702701371470.2914386167452736X-RAY DIFFRACTION96.1
3.4303-3.52310.2806896377081400.2687840767022726X-RAY DIFFRACTION96.4658364187
3.5231-3.62670.3084591280131530.2650031985062751X-RAY DIFFRACTION95.9682749504
3.6267-3.74370.2987850911821360.2623419510752731X-RAY DIFFRACTION96.2726662189
3.7437-3.87750.3150374458381540.2496110848962729X-RAY DIFFRACTION96.7774420947
3.8775-4.03260.2826042385031370.2449265654182758X-RAY DIFFRACTION96.8551354968
4.0326-4.21610.3005418279581400.2213758308222731X-RAY DIFFRACTION96.6992253284
4.2161-4.43820.2154281062071570.2119639725422743X-RAY DIFFRACTION96.6988996332
4.4382-4.71610.266704983281370.2001489530142763X-RAY DIFFRACTION97.0548862115
4.7161-5.07990.2281211140441480.199378844032750X-RAY DIFFRACTION96.4392678869
5.0799-5.59050.2686693112471440.2249179187562735X-RAY DIFFRACTION96.1268781302
5.5905-6.3980.2444626533741400.2366277442752746X-RAY DIFFRACTION95.373430271
6.398-8.05520.2382995476361440.228333633632674X-RAY DIFFRACTION94.1215764863
8.0552-49.52490.2208443947031390.1874504646852751X-RAY DIFFRACTION94.660989191
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)
10.0149209205424-0.0144257376644-0.01647351501980.01163542390730.01365658738730.01762993443440.08386449266090.339690942838-0.352273272668-0.316227084232-0.05646535469660.3052511176-0.0186437435846-0.1446493564713.11050801788E-71.1988247324-0.10426038727-0.0002789072245291.185140802870.03428758586961.3025821746144.611500012817.1756330619-20.6816066986
20.02615910917250.0108769063516-0.0164813177650.0103792113823-0.002434596107480.0120244189496-0.0673747676190.208539306364-0.945977626003-0.400136687016-0.0622917859255-0.1437611717350.8213999957940.0252298132446-4.9911655972E-71.274203756640.09635223267450.1511264354041.50057796398-0.291122729631.0271093235644.6710399051-44.4574502425-19.4303201714
30.22915173526-0.01644759018940.1217508717950.04148208476280.005043000058670.07711459044630.0888970491072-0.636221424287-0.6616073994060.574337696833-0.413675975634-0.2809811662440.4244735978560.146038635181-0.003772992880971.113239284790.0837870199279-0.1953395743410.8444591469450.375107499921.4893664755842.345561037-71.398698072135.3884897329
40.0556477854567-0.0002199269764830.007711188966410.1194458053240.02588723815140.0680174668441-0.0972582310975-0.162785448273-0.03517996223640.6774400835370.1802544196060.291225000253-0.144433634862-0.03067947328695.66881495723E-80.944786384350.222789453730.003861546761.12339652744-0.04464449015480.55114292624842.7661252773-39.189064525381.8481124703
50.04721830705660.03417010881380.02451403232420.04122787591570.006278411698630.0345972031158-0.09570449219390.52017056859-0.0717524808704-0.2620860371420.1336903394650.263017495570.3000199677910.02327237670924.37545477692E-71.07028369366-0.295023490013-0.2475908374471.60499035504-0.01354682950551.3171587217745.264117772444.323885447527.985370074
60.03794074916950.05050834816880.125216082160.07501034952710.1798783445630.446077470878-0.1314361292470.1533324338160.45780718618-0.7560048041070.129150435459-0.774914090673-0.1575669715170.3226636009850.1194921388150.61748076032-0.07781493320930.04103153161090.2614900740360.2559377587191.083153732346.314469515221.122633223-2.165510819
70.6695896981610.2029750933760.2511040685320.0832607983522-0.03435719355831.286375548440.2421554459840.836939803983-0.0189722506279-0.308094220433-0.0870257442829-0.1489925984980.2087603937380.5655966054451.240388017870.4496392454540.2651148266520.2093104925840.989047133042-0.01317559724990.24791949615645.7428345691-25.0984049925-15.0139417766
80.9398526370060.539387392786-0.7800011914811.209292408820.2275229675861.182717643030.2911761024970.117990364555-1.05486730360.0371071786897-0.171321606453-0.473103548710.5935721757510.4112317669570.07896664837080.4984649280760.281097272506-0.2469345189040.245407987507-0.1026085990211.1117364402944.270553392-58.514365175918.7141270596
91.33932774360.03850198718850.1661081932260.4513186961270.03299904159490.399016946793-0.0525300508999-0.0429793149525-0.6468201380430.2376277903050.118832350582-0.1462448693630.07878703688010.6747192131610.0002716565201720.5827606081280.080940795427-0.06372790945780.9170033889660.1589021209690.40416550907442.6433022528-45.781609517762.7578158302
100.1332505397270.07726410758090.01836846281850.07265592759460.009579184445930.00100382509762-0.246701346507-0.5684409407920.2235245329320.399442147148-0.24795288887-0.683065973116-0.2366249524350.185567567959-0.001932192090671.149633380520.0647931258297-0.2969790248341.32180088094-0.2376289376370.84449735769840.4447052153-2.8017810116274.8147480786
110.1163719192750.08745401952670.01635854523510.270188922929-0.145265572610.120958410367-0.0235377851031-0.505268742039-0.01583531391370.328025432481-0.251057291482-0.07257501395880.337452861636-0.02613747126334.73547196638E-81.098709618470.050178172165-0.2509442722560.87589285976-0.308431260341.0107518227944.021327216432.03365335344.8890289185
120.6215924219990.378522853561-0.01918359746521.93697456970.3878074859540.769896066802-0.1456012337670.1621867529960.5486073535510.133824117863-0.08955021340510.448884831906-0.33633628574-0.0949506903211-0.1146856615840.4509016527630.117208021442-0.007533426731090.01938211196260.08149005070460.95260258612717.728913225510.79788844239.80221259285
131.68074997729-0.0184626027641-0.2110413905841.37869652483-0.2319712469551.831312167020.1003114760510.5015772085250.108007499549-0.14540800079-0.03554669531670.198681559709-0.0217524946606-0.1224299452940.007632884824650.2960707294220.0660994426647-0.02437492330570.2932803954740.02561590993340.18936179581216.5408404142-18.8410149099-0.567418413927
141.23335420106-0.2481067056060.3972144111.233042813150.1407223076752.216813980710.195341193146-0.121562268044-0.6257345586950.08287389011380.008681968906520.2015638086120.148735386817-0.2342400975880.06297369733720.273142056355-0.0440190250826-0.08065784702010.06873661452250.06730895307450.37451463012515.0134057857-42.96858118919.8033140085
151.124420547560.0605731115730.4580748826611.000682598210.1199698332421.655856378870.10673170877-1.07151956381-0.3184775250850.531071148480.3315160972510.341708409984-0.0230458002387-0.7580561524030.2229475914710.2842303629-0.03862566922460.2722496285180.8014438574260.4325705348080.07653150195313.4200091656-37.461256173150.8754499141
161.690819633090.866455912839-0.5382552896161.32789855332-0.3799376432651.28350214638-0.332491873376-0.9983779512580.5436222044020.4516178608780.2564446419220.495169623689-0.657856703814-0.854115879402-0.1990766844090.8372154777270.5568751400750.1375740174561.3739960844-0.2539236722290.3505777611513.6954926108-7.9479535149461.7898709986
170.8484294688910.6041872552890.2502653925350.996879985153-0.6501264485072.1280723996-0.223353184598-0.3750429548270.08373226802480.2441495408040.02754229012120.102281779403-0.203196053185-0.388539285667-6.14563140335E-50.9846300625930.109322599532-0.04691802866750.613020811724-0.2872212696081.0515277337915.34027836317.838912815740.9569447355
180.156067003533-0.0403305043727-0.0992289059080.362084720201-0.09546534762150.189756808061-0.662040936235-0.1601239837821.00016110898-0.555998881160.1308168679510.367413789086-0.8514700076050.287620469244-0.001919513915870.9348088523880.00293366763132-0.02806603808150.619988795124-0.03388507501060.46907119854926.5894998516-13.131719611830.2988789502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 1:47
2X-RAY DIFFRACTION2chain B and resseq 1:47
3X-RAY DIFFRACTION3chain C and resseq 1:47
4X-RAY DIFFRACTION4chain D and resseq 1:47
5X-RAY DIFFRACTION5chain F and resseq 1:47
6X-RAY DIFFRACTION6chain A and resseq 48:124
7X-RAY DIFFRACTION7chain B and resseq 48:128
8X-RAY DIFFRACTION8chain C and resseq 48:128
9X-RAY DIFFRACTION9chain D and resseq 48:128
10X-RAY DIFFRACTION10chain E and resseq 49:128
11X-RAY DIFFRACTION11chain F and resseq 49:128
12X-RAY DIFFRACTION12chain A and resseq 130:416
13X-RAY DIFFRACTION13chain B and resseq 129:417
14X-RAY DIFFRACTION14chain C and resseq 129:417
15X-RAY DIFFRACTION15chain D and resseq 129:416
16X-RAY DIFFRACTION16chain E and resseq 129:405
17X-RAY DIFFRACTION17chain F and resseq 129:416
18X-RAY DIFFRACTION18chain G and resseq 1:9

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