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- PDB-3mmp: Structure of the Qb replicase, an RNA-dependent RNA polymerase co... -

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Basic information

Entry
Database: PDB / ID: 3mmp
TitleStructure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins
Components
  • Elongation factor Tu 2, Elongation factor Ts
  • RNA-directed RNA polymerase beta chain
KeywordsTRANSFERASE / RdRp / host-factor complex / translation
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / guanyl-nucleotide exchange factor activity / RNA-directed RNA polymerase / response to antibiotic / viral RNA genome replication / nucleotide binding ...guanyl-nucleotide exchange factor complex / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / guanyl-nucleotide exchange factor activity / RNA-directed RNA polymerase / response to antibiotic / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / GTPase activity / GTP binding / RNA binding / zinc ion binding / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RNA-directed RNA polymerase beta-chain / RNA replicase, beta-chain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / RNA-directed RNA polymerase, bacteriophage, catalytic domain ...RNA-directed RNA polymerase beta-chain / RNA replicase, beta-chain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Ubiquitin-associated (UBA) domain / Translation elongation factor EFTu/EF1A, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / UBA-like superfamily / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Helicase, Ruva Protein; domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / DNA/RNA polymerase superfamily / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-PXN / Elongation factor Ts / Elongation factor Tu 2 / RNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage Qbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKidmose, R.T. / Vasiliev, N.N. / Chetverin, A.B. / Knudsen, C.R. / Andersen, G.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure of the Qbeta replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins.
Authors: Kidmose, R.T. / Vasiliev, N.N. / Chetverin, A.B. / Andersen, G.R. / Knudsen, C.R.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 6, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
A: Elongation factor Tu 2, Elongation factor Ts
G: RNA-directed RNA polymerase beta chain
C: Elongation factor Tu 2, Elongation factor Ts
F: RNA-directed RNA polymerase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,8376
Polymers279,1004
Non-polymers7372
Water16,664925
1
A: Elongation factor Tu 2, Elongation factor Ts
G: RNA-directed RNA polymerase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,9183
Polymers139,5502
Non-polymers3681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-39 kcal/mol
Surface area51620 Å2
MethodPISA
2
C: Elongation factor Tu 2, Elongation factor Ts
F: RNA-directed RNA polymerase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,9183
Polymers139,5502
Non-polymers3681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-40 kcal/mol
Surface area51420 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13880 Å2
ΔGint-90 kcal/mol
Surface area100910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.710, 139.400, 101.870
Angle α, β, γ (deg.)90.00, 92.06, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21F
12A
22C
13A
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERPROPROCHAIN G AND (RESSEQ 7:113 OR RESSEQ 119:519 OR RESSEQ 533:573 )GB7 - 1137 - 113
121PHEPHESERSERCHAIN G AND (RESSEQ 7:113 OR RESSEQ 119:519 OR RESSEQ 533:573 )GB119 - 519119 - 519
131CYSCYSALAALACHAIN G AND (RESSEQ 7:113 OR RESSEQ 119:519 OR RESSEQ 533:573 )GB533 - 573533 - 573
211SERSERPROPROCHAIN F AND (RESSEQ 7:113 OR RESSEQ 119:519 OR RESSEQ 533:573 )FD7 - 1137 - 113
221PHEPHESERSERCHAIN F AND (RESSEQ 7:113 OR RESSEQ 119:519 OR RESSEQ 533:573 )FD119 - 519119 - 519
231CYSCYSALAALACHAIN F AND (RESSEQ 7:113 OR RESSEQ 119:519 OR RESSEQ 533:573 )FD533 - 573533 - 573
112LYSLYSGLYGLYCHAIN A AND (RESSEQ 1009:1041 OR RESSEQ 1064:1392 )AA1009 - 1041294 - 326
122THRTHRLEULEUCHAIN A AND (RESSEQ 1009:1041 OR RESSEQ 1064:1392 )AA1064 - 1392349 - 677
212LYSLYSGLYGLYCHAIN C AND (RESSEQ 1009:1041 OR RESSEQ 1064:1392 )CC1009 - 1041294 - 326
222THRTHRLEULEUCHAIN C AND (RESSEQ 1009:1041 OR RESSEQ 1064:1392 )CC1064 - 1392349 - 677
113ILEILESERSERCHAIN A AND (RESSEQ 3:282 )AA3 - 2824 - 283
213ILEILESERSERCHAIN C AND (RESSEQ 3:282 )CC3 - 2824 - 283

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Elongation factor Tu 2, Elongation factor Ts / EF-Tu 2 / P-43 / EF-Ts


Mass: 73954.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tufB, b3980, JW3943, tsf, b0170, JW0165 / Plasmid: pBAD33 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6P1, UniProt: P0CE48
#2: Protein RNA-directed RNA polymerase beta chain / RNA replicase beta chain


Mass: 65595.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Qbeta (virus) / Plasmid: pBAD33 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14647, RNA-directed RNA polymerase
#3: Chemical ChemComp-PXN / (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol / PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)


Mass: 368.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H36O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAINS A AND C ARE A CHIMERA OF UNP ENTRIES P0A6P1 AND P0CE48 WITH A SINGLE HIS AS LINKER

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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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M KCL, 0.05M Hepes pH 7.5, 27%-30% v/v pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 122568 / Num. obs: 122568 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.112 / Rsym value: 0.069 / Net I/σ(I): 18.29
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.87 / Rsym value: 0.571 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EFU

1efu


Resolution: 2.5→47.283 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 1993 1.63 %
Rwork0.21 --
obs0.2103 122547 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.625 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.95 Å2-0 Å2-0.2204 Å2
2---5.9852 Å2-0 Å2
3----5.9648 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18444 0 50 925 19419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818828
X-RAY DIFFRACTIONf_angle_d1.05325452
X-RAY DIFFRACTIONf_dihedral_angle_d16.7096978
X-RAY DIFFRACTIONf_chiral_restr0.0752888
X-RAY DIFFRACTIONf_plane_restr0.0043298
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11G4318X-RAY DIFFRACTIONPOSITIONAL0.04
12F4318X-RAY DIFFRACTIONPOSITIONAL0.04
21A2790X-RAY DIFFRACTIONPOSITIONAL0.054
22C2790X-RAY DIFFRACTIONPOSITIONAL0.054
31A2108X-RAY DIFFRACTIONPOSITIONAL0.023
32C2108X-RAY DIFFRACTIONPOSITIONAL0.023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.33531410.27298530X-RAY DIFFRACTION100
2.5625-2.63180.29431450.26618601X-RAY DIFFRACTION100
2.6318-2.70920.29761490.25578540X-RAY DIFFRACTION100
2.7092-2.79670.3211430.25948639X-RAY DIFFRACTION100
2.7967-2.89660.29461390.25158588X-RAY DIFFRACTION100
2.8966-3.01260.27571400.24878598X-RAY DIFFRACTION100
3.0126-3.14970.27521360.23558592X-RAY DIFFRACTION100
3.1497-3.31570.21981490.23378611X-RAY DIFFRACTION100
3.3157-3.52330.231420.21478630X-RAY DIFFRACTION100
3.5233-3.79530.23351350.20228591X-RAY DIFFRACTION100
3.7953-4.1770.20491280.18888641X-RAY DIFFRACTION100
4.177-4.78090.1781480.16638632X-RAY DIFFRACTION100
4.7809-6.02150.20491470.17548677X-RAY DIFFRACTION100
6.0215-47.29170.18191510.17178684X-RAY DIFFRACTION99

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