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- PDB-2r7x: Crystal Structure of Rotavirus SA11 VP1/RNA (UGUGACC)/GTP complex -

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Basic information

Entry
Database: PDB / ID: 2r7x
TitleCrystal Structure of Rotavirus SA11 VP1/RNA (UGUGACC)/GTP complex
Components
  • RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3')
  • RNA-dependent RNA polymerase
Keywordstransferase/RNA / Viral protein / RNA-dependent RNA polymerase / single subunit polymerase fold / fingers / palm / thumb / right hand configuration / RNA-directed RNA polymerase / transferase-RNA COMPLEX
Function / homology
Function and homology information


viral genome replication / virion component / RNA-directed RNA polymerase / nucleotide binding / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding
Similarity search - Function
Viral RNA-directed RNA polymerase, 4-helical domain / Tetracycline Repressor; domain 2 - #80 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1390 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1400 / Ribosomal Protein S5; domain 2 - #140 / Alpha-Beta Plaits - #2480 / Rotavirus VP1 RNA-directed RNA polymerase, C-terminal / Viral RNA-directed RNA polymerase, 4-helical domain / Rotavirus VP1 C-terminal domain / RNA-directed RNA polymerase, luteovirus ...Viral RNA-directed RNA polymerase, 4-helical domain / Tetracycline Repressor; domain 2 - #80 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1390 / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1400 / Ribosomal Protein S5; domain 2 - #140 / Alpha-Beta Plaits - #2480 / Rotavirus VP1 RNA-directed RNA polymerase, C-terminal / Viral RNA-directed RNA polymerase, 4-helical domain / Rotavirus VP1 C-terminal domain / RNA-directed RNA polymerase, luteovirus / Viral RNA-directed RNA-polymerase / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Tetracycline Repressor; domain 2 / Ribosomal Protein S5; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesSimian rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / molecular replacement / Resolution: 2.8 Å
AuthorsLu, X. / Harrison, S.C. / Tao, Y.J. / Patton, J.T. / Nibert, M.L.
CitationJournal: Structure / Year: 2008
Title: Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1.
Authors: Lu, X. / McDonald, S.M. / Tortorici, M.A. / Tao, Y.J. / Vasquez-Del Carpio, R. / Nibert, M.L. / Patton, J.T. / Harrison, S.C.
History
DepositionSep 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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
X: RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3')
Y: RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3')
A: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,0906
Polymers257,0444
Non-polymers1,0462
Water0
1
X: RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3')
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0453
Polymers128,5222
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-13.4 kcal/mol
Surface area44330 Å2
MethodPISA
2
Y: RNA (5'-R(*UP*GP*UP*GP*AP*CP*C)-3')
B: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0453
Polymers128,5222
Non-polymers5231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-13.5 kcal/mol
Surface area44370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.000, 143.766, 112.833
Angle α, β, γ (deg.)90.000, 90.650, 90.000
Int Tables number4
Space group name H-MP1211
Detailsthere are 2 biological units in the asymmetric unit

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Components

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


Mass: 2197.355 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein RNA-dependent RNA polymerase /


Mass: 126324.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus / Strain: SA11 / Gene: gene 1
Plasmid details: pCRBac-based transfer vector (invitrogen) is used to produce VP1 gene integrated ACNPV
Plasmid: pCRBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf21 / References: UniProt: O37061
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 microliter of VP1 at 10 mg/ml in 25 mM Na-HEPES, pH 7.8, 100 mM NaCl mixed with 2 microliter of crystallization buffer [25 mM Na-MES, pH 6.5, 1.5% (w/v) PEG 3350] and allowing the drop to ...Details: 1 microliter of VP1 at 10 mg/ml in 25 mM Na-HEPES, pH 7.8, 100 mM NaCl mixed with 2 microliter of crystallization buffer [25 mM Na-MES, pH 6.5, 1.5% (w/v) PEG 3350] and allowing the drop to equilibrate at 12 C by hanging-drop vapor diffusion with a well solution identical in composition to the drop except for the protein. With micro-seeding, thin, plate-like crystals appeared after 1 day and grew to full size in about two weeks., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Components of the solutions
IDNameCrystal-IDSol-ID
1Na-HEPES11
2NaClSodium chloride11
3Na-MES12
4PEG 335012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2006 / Details: Undulator A
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionRedundancy: 2.8 % / Av σ(I) over netI: 17.8 / Number: 137198 / Rmerge(I) obs: 0.051 / Χ2: 1 / D res high: 2.8 Å / D res low: 30 Å / Num. obs: 48859 / % possible obs: 81.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.02308310.0251.0092.9
4.786.028510.0370.992.8
4.184.7885.310.0350.9982.8
3.84.1887.210.0441.0012.9
3.533.885.510.0630.9932.8
3.323.538510.0890.9922.8
3.153.3285.410.1340.9932.9
3.023.1583.510.1951.0012.8
2.93.0276.910.27412.7
2.82.962.210.3390.9952.4
ReflectionResolution: 2.8→30 Å / Num. obs: 49581 / % possible obs: 81.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.051 / Χ2: 0.997 / Net I/σ(I): 17.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.92.40.33936990.99562.2
2.9-3.022.70.2744549176.9
3.02-3.152.80.19549861.00183.5
3.15-3.322.90.13450750.99385.4
3.32-3.532.80.08950410.99285
3.53-3.82.80.06351180.99385.5
3.8-4.182.90.04451831.00187.2
4.18-4.782.80.03550850.99885.3
4.78-6.022.80.03750880.9985
6.02-302.90.02550351.00983

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Phasing

Phasing
Method
MAD
molecular replacement
Phasing MRCor.coef. Fo:Fc: 0.41 / Packing: 0.307
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Rotation4 Å15 Åfast direct88.7 0
Translation4 Å15 Ågeneral88.7 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHARPphasing
DMphasing
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R7Q

2r7q


Resolution: 2.8→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3987 6.7 %RANDOM
Rwork0.233 ---
obs-49581 83.1 %-
Solvent computationBsol: 38.7 Å2
Displacement parametersBiso mean: 51.904 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17390 290 64 0 17744
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.1531.5
X-RAY DIFFRACTIONc_scbond_it3.6352
X-RAY DIFFRACTIONc_mcangle_it3.6732
X-RAY DIFFRACTIONc_scangle_it5.5942.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION4gtp.par

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