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- PDB-5tsn: Crystal structures of Norwalk virus polymerase bound to an RNA pr... -

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Basic information

Entry
Database: PDB / ID: 5tsn
TitleCrystal structures of Norwalk virus polymerase bound to an RNA primer-template duplex
Components
  • Norwalk virus polymerase
  • RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')
KeywordsTRANSFERASE/RNA / Norwalk virus / RNA dependent RNA polymerase / RNA primer-template complex / TRANSFERASE-RNA complex
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helix non-globular / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helix non-globular / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShaik, M.M. / Ng, K.K.
CitationJournal: Proteins / Year: 2017
Title: Norovirus RNA-dependent RNA polymerase: A computational study of metal-binding preferences.
Authors: Shaik, M.M. / Bhattacharjee, N. / Feliks, M. / Ng, K.K. / Field, M.J.
History
DepositionOct 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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: Norwalk virus polymerase
P: RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')
T: RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0375
Polymers61,9273
Non-polymers1102
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-45 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.760, 81.760, 189.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Norwalk virus polymerase


Mass: 56843.574 Da / Num. of mol.: 1 / Fragment: UNP residues 331-838
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q70ET3
#2: RNA chain RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')


Mass: 2541.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer RNA / Source: (synth.) Norwalk virus
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG8000, 25% glycerol, 100 mM Tris-HCl, pH 7.0, 50 mM potassium chloride, 10 mM manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→61.83 Å / Num. obs: 38050 / % possible obs: 99.4 % / Redundancy: 11.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 12 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 4.3 / CC1/2: 0.911 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BSO

3bso


Resolution: 2.1→49.908 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 1899 5 %
Rwork0.1742 --
obs0.1765 37950 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 316 2 275 4514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064388
X-RAY DIFFRACTIONf_angle_d0.8636022
X-RAY DIFFRACTIONf_dihedral_angle_d11.3012619
X-RAY DIFFRACTIONf_chiral_restr0.048666
X-RAY DIFFRACTIONf_plane_restr0.006722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.27881320.20942531X-RAY DIFFRACTION100
2.1525-2.21070.2891210.20632547X-RAY DIFFRACTION100
2.2107-2.27580.24471420.20982514X-RAY DIFFRACTION99
2.2758-2.34920.27041240.18852558X-RAY DIFFRACTION100
2.3492-2.43320.26511400.19632536X-RAY DIFFRACTION100
2.4332-2.53060.24761200.19682521X-RAY DIFFRACTION98
2.5306-2.64580.24221370.20062557X-RAY DIFFRACTION99
2.6458-2.78530.28141270.19662543X-RAY DIFFRACTION99
2.7853-2.95970.2431400.19692575X-RAY DIFFRACTION100
2.9597-3.18820.2211400.19472549X-RAY DIFFRACTION99
3.1882-3.5090.24131350.17572583X-RAY DIFFRACTION99
3.509-4.01660.21061600.1512604X-RAY DIFFRACTION100
4.0166-5.05970.1571490.13452624X-RAY DIFFRACTION98
5.0597-49.92260.191320.16472809X-RAY DIFFRACTION98
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)
10.35650.25630.70361.26020.47552.06980.1775-0.1185-0.1579-0.1027-0.11310.48470.1769-0.5819-0.06270.2425-0.0259-0.10280.31840.0190.3577-29.28820.54741.5582
20.2677-0.0810.0432.3139-0.70591.15240.1004-0.0209-0.0683-0.3193-0.1048-0.0870.20330.15150.02160.23930.0677-0.04490.2435-0.00720.1984-8.398124.0487-7.0786
30.23120.54160.22613.4975-0.78710.89340.06550.03540.025-0.2770.06240.63120.1177-0.1195-0.15540.28590.0376-0.04760.21850.02530.2723-18.434435.2754-14.7827
40.7641.0369-0.09012.0159-1.31222.1508-0.0097-0.1841-0.10610.08790.03290.0916-0.1352-0.2737-0.0230.22160.05890.06330.32290.0480.264-19.273341.511414.6558
55.20950.7942-1.81525.5421-1.25116.92440.0658-0.6971-0.00960.5182-0.1554-0.0801-0.09090.27860.05270.24880.0009-0.02270.32710.01820.2173-6.992751.202215.2534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 280 )
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 400 )
4X-RAY DIFFRACTION4chain 'A' and (resid 401 through 466 )
5X-RAY DIFFRACTION5chain 'A' and (resid 467 through 505 )

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