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- PDB-3bsn: Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate an... -

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Basic information

Entry
Database: PDB / ID: 3bsn
TitleNorwalk Virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA
Components
  • RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')
  • RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*GP*(N5M))-3')
  • RNA dependent RNA polymerase
KeywordsTransferase/RNA / RNA-dependent RNA polymerase / viral replication / antiviral enzyme inhibitor / Helicase / Hydrolase / Nucleotide-binding / Nucleotidyltransferase / RNA replication / RNA-directed RNA polymerase / Transferase / Transferase-RNA COMPLEX
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / host cell / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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
: / 5-nitrocytidine 5'-(tetrahydrogen triphosphate) / RNA / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZamyatkin, D.F. / Ng, K.K.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural insights into mechanisms of catalysis and inhibition in norwalk virus polymerase.
Authors: Zamyatkin, D.F. / Parra, F. / Alonso, J.M. / Harki, D.A. / Peterson, B.R. / Grochulski, P. / Ng, K.K.
History
DepositionDec 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_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 / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA dependent RNA 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*GP*(N5M))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,37011
Polymers62,3093
Non-polymers1,0618
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.310, 93.850, 96.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA dependent RNA polymerase


Mass: 56843.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Genus: Norovirus / Strain: Ast6139/01/Sp / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q70ET3, RNA-directed RNA polymerase

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RNA chain , 2 types, 2 molecules PT

#2: RNA chain RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3')


Mass: 2557.577 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: chemically synthesized self-complementary RNA oligonucleotide with 2-base overhang
#3: RNA chain RNA (5'-R(*UP*GP*CP*CP*CP*GP*GP*GP*(N5M))-3')


Mass: 2907.756 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: chemically synthesized self-complementary RNA oligonucleotide that was extended by a single 5-nitrocytidine monophosphate residue during crystallization

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Non-polymers , 4 types, 355 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-N5C / 5-nitrocytidine 5'-(tetrahydrogen triphosphate)


Mass: 528.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N4O16P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% (w/v) PEG 8000, 25% (w/v) glycerol, 100 mM Tris-HCl, 50 mM KCl, 4 mM MgCl2, 10 mM MnCl2, 14 mM 2-mercaptoethanol, 0.1% (w/v) CHAPS, 0.5 mM RNA duplex, 1 mM NTP, 0.03 mM polymerase, pH 7. ...Details: 16% (w/v) PEG 8000, 25% (w/v) glycerol, 100 mM Tris-HCl, 50 mM KCl, 4 mM MgCl2, 10 mM MnCl2, 14 mM 2-mercaptoethanol, 0.1% (w/v) CHAPS, 0.5 mM RNA duplex, 1 mM NTP, 0.03 mM polymerase, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2glycerol11
3Tris-HCl11
4KCl11
5MgCl211
6MnCl211
72-mercaptoethanol11
8CHAPS11
9NTP11
10PEG 800012
11glycerol12
12Tris-HCl12
13KCl12
14MgCl212
15MnCl212
162-mercaptoethanol12
17CHAPS12
18NTP12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2007
Details: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)
RadiationMonochromator: sagittally bent second crystal of double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 58959 / Num. obs: 58959 / % possible obs: 93.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 13.7
Reflection shellResolution: 1.8→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.3 / Num. unique all: 11566 / Rsym value: 0.614 / % possible all: 78.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SH0

1sh0


Resolution: 1.8→19.71 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.291 / SU ML: 0.1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23585 2989 5.1 %RANDOM
Rwork0.20069 ---
all0.20251 58959 --
obs0.20251 58754 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.254 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å20 Å20 Å2
2---0.86 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 361 59 347 4529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224326
X-RAY DIFFRACTIONr_angle_refined_deg12.0935925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8765477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59923.75160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97215669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.961524
X-RAY DIFFRACTIONr_chiral_restr0.0620.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023105
X-RAY DIFFRACTIONr_nbd_refined0.1760.21939
X-RAY DIFFRACTIONr_nbtor_refined0.2910.22912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2374
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.210
X-RAY DIFFRACTIONr_mcbond_it1.84522469
X-RAY DIFFRACTIONr_mcangle_it2.5762.53883
X-RAY DIFFRACTIONr_scbond_it3.5743.52252
X-RAY DIFFRACTIONr_scangle_it4.8844.52042
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 156 -
Rwork0.314 2791 -
obs-2947 100 %

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