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- PDB-3h5y: Norovirus polymerase+primer/template+CTP complex at 6 mM MnCl2 -

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Basic information

Entry
Database: PDB / ID: 3h5y
TitleNorovirus polymerase+primer/template+CTP complex at 6 mM MnCl2
Components
  • 5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'
  • 5'-R(P*UP*GP*CP*CP*CP*GP*GP*GP*C)-3'
  • RNA dependent RNA polymeraseRNA-dependent RNA polymerase
KeywordsTransferase/RNA / caliciviruses / viral RNA polymerase / Hydrolase / Nucleotide-binding / Nucleotidyltransferase / Protease / RNA replication / RNA-directed RNA polymerase / Thiol protease / Transferase / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / 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
CYTIDINE-5'-TRIPHOSPHATE / : / RNA / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.77 Å
AuthorsZamyatkin, D.F. / Parra, F. / Machin, A. / Grochulski, P. / Ng, K.K.S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Binding of 2'-amino-2'-deoxycytidine-5'-triphosphate to norovirus polymerase induces rearrangement of the active site.
Authors: Zamyatkin, D.F. / Parra, F. / Machin, A. / Grochulski, P. / Ng, K.K.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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.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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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: 5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'
T: 5'-R(P*UP*GP*CP*CP*CP*GP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,33512
Polymers62,2643
Non-polymers1,0719
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-67 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.200, 93.600, 96.300
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 / 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 / Gene: polymerase / 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 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 5'-R(P*UP*GP*CP*CP*CP*GP*GP*GP*C)-3'


Mass: 2862.759 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized self-complementary RNA oligonucleotide that was extended by a single cytidine-5'-monophosphate residue during crystallization

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Non-polymers , 4 types, 381 molecules

#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 160 g/L PEG 8000, 250 g/L glycerol, 100 mM Tris-Cl, 50 mM KCl, 4 mM MgCl2, 6 mM MnCl2, 14 mM mercaptoethanol, 1 g/L CHAPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Glycerol11
3Tris-HClTris11
4KCl11
5MgCl211
6MnCl211
72-mercaptoethanol11
8CHAPS11
9PEG 800012
10Glycerol12
11Tris-HClTris12
12KCl12
13MgCl212
14MnCl212
152-mercaptoethanol12
16CHAPS12

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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: Feb 25, 2008
Details: WHITE BEAM SLITS, DOUBLE CRYSTAL MONOCHROMATOR (DCM), VERTICALLY FOCUSING MIRROR (VFM)
RadiationMonochromator: CRYO-COOLED FIRST AND 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: 1.77→20 Å / Num. all: 65904 / Num. obs: 65904 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 23.1
Reflection shellResolution: 1.77→1.97 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 3.2 / Num. unique all: 17876 / Rsym value: 0.622 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0066refinement
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3BSO

3bso


Resolution: 1.77→19.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.616 / SU ML: 0.083 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 3296 5 %RANDOM
Rwork0.20443 ---
all0.20615 62607 --
obs0.20615 62607 100 %-
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: 34.253 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2---1.97 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.77→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 344 57 372 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224265
X-RAY DIFFRACTIONr_angle_refined_deg1.0912.0885840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9925471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55423.671158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94215661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7261524
X-RAY DIFFRACTIONr_chiral_restr0.0690.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213050
X-RAY DIFFRACTIONr_mcbond_it1.31622373
X-RAY DIFFRACTIONr_mcangle_it2.2232.53841
X-RAY DIFFRACTIONr_scbond_it2.9723.51892
X-RAY DIFFRACTIONr_scangle_it4.3754.51999
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 239 -
Rwork0.292 4541 -
obs-4541 100 %

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