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- PDB-3nah: Crystal structures and functional analysis of murine norovirus RN... -

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Basic information

Entry
Database: PDB / ID: 3nah
TitleCrystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase
ComponentsRNA dependent RNA polymeraseRNA-dependent RNA polymerase
KeywordsTRANSFERASE / RNA-dependent RNA polymerase / Murine norovirus
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / 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 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / 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 / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / ML / Resolution: 2.75 Å
AuthorsKim, K.H. / Lee, J.H. / Alam, I. / Park, Y. / Kang, S.
CitationJournal: To be Published
Title: Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase
Authors: Kim, K.H. / Lee, J.H. / Alam, I. / Park, Y. / Kang, S.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: RNA dependent RNA polymerase
B: RNA dependent RNA polymerase
C: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,8476
Polymers175,5593
Non-polymers2883
Water2,630146
1
A: RNA dependent RNA polymerase
B: RNA dependent RNA polymerase
C: RNA dependent RNA polymerase
hetero molecules

A: RNA dependent RNA polymerase
B: RNA dependent RNA polymerase
C: RNA dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,69412
Polymers351,1176
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area13120 Å2
ΔGint-57 kcal/mol
Surface area121700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.833, 196.543, 109.156
Angle α, β, γ (deg.)90.000, 114.210, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA dependent RNA polymerase / RNA-dependent RNA polymerase / RdRp


Mass: 58519.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q80J95
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.37 Å3/Da / Density % sol: 63.47 % / Mosaicity: 1.434 °
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 1M (NH4)2SO4, 100mM cacodylate (pH 6.5), VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.239 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.239 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 58979 / Num. obs: 55441 / % possible obs: 94 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.186 / Χ2: 0.982 / Net I/σ(I): 4.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.433 / Num. unique all: 4512 / Χ2: 0.769 / % possible all: 76.3

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Phasing

PhasingMethod: ML

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→44.06 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.737 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.352 / SU ML: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.303 2824 5.1 %RANDOM
Rwork0.221 ---
obs0.225 55441 92.25 %-
all-60098 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.35 Å2 / Biso mean: 23.286 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.75→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11549 0 15 146 11710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211846
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.97116053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79751453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5823.235544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.929152037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.87915106
X-RAY DIFFRACTIONr_chiral_restr0.0970.21705
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219079
X-RAY DIFFRACTIONr_mcbond_it0.4471.57274
X-RAY DIFFRACTIONr_mcangle_it0.862211730
X-RAY DIFFRACTIONr_scbond_it1.21834572
X-RAY DIFFRACTIONr_scangle_it2.0834.54323
LS refinement shellResolution: 2.751→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 113 -
Rwork0.271 2219 -
all-2332 -
obs--52.66 %

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