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- PDB-8u1w: Structure of Norovirus (Hu/GII.4/Sydney/NSW0514/2012/AU) protease... -

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Basic information

Entry
Database: PDB / ID: 8u1w
TitleStructure of Norovirus (Hu/GII.4/Sydney/NSW0514/2012/AU) protease bound to inhibitor NV-004
ComponentsPeptidase C37
KeywordsVIRAL PROTEIN/INHIBITOR / Protease / 3-chymotrypsin-like protease / 3CL-pro / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
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 / 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 / RNA-directed RNA polymerase, C-terminal domain ...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 / 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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide / ACETATE ION / Chem-FHR / Genome polyprotein
Similarity search - Component
Biological speciesNorovirus Hu/GII.4/Sydney/NSW0514/2012/AU
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsEruera, A.R. / Campbell, A.C. / Krause, K.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Ministry of Business, Innovation and Employment (New Zealand)UOOX1904 New Zealand
CitationJournal: Viruses / Year: 2023
Title: Crystal Structure of Inhibitor-Bound GII.4 Sydney 2012 Norovirus 3C-Like Protease.
Authors: Eruera, A.R. / McSweeney, A.M. / McKenzie-Goldsmith, G.M. / Opel-Reading, H.K. / Thomas, S.X. / Campbell, A.C. / Stubbing, L. / Siow, A. / Hubert, J.G. / Brimble, M.A. / Ward, V.K. / Krause, K.L.
History
DepositionSep 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase C37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4466
Polymers19,3301
Non-polymers1,1155
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.442, 53.415, 49.992
Angle α, β, γ (deg.)90.00, 102.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

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Components

#1: Protein Peptidase C37


Mass: 19330.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Production host: Escherichia coli (E. coli) / References: UniProt: K4L8Z7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FHR / ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 452.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H32N4O4 / Feature type: SUBJECT OF INVESTIGATION
References: ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% w/v PEG 3350, 8% Tacsimate pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95364 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 1.84→48.85 Å / Num. obs: 17894 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.029 / Rrim(I) all: 0.047 / Net I/σ(I): 14.2
Reflection shellResolution: 1.84→1.88 Å / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1050 / CC1/2: 0.85 / Rpim(I) all: 0.339 / Rrim(I) all: 0.546 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→48.85 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 895 5 %Random Selection
Rwork0.1654 ---
obs0.1667 17892 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 70 102 1368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061297
X-RAY DIFFRACTIONf_angle_d0.8951760
X-RAY DIFFRACTIONf_dihedral_angle_d15.703451
X-RAY DIFFRACTIONf_chiral_restr0.058197
X-RAY DIFFRACTIONf_plane_restr0.006221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.950.26361440.21122744X-RAY DIFFRACTION99
1.95-2.10.21021500.17072854X-RAY DIFFRACTION100
2.1-2.310.19181490.17172820X-RAY DIFFRACTION100
2.31-2.650.20661510.18362851X-RAY DIFFRACTION100
2.65-3.340.20131490.17632840X-RAY DIFFRACTION100
3.34-48.850.16851520.14652888X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.8064 Å / Origin y: -14.3441 Å / Origin z: 7.53 Å
111213212223313233
T0.1944 Å2-0.0039 Å20.0134 Å2-0.1851 Å2-0.0045 Å2--0.1991 Å2
L1.4273 °2-0.4585 °20.1369 °2-1.2945 °2-0.0903 °2--1.7235 °2
S0.005 Å °-0.067 Å °0.0412 Å °0.067 Å °0.048 Å °0.1637 Å °-0.0667 Å °-0.0457 Å °0 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 173)

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