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- PDB-9d9y: Human norovirus GI.1 Norwalk protease in complex with rupintrivir -

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Basic information

Entry
Database: PDB / ID: 9d9y
TitleHuman norovirus GI.1 Norwalk protease in complex with rupintrivir
Components3C-like protease
KeywordsVIRAL PROTEIN / Viral protease with inhibitor
Function / homology
Function and homology information


calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication ...calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / metal ion binding / membrane
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. / 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
Chem-AG7 / Genome polyprotein
Similarity search - Component
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhao, B. / Pham, S.H. / Neetu, N. / Sankaran, B. / Prasad, B.V.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI057788 United States
Robert A. Welch FoundationQ-1279 United States
CitationJournal: J.Virol. / Year: 2025
Title: Conformational flexibility is a critical factor in designing broad-spectrum human norovirus protease inhibitors.
Authors: Pham, S. / Zhao, B. / Neetu, N. / Sankaran, B. / Patil, K. / Ramani, S. / Song, Y. / Estes, M.K. / Palzkill, T. / Prasad, B.V.V.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like protease
B: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8224
Polymers38,6202
Non-polymers1,2012
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.464, 118.464, 66.571
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21B-424-

HOH

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Components

#1: Protein 3C-like protease / 3CLpro / Calicivirin / NS6


Mass: 19310.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Gene: ORF1 / Production host: Escherichia coli B (bacteria) / References: UniProt: Q83883, calicivirin
#2: Chemical ChemComp-AG7 / 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER / RUPINTRIVIR, bound form


Mass: 600.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H41FN4O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antivirus, protease inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Lithium sulfate, 0.1M Tris, 1.0 M Sodium/Potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.8→52.98 Å / Num. obs: 44383 / % possible obs: 99.95 % / Redundancy: 8.7 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.032 / Rrim(I) all: 0.096 / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2155 / CC1/2: 0.761 / CC star: 0.93 / Rpim(I) all: 0.336 / Rrim(I) all: 0.887 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→52.98 Å / SU ML: 0.1805 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.1381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 1438 3.24 %
Rwork0.1748 42924 -
obs0.1756 44362 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.36 Å2
Refinement stepCycle: LAST / Resolution: 1.8→52.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 86 232 2776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112608
X-RAY DIFFRACTIONf_angle_d1.2913538
X-RAY DIFFRACTIONf_chiral_restr0.0742396
X-RAY DIFFRACTIONf_plane_restr0.0127446
X-RAY DIFFRACTIONf_dihedral_angle_d10.0477358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.26851420.23444205X-RAY DIFFRACTION99.86
1.86-1.940.19771410.194230X-RAY DIFFRACTION99.95
1.94-2.030.21831420.16994225X-RAY DIFFRACTION99.93
2.03-2.130.19811410.18174222X-RAY DIFFRACTION99.86
2.13-2.270.22181430.16914246X-RAY DIFFRACTION99.95
2.27-2.440.1971430.17524278X-RAY DIFFRACTION100
2.44-2.690.21071430.19654277X-RAY DIFFRACTION100
2.69-3.080.21941440.19474316X-RAY DIFFRACTION100
3.08-3.880.20241460.16234362X-RAY DIFFRACTION100
3.88-52.980.1661530.16014563X-RAY DIFFRACTION99.94

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