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- PDB-9dap: Human norovirus GII.3 protease in complex with rupintrivir -

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Basic information

Entry
Database: PDB / ID: 9dap
TitleHuman norovirus GII.3 protease in complex with rupintrivir
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / Viral protease with inhibitor
Function / homology
Function and homology information


host cell / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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
Chem-AG7 / Genome polyprotein
Similarity search - Component
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsPham, 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 22, 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: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9482
Polymers19,3471
Non-polymers6011
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.329, 97.329, 43.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Genome polyprotein


Mass: 19347.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Production host: Escherichia coli B (bacteria) / References: UniProt: B2DD26
#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.: 1 / Source method: obtained synthetically / Formula: C31H41FN4O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antivirus, protease inhibitor*YM
Has ligand of interestY
Has protein modificationY

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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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.3 M Sodium Formate, 0.1 M Sodium Citrate Tribasic:HCl, 22.5 % (v/v) PurePEGs Cocktail

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→48.66 Å / Num. obs: 6699 / % possible obs: 99.78 % / Redundancy: 1.1 % / Biso Wilson estimate: 50.06 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04753 / Rpim(I) all: 0.04753 / Rrim(I) all: 0.06721 / Net I/σ(I): 9.86
Reflection shellResolution: 2.71→3.41 Å / Redundancy: 1 % / Mean I/σ(I) obs: 3.85 / Num. unique obs: 6292 / CC1/2: 0.963 / CC star: 0.991 / % possible all: 99.67

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
iMOSFLMdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→48.66 Å / SU ML: 0.1818 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 318 4.76 %
Rwork0.1864 6367 -
obs0.1889 6685 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.27 Å2
Refinement stepCycle: LAST / Resolution: 2.71→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 43 0 1260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641290
X-RAY DIFFRACTIONf_angle_d1.00651748
X-RAY DIFFRACTIONf_chiral_restr0.0531195
X-RAY DIFFRACTIONf_plane_restr0.0076221
X-RAY DIFFRACTIONf_dihedral_angle_d15.5643458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-3.410.29721650.25943117X-RAY DIFFRACTION99.67
3.41-48.660.21371530.15793250X-RAY DIFFRACTION99.91
Refinement TLS params.Method: refined / Origin x: -31.8519824581 Å / Origin y: -25.4506536934 Å / Origin z: 1.5030171816 Å
111213212223313233
T0.319308307315 Å2-0.018015792616 Å2-0.0136716697205 Å2-0.316881438624 Å2-0.0375812930653 Å2--0.282268825999 Å2
L2.83513076851 °2-0.739197987823 °2-0.00827904385745 °2-1.96505488844 °2-0.444455580858 °2--0.769385240569 °2
S0.00787835686272 Å °0.00730320194171 Å °0.162288522254 Å °-0.151598019665 Å °-0.00068094084821 Å °0.00680907334689 Å °-0.00834335599332 Å °0.0474232092636 Å °-7.93063772178E-9 Å °
Refinement TLS groupSelection details: all

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