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- PDB-9da7: Human norovirus GII.4 Houston protease in complex with rupintrivir -

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Basic information

Entry
Database: PDB / ID: 9da7
TitleHuman norovirus GII.4 Houston protease in complex with rupintrivir
ComponentsPeptidase C37
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: 2.5 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: Peptidase C37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9052
Polymers19,3041
Non-polymers6011
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.569, 56.569, 95.064
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

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Components

#1: Protein Peptidase C37


Mass: 19304.264 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: Q6REV3
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97936 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.5→48.99 Å / Num. obs: 12340 / % possible obs: 99.52 % / Redundancy: 12.4 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1085 / Rpim(I) all: 0.03192 / Rrim(I) all: 0.1133 / Net I/σ(I): 7.05
Reflection shellResolution: 2.5→3.15 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 1.34 / Num. unique obs: 6035 / CC1/2: 0.972 / CC star: 0.993 / % possible all: 99.78

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.99 Å / SU ML: 0.1566 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.1275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2915 326 5.06 %
Rwork0.2515 6113 -
obs0.2536 6439 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 43 17 1261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721273
X-RAY DIFFRACTIONf_angle_d1.051722
X-RAY DIFFRACTIONf_chiral_restr0.0596191
X-RAY DIFFRACTIONf_plane_restr0.0094217
X-RAY DIFFRACTIONf_dihedral_angle_d15.6413452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-3.150.38971600.32043009X-RAY DIFFRACTION99.78
3.15-48.990.25741660.22713104X-RAY DIFFRACTION99.3

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