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- PDB-9df5: Human norovirus GII.3 protease -

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Basic information

Entry
Database: PDB / ID: 9df5
TitleHuman norovirus GII.3 protease
ComponentsPeptidase C37
KeywordsVIRAL PROTEIN / Viral protease
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / host cell / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / 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
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 29, 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
B: Peptidase C37


Theoretical massNumber of molelcules
Total (without water)38,9572
Polymers38,9572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.525, 78.525, 105.686
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

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Components

#1: Protein Peptidase C37


Mass: 19478.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Production host: Escherichia coli B (bacteria) / References: UniProt: B2DD26
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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1-0.35M KSCN, 15-25% PEG 3,350, 0.1M Bis-Tris Propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.8→63.03 Å / Num. obs: 8595 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 59.2 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.028 / Rrim(I) all: 0.085 / Net I/σ(I): 18.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 415 / CC1/2: 0.915 / CC star: 0.977 / Rpim(I) all: 0.157 / Rrim(I) all: 0.528 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→63.03 Å / SU ML: 0.3591 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.6708
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2965 430 5 %
Rwork0.2517 8164 -
obs0.2539 8594 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.74 Å2
Refinement stepCycle: LAST / Resolution: 2.8→63.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 0 0 2269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282324
X-RAY DIFFRACTIONf_angle_d0.57193148
X-RAY DIFFRACTIONf_chiral_restr0.0468356
X-RAY DIFFRACTIONf_plane_restr0.006395
X-RAY DIFFRACTIONf_dihedral_angle_d15.5326841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.36121400.31512651X-RAY DIFFRACTION100
3.21-4.040.32721400.27162679X-RAY DIFFRACTION99.65
4.04-63.030.25931500.22222834X-RAY DIFFRACTION99.63

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