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- PDB-9pjf: GII.4 Human Norovirus 3CL protease bound to compound 27 -

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Basic information

Entry
Database: PDB / ID: 9pjf
TitleGII.4 Human Norovirus 3CL protease bound to compound 27
Components
  • (BOC)F(ALC)(ELL) peptide
  • Peptidase C37
KeywordsVIRAL PROTEIN/INHIBITOR / Norovirus / Protease / Inhibitor / 3CLpro / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex
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 / metal ion 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 / Reverse transcriptase/Diguanylate cyclase 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsCampbell, A.C. / Opel-Reading, H.K. / Krause, K.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Ministry of Business, Innovation and Employment (New Zealand)UOOX1904 New Zealand
CitationJournal: Acs Infect Dis. / Year: 2025
Title: Broad-Spectrum Peptidomimetic Inhibitors of Norovirus and Coronavirus 3C-like Proteases.
Authors: Brimble, M.A. / Stubbing, L.A. / Hermant, Y.O. / Yang, S.H. / Hubert, J.G. / Pearl, E.S. / McSweeney, A.M. / Young, V.L. / Campbell, A.C. / Opel-Reading, H.K. / McKenzie-Goldsmith, G.M. / ...Authors: Brimble, M.A. / Stubbing, L.A. / Hermant, Y.O. / Yang, S.H. / Hubert, J.G. / Pearl, E.S. / McSweeney, A.M. / Young, V.L. / Campbell, A.C. / Opel-Reading, H.K. / McKenzie-Goldsmith, G.M. / Putha, L. / Mortuza, R. / Wang, H. / Hurst, B.L. / Julander, J. / Harris, L.D. / Krause, K.L. / Ward, V.K.
History
DepositionJul 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase C37
B: Peptidase C37
C: (BOC)F(ALC)(ELL) peptide
D: (BOC)F(ALC)(ELL) peptide


Theoretical massNumber of molelcules
Total (without water)39,7744
Polymers39,7744
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-21 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.683, 63.945, 96.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-297-

HOH

21A-402-

HOH

31B-253-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 9 or resid 11...
d_2ens_1(chain "B" and (resid 4 through 9 or resid 11...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERILEILEAA4 - 94 - 9
d_12ASNASNPROPROAA11 - 2211 - 22
d_13LEULEUGLYGLYAA24 - 7024 - 70
d_14ILEILEALAALAAA72 - 9972 - 99
d_15METMETGLYGLYAA101 - 102101 - 102
d_16HISHISGLNGLNAA104 - 117104 - 117
d_17GLYGLYGLYGLYAA119 - 124119 - 124
d_18LEULEUTYRTYRAA132 - 143132 - 143
d_19TYRTYRHISHISAA145 - 157145 - 157
d_110ALAALAARGARGAA159 - 162159 - 162
d_111ASNASNGLYGLYAA165 - 173165 - 173
d_11228282828AC201
d_21SERSERILEILEBB4 - 91 - 6
d_22ASNASNPROPROBB11 - 228 - 19
d_23LEULEUGLYGLYBB24 - 7021 - 67
d_24ILEILEALAALABB72 - 9969 - 96
d_25METMETGLYGLYBB101 - 10298 - 99
d_26HISHISGLNGLNBB104 - 117101 - 114
d_27GLYGLYTYRTYRBB119 - 143116 - 133
d_28TYRTYRHISHISBB145 - 157135 - 147
d_29ALAALAGLYGLYBB159 - 173149 - 161
d_21028282828BD201

NCS oper: (Code: givenMatrix: (-0.977500700902, 0.200713405397, -0.0648576027107), (0.205287552266, 0.834597197535, -0.511179556272), (-0.0484706160477, -0.512992833049, -0.857023309263)Vector: -3. ...NCS oper: (Code: given
Matrix: (-0.977500700902, 0.200713405397, -0.0648576027107), (0.205287552266, 0.834597197535, -0.511179556272), (-0.0484706160477, -0.512992833049, -0.857023309263)
Vector: -3.48331603569, 18.8639251414, 52.5721840817)

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Components

#1: Protein Peptidase C37


Mass: 19330.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Production host: Escherichia coli (E. coli) / References: UniProt: K4L8Z7
#2: Protein/peptide (BOC)F(ALC)(ELL) peptide


Mass: 556.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Na formate, 0.1 M BICINE pH 8.5, 20% PEG MME 5K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.47→48.26 Å / Num. obs: 64564 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.67 Å2 / CC1/2: 1 / Net I/σ(I): 19.4
Reflection shellResolution: 1.47→1.5 Å / Num. unique obs: 3126 / CC1/2: 0.928

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→48.26 Å / SU ML: 0.1227 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.5288
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.184 1930 2.99 %
Rwork0.162 62589 -
obs0.1627 64519 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.44 Å2
Refinement stepCycle: LAST / Resolution: 1.47→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 80 332 2940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172765
X-RAY DIFFRACTIONf_angle_d1.55853768
X-RAY DIFFRACTIONf_chiral_restr0.1158426
X-RAY DIFFRACTIONf_plane_restr0.0105480
X-RAY DIFFRACTIONf_dihedral_angle_d18.9687985
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.832875921902 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.510.19191310.18014390X-RAY DIFFRACTION99.34
1.51-1.550.21271370.16894405X-RAY DIFFRACTION99.98
1.55-1.590.18491370.15454430X-RAY DIFFRACTION100
1.59-1.640.17411390.15944430X-RAY DIFFRACTION99.98
1.64-1.70.17991390.15694414X-RAY DIFFRACTION100
1.7-1.770.17341390.15314419X-RAY DIFFRACTION99.98
1.77-1.850.18021380.15874432X-RAY DIFFRACTION99.98
1.85-1.950.17831310.15644474X-RAY DIFFRACTION100
1.95-2.070.19271410.15754457X-RAY DIFFRACTION99.93
2.07-2.230.17161390.15894454X-RAY DIFFRACTION100
2.23-2.460.23381380.17274488X-RAY DIFFRACTION99.96
2.46-2.810.20981350.17734500X-RAY DIFFRACTION99.89
2.81-3.540.18781440.16434567X-RAY DIFFRACTION99.96
3.54-48.260.15731420.15484729X-RAY DIFFRACTION99.45
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.877564347528-0.3077638921130.3360794905981.04057155672-0.3154152228051.098561063240.05062648996820.00254520454347-0.0791312809002-0.04075355570830.008089991409210.01880240765130.04846179093590.06565162243660.03732836625490.1011162717170.0130592305979-0.01878652332450.11671298129-0.003705767386720.1259948035825.1690317728215.271999845439.7676965082
20.788263885027-0.08844682972310.1746851733550.8153755252270.2043057806350.694084933066-0.0350013416230.0593862319650.0446373576518-0.0747713914042-0.07834859086570.0204215624183-0.0690509157088-0.0463133034791-0.08578350775560.1680650379070.0236464854757-0.04043225011560.158265940079-0.01949726025450.131186414791-8.6204904590911.511261969310.4442853127
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid 1 through 201)AA - B1 - 201
22(chain 'B' and resid 4 through 201)BC - D4 - 201

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