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- PDB-9da0: Human norovirus GII.4 Houston R112A mutant protease in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9da0
TitleHuman norovirus GII.4 Houston R112A mutant 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: 2.28 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

Downloads & links

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Assembly

Deposited unit
A: Peptidase C37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8192
Polymers19,2181
Non-polymers6011
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.100, 93.100, 44.660
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 Peptidase C37


Mass: 19218.146 Da / Num. of mol.: 1 / Mutation: R112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Gene: ORF1 / Production host: Escherichia coli B (bacteria) / References: UniProt: A0A7S9NT71
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.2 M Lithium acetate dihydrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.28→46.55 Å / Num. obs: 13538 / % possible obs: 92.03 % / Redundancy: 11 % / Biso Wilson estimate: 41.62 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1053 / Rpim(I) all: 0.03333 / Rrim(I) all: 0.1105 / Net I/σ(I): 15.47
Reflection shellResolution: 2.28→2.61 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.27 / Num. unique obs: 4067 / CC1/2: 0.647 / CC star: 0.886 / % 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: 2.28→46.55 Å / SU ML: 0.3071 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.2119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 480 5.01 %
Rwork0.1985 9109 -
obs0.2002 9589 92.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.19 Å2
Refinement stepCycle: LAST / Resolution: 2.28→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 43 38 1313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031318
X-RAY DIFFRACTIONf_angle_d0.71451788
X-RAY DIFFRACTIONf_chiral_restr0.049198
X-RAY DIFFRACTIONf_plane_restr0.0059227
X-RAY DIFFRACTIONf_dihedral_angle_d14.0256466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.610.26281700.26143240X-RAY DIFFRACTION100
2.61-3.290.29351500.23942869X-RAY DIFFRACTION87.51
3.29-46.550.20021600.16653000X-RAY DIFFRACTION88.79
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)
15.65234571384-0.443653964894-1.155369143556.808302407830.9185089118155.8556567116-0.197601182205-0.1748970852270.0187791947247-0.1968108123440.170758450590.603275507182-0.014047586123-0.09700802344880.08599889974760.2511902844340.0064158580049-0.03346209847840.320379598970.04550914576910.34523550430324.978569968627.83690697636.13906699771
24.2049652255-5.09246945239-6.112754769137.518707913656.81512774529.492683438360.312260196437-0.2229366025090.0973127328083-0.02762559079520.0261133875997-0.291469491915-0.0848654299116-0.184037419061-0.469003038170.3360563021180.0218534731406-0.006682955336280.4451406219110.03338848460820.34254506043533.893651287328.743545818312.5797345033
36.079318318663.385185951471.433577385677.929148755671.978622540737.422862745680.17290692584-0.6136784929760.1008024264280.5784056209-0.367250397241.000781109080.128165574735-1.502538786310.2988792214470.3172921087770.0342975413150.1211082901680.553445158014-0.01791662730890.35884351160619.93322418723.932239654315.5262002131
46.18540455008-4.35974602584-0.7027689737285.0419945582-0.6104585699551.092564167510.2787833185020.40601209677-0.414454907228-0.22267042508-0.3009188918210.182820754230.08262753051740.121902647102-0.03450763835580.320360338533-0.0701063889001-0.05150270687020.258991527855-0.01808075419670.36667974437627.904612232716.5582820398-1.35269153743
56.72104475139-1.856182519270.6868818996952.54654884834-0.748798666930.7506771870010.2734082674850.288437931544-0.541462320312-0.328307183264-0.163953282749-0.118154920026-0.2309198707250.157974689835-0.07090628226410.3553132426230.01990915751840.05568944378320.34420193873-0.04798731318280.22220853443937.812668435118.7582258502-5.5970703418
66.05304479340.821451154056-0.1039016553957.89054923201-0.2580180687485.414038344850.0808650774093-0.0335406007778-0.3254093101390.227339941539-0.1591848505250.4698918897520.113132777583-0.2154240792230.02305448119290.1805781635370.00139247742319-0.03990312278380.288063000452-0.02455547738620.35974032317728.774854635817.22152453-2.07146102922
78.623355232711.49281176087-1.905266746257.848184735280.06185568483912.10809809945-0.44232100740.207509061664-0.400695817118-0.567313672126-0.124633023537-0.632164800402-0.07657196588620.1601994490070.7133306116420.4306625081830.04199084896880.05706136482040.273199539948-0.007464239093050.39122193009237.864062112720.5898033467-5.26155540922
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )1 - 431 - 43
22chain 'A' and (resid 44 through 59 )44 - 5944 - 59
33chain 'A' and (resid 60 through 69 )60 - 6960 - 69
44chain 'A' and (resid 70 through 93 )70 - 9370 - 93
55chain 'A' and (resid 94 through 121 )94 - 12194 - 121
66chain 'A' and (resid 122 through 160 )122 - 160122 - 151
77chain 'A' and (resid 161 through 174 )161 - 174152 - 165

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