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- PDB-3ur6: 1.5A resolution structure of apo Norwalk Virus Protease -

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Basic information

Entry
Database: PDB / ID: 3ur6
Title1.5A resolution structure of apo Norwalk Virus Protease
Components3C-like protease
KeywordsHYDROLASE / PROTEASE / NOROVIRUS / NORWALK VIRUS / ANTIVIRAL INHIBITORS / DIPEPTIDYL INHIBITOR
Function / homology
Function and homology information


calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...calicivirin / host cell membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / membrane
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 / Trypsin-like serine proteases ...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 / Trypsin-like serine proteases / Thrombin, subunit H / 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. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLovell, S. / Battaile, K.P. / Kim, Y. / Tiew, K.C. / Mandadapu, S.R. / Alliston, K.R. / Groutas, W.C. / Chang, K.O.
CitationJournal: J.Virol. / Year: 2012
Title: Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses.
Authors: Kim, Y. / Lovell, S. / Tiew, K.C. / Mandadapu, S.R. / Alliston, K.R. / Battaile, K.P. / Groutas, W.C. / Chang, K.O.
History
DepositionNov 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like protease
B: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)40,2522
Polymers40,2522
Non-polymers00
Water3,351186
1
A: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)20,1261
Polymers20,1261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3C-like protease


Theoretical massNumber of molelcules
Total (without water)20,1261
Polymers20,1261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.244, 35.932, 112.974
Angle α, β, γ (deg.)90.000, 97.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3C-like protease / / 3CLpro


Mass: 20126.131 Da / Num. of mol.: 2 / Fragment: unp residues 1101-1281
Source method: isolated from a genetically manipulated source
Details: N-terminal hexahistidine tag / Source: (gene. exp.) Norovirus / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q83883, calicivirin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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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: 1.86 Å3/Da / Density % sol: 33.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20% PEG 3350, 100 mM sodium thiocyanate, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→111.89 Å / Num. all: 47402 / Num. obs: 47402 / % possible obs: 99.09 % / Observed criterion σ(F): 153587 / Observed criterion σ(I): 153587 / Redundancy: 3.24 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.6179
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.5-1.583.140.562.0821664689999.68
1.58-1.683.220.353.2821134655799.88
1.68-1.793.370.215.1320881619299.91
1.79-1.943.280.138.0818739570599.82
1.94-2.123.230.0812.5517092529399.57
2.12-2.373.40.0617.2116210477299.13
2.37-2.743.170.0520.213318420798.7
2.74-3.353.160.0327.7511122351897.51
3.35-4.743.20.0336.288735272796.2
4.74-111.893.060.0235.394692153295.03

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
MOLREPphasing
PHENIXdev_845refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FYQ

2fyq


Resolution: 1.5→36.568 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.861 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.1 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 2400 5.08 %RANDOM
Rwork0.1797 ---
obs0.181 47378 94.14 %-
all-47378 --
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.832 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 84.32 Å2 / Biso mean: 24.9109 Å2 / Biso min: 9.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.6801 Å20 Å21.7333 Å2
2--5.4639 Å2-0 Å2
3----4.1143 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 0 186 2680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142576
X-RAY DIFFRACTIONf_angle_d1.4593506
X-RAY DIFFRACTIONf_chiral_restr0.084399
X-RAY DIFFRACTIONf_plane_restr0.009447
X-RAY DIFFRACTIONf_dihedral_angle_d13.467904
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51710.3551480.31822732288095
1.5171-1.53490.32391450.30472820296595
1.5349-1.55360.34581410.30812821296294
1.5536-1.57330.32371330.29682776290995
1.5733-1.5940.29941700.27742759292995
1.594-1.61580.27481480.25042894304296
1.6158-1.63890.25471370.23792684282194
1.6389-1.66340.25641500.22722792294294
1.6634-1.68940.29641530.2252900305397
1.6894-1.71710.271490.21352849299897
1.7171-1.74670.25241230.2072825294897
1.7467-1.77840.2751400.19412895303597
1.7784-1.81260.21481440.19342781292596
1.8126-1.84960.23651650.18042858302396
1.8496-1.88990.21261660.17452807297396
1.8899-1.93380.23141590.182732289195
1.9338-1.98220.20221180.17132863298195
1.9822-2.03580.19861820.1732672285494
2.0358-2.09570.21621410.172782292393
2.0957-2.16330.21221320.17342818295095
2.1633-2.24060.20911670.16732842300996
2.2406-2.33030.20171480.16462766291495
2.3303-2.43630.18321450.15942742288793
2.4363-2.56470.1911620.18262718288093
2.5647-2.72540.2151450.1792663280892
2.7254-2.93570.16881480.17752643279190
2.9357-3.2310.20571440.17082651279589
3.231-3.69820.18081630.16542663282691
3.6982-4.65780.14681440.13722629277390
4.6578-36.57930.1941320.18242622275489
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)
12.1773-0.4526-0.51061.8879-1.08411.9038-0.035-0.1580.18730.15010.0642-0.0486-0.13830.0798-0.01960.12440.0179-0.0120.0845-0.01250.11243.22691.190922.0081
22.75180.05761.27472.1115-1.35172.6987-0.04880.03020.134-0.095-0.1153-0.2708-0.04120.23040.17830.1140.02190.01620.1219-0.00160.150910.86352.7619.5011
32.07380.4626-0.33360.856-0.61464.02660.01150.12850.0431-0.10840.0690.07780.0228-0.1972-0.1050.16020.0132-0.01030.0626-0.00130.1393-3.4896-4.800812.894
40.72511.1619-0.51382.8122-1.72362.5132-0.03690.06790.1894-0.24750.14070.2914-0.055-0.3132-0.09860.17850.0358-0.01950.20690.0270.1716-6.91673.35996.5069
52.753-0.6825-0.33923.82170.47682.5305-0.04460.1997-0.0723-0.17340.10140.25080.1516-0.215-0.04720.1357-0.006-0.01230.10020.00640.1118-4.9779-1.864111.23
61.5380.2434-0.25831.61530.31022.01480.0757-0.2429-0.03990.151-0.0577-0.1125-0.00750.1342-0.03610.1223-0.0001-0.00530.20940.06560.1281-8.7905-7.987838.39
71.6779-0.8424-0.27742.7210.84113.7204-0.0127-0.22850.03060.3105-0.02650.29370.1226-0.36790.02420.142-0.01060.03310.2450.02170.173-17.0377-7.374242.0062
80.2769-0.82570.50152.5449-1.26421.41730.0323-0.4802-0.27510.1257-0.1715-0.10690.00910.03310.10040.16630.02240.01970.25690.10530.186-3.5122-18.750738.2697
90.5929-0.05180.0530.1156-0.03560.05010.1145-0.31730.20480.30170.0879-0.059-0.3037-0.1225-0.09360.32110.05130.0710.3090.17870.24531.047-19.746646.4513
101.1687-0.0846-2.05211.78932.58388.4798-0.0394-0.2668-0.14850.3737-0.139-0.10050.25810.1830.11910.2549-0.00190.00880.3140.13860.1974-0.4359-20.795450.737
112.13240.719-0.65440.5009-0.6911.0586-0.33020.6719-0.3335-0.17730.2398-0.23210.3159-0.15540.13570.231-0.05210.02150.46170.08960.335612.3588-17.296238.8468
121.5719-0.2664-0.30053.24310.04321.9767-0.1316-0.4634-0.2468-0.02140.035-0.00030.07890.17970.06280.14120.00430.02790.27190.10390.1628-3.0018-19.050541.6126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:43)A0 - 43
2X-RAY DIFFRACTION2chain 'A' and (resseq 44:69)A44 - 69
3X-RAY DIFFRACTION3chain 'A' and (resseq 70:93)A70 - 93
4X-RAY DIFFRACTION4chain 'A' and (resseq 94:121)A94 - 121
5X-RAY DIFFRACTION5chain 'A' and (resseq 122:173)A122 - 173
6X-RAY DIFFRACTION6chain 'B' and (resseq -2:43)B-2 - 43
7X-RAY DIFFRACTION7chain 'B' and (resseq 44:70)B44 - 70
8X-RAY DIFFRACTION8chain 'B' and (resseq 71:93)B71 - 93
9X-RAY DIFFRACTION9chain 'B' and (resseq 94:111)B94 - 111
10X-RAY DIFFRACTION10chain 'B' and (resseq 112:121)B112 - 121
11X-RAY DIFFRACTION11chain 'B' and (resseq 122:135)B122 - 135
12X-RAY DIFFRACTION12chain 'B' and (resseq 136:173)B136 - 173

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