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- PDB-4in1: Structural Basis of Substrate Specificity and Protease Inhibition... -

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Basic information

Entry
Database: PDB / ID: 4in1
TitleStructural Basis of Substrate Specificity and Protease Inhibition in Norwalk Virus
Components3C-like protease
KeywordsHYDROLASE / Protease
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 Hu/1968/US
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPrasad, B.V.V. / Muhaxhiri, Z. / Deng, L. / Shanker, S. / Sankaran, B. / Estes, M.K. / Palzkill, T. / Song, Y.
CitationJournal: J.Virol. / Year: 2013
Title: Structural basis of substrate specificity and protease inhibition in norwalk virus.
Authors: Muhaxhiri, Z. / Deng, L. / Shanker, S. / Sankaran, B. / Estes, M.K. / Palzkill, T. / Song, Y. / Prasad, B.V.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4382
Polymers19,3421
Non-polymers961
Water2,720151
1
A: 3C-like protease
hetero molecules

A: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8774
Polymers38,6842
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area4000 Å2
ΔGint-76 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.197, 124.197, 49.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 3C-like protease / / Genome polyprotein


Mass: 19342.223 Da / Num. of mol.: 1 / Fragment: norwalk virus protease (unp residues 1101-1281) / Mutation: I179T, N180A, F181L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/1968/US / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83883, calicivirin
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293.15 K / pH: 6.8
Details: 1.9 M lithium sulfate and 0.1 M sodium cacodylate, 25% glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2011
RadiationMonochromator: ROSENBAUM-ROCK HIGH-RESOLUTION DOUBLE-CRYSTAL MONOCHROMATOR. LN2 COOLED FIRST CRYSTAL, SAGITTAL FOCUSING 2ND CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 14341 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.105
Reflection shellResolution: 2.05→2.09 Å / % possible all: 5.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→35.85 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 704 5.08 %
Rwork0.163 --
obs0.165 13848 94.4 %
all-14341 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.94 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1022 Å2-0 Å20 Å2
2---0.1022 Å20 Å2
3---0.2045 Å2
Refinement stepCycle: LAST / Resolution: 2.05→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 5 151 1452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061359
X-RAY DIFFRACTIONf_angle_d1.0151854
X-RAY DIFFRACTIONf_dihedral_angle_d12.773482
X-RAY DIFFRACTIONf_chiral_restr0.068210
X-RAY DIFFRACTIONf_plane_restr0.004239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.20830.1961420.15832430X-RAY DIFFRACTION90
2.2083-2.43050.23981390.16452515X-RAY DIFFRACTION92
2.4305-2.78210.21521400.1712588X-RAY DIFFRACTION94
2.7821-3.50460.17541280.15312716X-RAY DIFFRACTION97
3.5046-35.85810.20081550.16722895X-RAY DIFFRACTION98
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)
10.4486-0.3664-0.28470.34120.07960.67560.01820.0819-0.071-0.00880.02690.0111-0.09580.1357-0.0350.14460.033-0.00230.1754-0.03770.138834.541931.6028-3.4764
20.650.2201-0.12390.1883-0.12070.07770.2678-0.21330.0488-0.02970.0393-0.2233-0.44430.44630.07810.1768-0.05440.09470.2932-0.09360.267945.700341.043-8.55
30.5918-0.0862-0.47880.26050.09670.38930.2290.18130.1837-0.0767-0.0081-0.048-0.4717-0.063-0.14030.22040.00790.0550.202-0.02730.162735.518644.4337-6.1751
40.9129-0.35490.03140.5604-0.00490.4083-0.0090.3307-0.3149-0.1108-0.09590.05280.160.0742-0.02080.18690.03980.0130.2033-0.04030.141132.73132.3454-15.4317
50.3489-0.197-0.01920.48590.22040.2373-0.06070.01730.10170.1192-0.011-0.07930.1221-0.08630.04920.18320.0209-0.00610.1609-0.01830.176727.990830.22933.9259
60.237-0.2562-0.16490.30430.13680.1568-0.1428-0.1074-0.05110.21180.0639-0.02530.08110.0388-0.20480.13760.06630.06910.0989-0.03780.148929.295335.694712.6733
70.48380.0990.38240.64830.22040.3366-0.1659-0.1120.10170.05050.09160.04220.0130.2738-0.04950.17360.02470.04410.2015-0.01540.154829.464540.527713.2546
80.18690.0539-0.05430.2820.01910.1179-0.15780.0072-0.02840.11850.2229-0.02260.17990.1093-0.02380.18730.10170.02980.2328-0.00010.182635.446728.622210.7425
90.72730.0601-0.09870.8522-0.0460.8368-0.0626-0.0507-0.24270.14430.10750.1510.0979-0.1860.0170.12170.01840.01080.16070.00510.16926.873731.8626.7523
100.1301-0.0023-0.11350.11380.06540.1292-0.03660.0503-0.11450.1707-0.01060.0688-0.1279-0.3319-0.0290.24160.09530.01730.33160.02460.217918.353849.717911.7522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:31)
2X-RAY DIFFRACTION2chain 'A' and (resseq 32:43)
3X-RAY DIFFRACTION3chain 'A' and (resseq 44:60)
4X-RAY DIFFRACTION4chain 'A' and (resseq 61:70)
5X-RAY DIFFRACTION5chain 'A' and (resseq 71:93)
6X-RAY DIFFRACTION6chain 'A' and (resseq 94:111)
7X-RAY DIFFRACTION7chain 'A' and (resseq 112:121)
8X-RAY DIFFRACTION8chain 'A' and (resseq 122:141)
9X-RAY DIFFRACTION9chain 'A' and (resseq 142:170)
10X-RAY DIFFRACTION10chain 'A' and (resseq 171:181)

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