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- PDB-4in2: Structural Basis of Substrate Specificity and Protease Inhibition... -

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Basic information

Entry
Database: PDB / ID: 4in2
TitleStructural Basis of Substrate Specificity and Protease Inhibition in Norwalk Virus
ComponentsC-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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,1532
Polymers39,1532
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: C-like protease

B: C-like protease


Theoretical massNumber of molelcules
Total (without water)39,1532
Polymers39,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.582, 97.582, 270.458
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein C-like protease / Genome polyprotein


Mass: 19576.535 Da / Num. of mol.: 2 / Fragment: norwalk virus protease (unp residues 1100-1281)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus / Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83883, calicivirin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 4.75 Å3/Da / Density % sol: 74.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6-1.8 M lithium sulfate and 0.1 M sodium cacodylate, 30% glycerol, pH 6.5, 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: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2008
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: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 30866 / Num. obs: 30866 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.44 Å / % possible all: 100

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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: 2.401→48.791 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1490 4.99 %
Rwork0.1879 --
obs0.1892 29836 97.11 %
all-30866 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.423 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.8227 Å2-0 Å2-0 Å2
2--6.8227 Å2-0 Å2
3----13.6454 Å2
Refinement stepCycle: LAST / Resolution: 2.401→48.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 0 130 2692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072624
X-RAY DIFFRACTIONf_angle_d1.0743558
X-RAY DIFFRACTIONf_dihedral_angle_d14.851927
X-RAY DIFFRACTIONf_chiral_restr0.071403
X-RAY DIFFRACTIONf_plane_restr0.005455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4015-2.4790.26171120.22472427X-RAY DIFFRACTION93
2.479-2.56760.28381200.22922407X-RAY DIFFRACTION93
2.5676-2.67040.27391250.21782424X-RAY DIFFRACTION94
2.6704-2.79190.25761360.21222513X-RAY DIFFRACTION96
2.7919-2.93910.25741440.19892519X-RAY DIFFRACTION97
2.9391-3.12320.23131460.19822559X-RAY DIFFRACTION98
3.1232-3.36420.23961390.18772603X-RAY DIFFRACTION99
3.3642-3.70270.19571330.16292613X-RAY DIFFRACTION99
3.7027-4.23820.17011520.15242661X-RAY DIFFRACTION99
4.2382-5.33870.15311410.14332705X-RAY DIFFRACTION100
5.3387-48.8010.2461420.24382915X-RAY DIFFRACTION100
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)
10.95030.19410.76920.7138-0.03730.6837-0.13130.2926-0.0443-0.3082-0.1452-0.04940.0130.23780.00750.32840.13870.10940.3122-0.01030.312910.434135.085221.2071
20.1221-0.004-0.22610.4454-0.09840.42320.11570.11170.0712-0.2217-0.0352-0.1725-0.07850.2117-0.00740.3220.07110.04480.27560.03810.28398.296549.1221.2316
30.3768-0.01640.41550.4221-0.37440.78470.31610.14250.0748-0.1760.04660.3194-0.0755-0.2568-0.12640.29150.09650.02550.18690.03060.24610.505851.711421.8089
41.8054-0.5450.97070.4154-0.23760.5374-0.21590.4643-0.1362-0.3327-0.30670.0394-0.0262-0.08750.02260.55710.19230.09070.4698-0.0430.2576.048643.119410.5642
50.3967-0.0732-0.02270.47110.05230.9242-0.02910.2096-0.1775-0.2150.0277-0.04230.18020.016-0.04960.48550.04850.05840.481-0.02170.423-4.812835.393827.0965
60.80960.0482-0.20710.6807-0.62290.685-0.1542-0.0750.0770.0564-0.0951-0.44610.17980.3031-0.17910.46990.26280.15480.23060.02030.380612.872734.707729.6754
70.2988-0.0974-0.12070.28840.0220.5744-0.3222-0.2055-0.13760.45290.16960.01960.1825-0.00050.04270.36380.13250.07730.33120.06230.33153.920939.742737.3498
81.3056-0.4774-0.1970.4206-0.31870.922-0.0712-0.3232-0.45660.36290.02950.12960.9386-0.1355-0.06290.44210.0660.07570.24930.06170.32172.364735.374131.6772
90.3281-0.2771-0.12410.61020.51050.48730.13020.4449-0.0111-0.0505-0.00260.2277-0.08830.0639-0.02530.18920.04740.00430.45350.03460.4044-9.969146.27233.7234
100.1313-0.02050.07350.07340.08280.1375-0.0787-0.13330.01090.14620.01220.1088-0.2584-0.0991-0.03660.58760.38640.14460.1118-0.03120.347921.978631.127619.6002
110.8733-0.0538-0.76650.9144-0.26380.81440.1096-0.18240.21460.08050.2373-0.171-1.16540.31850.15040.792-0.02580.06140.1567-0.08420.326533.633637.435120.8073
120.6721-0.0612-0.311.39550.5570.38710.0178-0.2193-0.01140.3726-0.0229-0.42290.02180.5565-0.06550.5484-0.06780.02340.3828-0.07160.328340.180333.272521.3527
130.197-0.2164-0.35140.2230.38490.6322-0.052-0.31560.12640.27970.04620.1354-0.40580.1196-0.4720.6660.2140.18570.3593-0.09020.224328.620430.115730.6575
140.2472-0.06670.09870.69230.03132.0892-0.0022-0.0321-0.26810.1193-0.01580.27460.1751-0.48380.09060.33470.01440.04980.1818-0.07180.281931.755519.449912.1163
152.0030.31380.07470.0688-0.10511.20240.13740.27810.67640.007-0.00440.117-0.6863-0.2394-0.11810.50020.14160.15020.35990.01470.37519.935133.048510.5745
161.4844-0.1248-0.32840.35460.0950.4450.16820.5370.1745-0.106-0.0966-0.0848-0.4818-0.0271-0.12780.43440.07370.08830.3307-0.04520.353132.250628.85163.3929
171.7441.1949-0.36921.73290.21741.78590.00750.4955-0.5349-0.34970.2123-0.3542-0.5303-0.2729-0.07080.4270.06390.06970.3727-0.01940.325434.067626.80221.7548
181.12661.3243-0.24551.7893-0.52220.37370.03170.0172-0.30240.4873-0.0797-0.3149-0.4573-0.1875-0.14350.43170.16370.05560.2389-0.01610.239924.908527.08619.9867
190.28920.14440.15960.64680.11190.44130.03390.01630.022-0.26280.03470.1384-0.11720.1534-0.01320.43440.0670.0380.2065-0.0090.240233.520125.36844.9806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:12 )A0 - 12
2X-RAY DIFFRACTION2( CHAIN A AND RESID 13:43 )A13 - 43
3X-RAY DIFFRACTION3( CHAIN A AND RESID 44:59 )A44 - 59
4X-RAY DIFFRACTION4( CHAIN A AND RESID 60:69 )A60 - 69
5X-RAY DIFFRACTION5( CHAIN A AND RESID 70:81 )A70 - 81
6X-RAY DIFFRACTION6( CHAIN A AND RESID 82:93 )A82 - 93
7X-RAY DIFFRACTION7( CHAIN A AND RESID 94:141 )A94 - 141
8X-RAY DIFFRACTION8( CHAIN A AND RESID 142:170 )A142 - 170
9X-RAY DIFFRACTION9( CHAIN A AND RESID 171:179 )A171 - 179
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1:12 )B1 - 12
11X-RAY DIFFRACTION11( CHAIN B AND RESID 13:43 )B13 - 43
12X-RAY DIFFRACTION12( CHAIN B AND RESID 44:60 )B44 - 60
13X-RAY DIFFRACTION13( CHAIN B AND RESID 61:70 )B61 - 70
14X-RAY DIFFRACTION14( CHAIN B AND RESID 71:81 )B71 - 81
15X-RAY DIFFRACTION15( CHAIN B AND RESID 82:93 )B82 - 93
16X-RAY DIFFRACTION16( CHAIN B AND RESID 94:112 )B94 - 112
17X-RAY DIFFRACTION17( CHAIN B AND RESID 113:121 )B113 - 121
18X-RAY DIFFRACTION18( CHAIN B AND RESID 122:149 )B122 - 149
19X-RAY DIFFRACTION19( CHAIN B AND RESID 150:181 )B150 - 181

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