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- PDB-4xbd: 1.45A resolution structure of Norovirus 3CL protease complex with... -

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Entry
Database: PDB / ID: 4xbd
Title1.45A resolution structure of Norovirus 3CL protease complex with a covalently bound dipeptidyl inhibitor (1R,2S)-2-({N-[(benzyloxy)carbonyl]-3-cyclohexyl-L-alanyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid (Orthorhombic P Form)
Components3C-LIKE PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / NOROVIRUS / NORWALK VIRUS / ANTIVIRAL INHIBITORS / DIPEPTIDYL INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
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
Chem-M40 / Genome polyprotein
Similarity search - Component
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsLovell, S. / Battaile, K.P. / Mehzabeen, N. / Kankanamalage, A.C.G. / Kim, Y. / Weerawarna, P.M. / Uy, R.A.Z. / Damalanka, V.C. / Mandadapu, S.R. / Alliston, K.R. ...Lovell, S. / Battaile, K.P. / Mehzabeen, N. / Kankanamalage, A.C.G. / Kim, Y. / Weerawarna, P.M. / Uy, R.A.Z. / Damalanka, V.C. / Mandadapu, S.R. / Alliston, K.R. / Groutas, W.C. / Chang, K.-O.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structure-Guided Design and Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. Structure-Activity Relationships and Biochemical, X-ray Crystallographic, Cell-Based, and In Vivo Studies.
Authors: Galasiti Kankanamalage, A.C. / Kim, Y. / Weerawarna, P.M. / Uy, R.A. / Damalanka, V.C. / Mandadapu, S.R. / Alliston, K.R. / Mehzabeen, N. / Battaile, K.P. / Lovell, S. / Chang, K.O. / Groutas, W.C.
History
DepositionDec 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3034
Polymers40,2522
Non-polymers1,0512
Water3,927218
1
A: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6522
Polymers20,1261
Non-polymers5261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6522
Polymers20,1261
Non-polymers5261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-4 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.466, 66.907, 126.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3C-LIKE PROTEASE


Mass: 20126.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus (strain GI/Human/United States/Norwalk/1968)
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: Chemical ChemComp-M40 / (1R,2S)-2-({N-[(benzyloxy)carbonyl]-3-cyclohexyl-L-alanyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid


Mass: 525.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H35N3O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG3350, 200 mM sodium thiocyanate

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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: Nov 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.94 Å / Num. obs: 57354 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 19.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 18.9 / Num. measured all: 371208
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2% possible all
1.45-1.486.51.0541.81945329720.635100
7.67-45.945.60.02362.626214660.99999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.99 Å45.94 Å
Translation3.99 Å45.94 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→35.654 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.84 / Phase error: 18.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 2905 5.07 %RANDOM
Rwork0.1725 54369 --
obs0.1738 57274 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.85 Å2 / Biso mean: 24.3087 Å2 / Biso min: 9.16 Å2
Refinement stepCycle: final / Resolution: 1.45→35.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 58 218 2692
Biso mean--25.43 32.05 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082572
X-RAY DIFFRACTIONf_angle_d1.023507
X-RAY DIFFRACTIONf_chiral_restr0.084407
X-RAY DIFFRACTIONf_plane_restr0.008438
X-RAY DIFFRACTIONf_dihedral_angle_d14.652929
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.45-1.47380.30431210.273225432664
1.4738-1.49920.25511240.241525982722
1.4992-1.52650.23881430.22925042647
1.5265-1.55580.24081470.209725702717
1.5558-1.58760.20381340.207625272661
1.5876-1.62210.24151500.20525572707
1.6221-1.65980.21941480.184825482696
1.6598-1.70130.24181130.183726052718
1.7013-1.74730.17761430.174325252668
1.7473-1.79870.22161420.169325792721
1.7987-1.85680.19331370.165525862723
1.8568-1.92320.20251370.162325512688
1.9232-2.00020.21061420.159425672709
2.0002-2.09120.18321190.158926272746
2.0912-2.20140.18741560.156425612717
2.2014-2.33930.17771340.157125992733
2.3393-2.51990.1831450.169225972742
2.5199-2.77340.1961370.176826062743
2.7734-3.17450.20931330.179326542787
3.1745-3.99870.18961390.169726692808
3.9987-35.66460.19681610.164927962957
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)
12.3964-0.0283-0.20971.8459-0.45252.70.0358-0.06150.0113-0.0575-0.0063-0.07590.0058-0.0534-0.02430.097-0.01080.00520.08580.00630.1011-7.65269.1816-24.6387
26.20672.14073.49582.27851.07485.1277-0.272-0.42490.6375-0.0113-0.0003-0.1588-0.7176-0.08250.2670.2773-0.02110.02810.2189-0.07690.2771-2.542623.8232-18.9753
35.42360.06932.28770.85080.82564.5091-0.140.21980.7353-0.03550.2008-0.059-0.88990.38510.02590.2917-0.07710.06840.15870.01030.2877-0.294520.5469-28.888
45.33381.3474-0.69867.1796-2.65084.24240.1214-0.5134-0.14350.1352-0.1566-0.32860.01470.56920.01960.1108-0.01180.00220.20970.00190.16223.68439.5733-19.4826
51.21730.33690.18051.1178-0.79433.27270.10210.2887-0.0184-0.14460.0410.0140.0653-0.2576-0.16020.19510.0060.0010.17530.00790.1773-11.37865.8472-32.0654
61.58110.10290.14071.1409-0.02462.62270.09390.21690.1816-0.19570.09880.1134-0.0658-0.5239-0.17740.20260.02560.00230.26590.01640.147-16.546511.5448-38.2916
74.68741.7627-1.13753.4706-0.024.16180.0335-0.19950.1796-0.4231-0.190.5733-0.4754-0.63010.09780.23430.0685-0.02120.30890.00870.1929-14.997314.8198-40.1428
82.8074-0.4419-0.17453.83650.20663.2040.01890.3368-0.1519-0.1369-0.03180.02910.2639-0.236-0.01340.1412-0.00680.00620.1285-0.00580.0935-12.60737.9819-33.8498
91.3484-0.1275-0.00391.08250.00233.09960.0064-0.04380.0455-0.00720.0628-0.02820.0078-0.1919-0.06910.1255-0.0188-0.01480.12250.03850.1576-16.9542.6524-7.7372
105.265-2.4294-0.46713.3586-0.99410.6853-0.2828-0.2461.1880.3561-0.04080.5747-0.7721-0.67490.37910.35230.0818-0.03230.2801-0.05640.5487-23.751914.9737-3.4768
116.9338-2.53773.46552.5386-2.10644.5128-0.3292-0.71380.4110.46890.19020.2684-0.4261-0.85820.11410.23560.04820.03370.3507-0.01640.2504-25.43725.74921.3985
124.2998-1.126-1.63522.61910.19551.80820.09910.08810.17-0.19230.04450.4030.0661-0.729-0.05650.1264-0.0377-0.05170.29470.06610.2236-27.4432.0789-13.502
131.2190.1531-0.54841.4224-0.98992.50860.0558-0.1827-0.32470.1231-0.0340.00720.4093-0.03090.02940.2182-0.0324-0.03950.14210.05490.194-11.0822-5.0786-4.9668
140.4780.011-0.0360.0952-0.14351.57840.067-0.2941-0.02690.145-0.133-0.13410.11830.36660.06220.2790.017-0.02250.21650.06620.2139-6.9803-4.74783.2654
152.4183-1.01-0.5282.70241.5513.0026-0.075-0.11550.08410.5115-0.0032-0.02020.0507-0.24780.05930.29510.0165-0.01260.2520.10450.2163-10.0576-3.38747.7845
163.18950.6674-0.42434.09490.05622.2166-0.0607-0.0566-0.3768-0.0991-0.0065-0.17090.44440.18540.02570.21440.0044-0.01370.13450.0510.1724-8.4375-4.5903-4.8798
173.36150.0986-0.16934.03790.93773.6064-0.0752-0.4984-0.11040.0936-0.0116-0.10160.47370.01710.04740.2058-0.006-0.02020.15520.08560.1493-10.1398-4.11161.2073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 31 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 43 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 59 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 69 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 93 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 94 through 111 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 112 through 121 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 173 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 0 through 31 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 43 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 44 through 60 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 61 through 70 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 71 through 93 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 94 through 111 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 112 through 121 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 122 through 149 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 150 through 173 )B0

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