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- PDB-4xbc: 1.60 A resolution structure of Norovirus 3CL protease complex wit... -

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Basic information

Entry
Database: PDB / ID: 4xbc
Title1.60 A 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 (Hexagonal 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 Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity ...calicivirin / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / extracellular region / ATP binding / membrane / metal ion 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 / 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: 1.6 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_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_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-LIKE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8463
Polymers20,1261
Non-polymers7202
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint3 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.853, 121.853, 51.498
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-202-

PG4

21A-376-

HOH

31A-378-

HOH

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Components

#1: Protein 3C-LIKE PROTEASE


Mass: 20126.131 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C24H35N3O8S
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20% (w/v) PEG3350, 200 mM ammonium citrate

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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: 1.6→46.28 Å / Num. obs: 30219 / % possible obs: 100 % / Redundancy: 19.2 % / Biso Wilson estimate: 15.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.166 / Net I/σ(I): 16.3 / Num. measured all: 579016
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2% possible all
1.6-1.6316.91.69222478714710.711100
8.76-46.28150.04353.335442360.99999.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.14 Å46.28 Å
Translation3.14 Å46.28 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→36.854 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.73 / Phase error: 15.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 1530 5.07 %RANDOM
Rwork0.1634 28660 --
obs0.1639 30190 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.47 Å2 / Biso mean: 17.1933 Å2 / Biso min: 4.73 Å2
Refinement stepCycle: final / Resolution: 1.6→36.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 49 160 1492
Biso mean--20.14 28.97 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091409
X-RAY DIFFRACTIONf_angle_d1.2341919
X-RAY DIFFRACTIONf_chiral_restr0.083218
X-RAY DIFFRACTIONf_plane_restr0.007241
X-RAY DIFFRACTIONf_dihedral_angle_d15.611525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.65170.25731360.248325512687
1.6517-1.71070.23291210.218225772698
1.7107-1.77920.20121330.198125612694
1.7792-1.86020.20691480.170825432691
1.8602-1.95830.17431530.15525462699
1.9583-2.08090.17151560.152325672723
2.0809-2.24160.16331250.144826062731
2.2416-2.46710.15441310.14426122743
2.4671-2.8240.17331480.163226142762
2.824-3.55750.18711440.159726562800
3.5575-36.86380.14971350.16128272962
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)
15.60970.55741.11213.76391.0673.4874-0.0523-0.1155-0.24570.11090.06130.15090.1315-0.1243-0.02890.0790.03720.01340.0627-00.062831.102824.9424-2.9557
22.62440.33890.82481.29070.51732.43630.0190.03540.05220.00820.0464-0.0975-0.02710.159-0.06030.06480.01360.00940.0605-0.0090.062335.157735.6479-2.6755
35.43181.98891.07772.4215-2.97926.93610.0290.0831-0.0397-0.04770.01-0.482-0.19150.8518-0.06980.0955-0.01390.00690.1911-0.0190.223644.789841.493-7.3167
43.4929-0.1855-3.08462.4122-0.59148.00590.14440.11170.3388-0.01450.13090.0257-0.31470.0094-0.26580.1298-0.01090.0130.06980.00340.134234.816544.1855-5.3926
51.3437-0.2326-0.43151.35740.18162.1626-0.0154-0.0060.02320.03220.03440.0086-0.0182-0.128-0.01180.0865-0.0096-0.01410.0736-0.01660.0828.828330.2706-1.3822
61.1825-0.5261-0.60186.18551.85411.70130.032-0.0710.00770.2078-0.07080.14950.08530.05590.02530.11080.0190.01860.10610.01270.040427.660134.557712.5279
72.97471.5972-0.93994.8087-0.92052.96880.1589-0.22920.16980.3352-0.2851-0.2867-0.16850.33240.11550.0950.00570.00580.1744-0.00320.09428.210639.022913.2081
83.71672.0208-0.82932.32811.02412.0610.1027-0.2991-0.32070.3624-0.1134-0.06560.20560.24060.01180.14770.0369-0.01170.11350.00450.114835.536728.718710.4829
93.04681.11011.53522.50151.21634.40090.0009-0.1361-0.10660.08850.07590.17650.0302-0.1629-0.080.04990.02420.01310.07250.00710.087826.022131.32326.6371
108.7535-0.1196-6.42741.48550.37984.7770.25750.3930.6004-0.155-0.04770.1069-0.445-0.6759-0.22570.20140.0535-0.00960.2139-0.00020.172618.845645.86297.5886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 12 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 31 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 43 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 60 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 61 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 141 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 142 through 170 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 171 through 181 )A0

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