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- PDB-4dcd: 1.6A resolution structure of PolioVirus 3C Protease Containing a ... -

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Basic information

Entry
Database: PDB / ID: 4dcd
Title1.6A resolution structure of PolioVirus 3C Protease Containing a covalently bound dipeptidyl inhibitor
ComponentsGenome polyprotein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / POLIOVIRUS / ANTIVIRAL INHIBITORS / DIPEPTIDYL INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / 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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-K36 / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 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
DepositionJan 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3May 20, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_conn / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4395
Polymers20,6071
Non-polymers8324
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.083, 58.607, 107.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Genome polyprotein / Protease 3C


Mass: 20607.389 Da / Num. of mol.: 1 / Fragment: unp residues 1566-1748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Strain: Mahoney / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03300, picornain 3C
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-K36 / (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid / GC376 / GC376


Type: peptide-like / Mass: 485.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H31N3O8S / Comment: medication, antivirus*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsWHEN THE K36 LIGAND IS MIXED WITH THE POLIOVIRUS PROTEASE, IT FORMS A COVALENT COMPLEX WITH A ...WHEN THE K36 LIGAND IS MIXED WITH THE POLIOVIRUS PROTEASE, IT FORMS A COVALENT COMPLEX WITH A LINKAGE BETWEEN C21 OF THE LIGAND AND THE SULFUR ATOM (SG) OF CYS147. THE BISULFITE FUNCTIONAL GROUP IS REMOVED DURING THIS REACTION.

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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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (w/v) PEG 5000 MME, 100 mM MES, 200 mM ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→53.995 Å / Num. all: 23731 / Num. obs: 23731 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.049
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3442 / Rsym value: 0.536 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å51.51 Å
Translation2.5 Å51.51 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.3.0phasing
PHENIXdev_892refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1L1N

1l1n


Resolution: 1.69→40.52 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.2 / Phase error: 18.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 2228 5.11 %RANDOM
Rwork0.1658 ---
obs0.167 23726 95.97 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.299 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 58.71 Å2 / Biso mean: 22.6886 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1--3.844 Å2-0 Å20 Å2
2---3.0155 Å20 Å2
3---6.8595 Å2
Refinement stepCycle: LAST / Resolution: 1.69→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1370 0 43 130 1543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091455
X-RAY DIFFRACTIONf_angle_d1.3081977
X-RAY DIFFRACTIONf_chiral_restr0.109228
X-RAY DIFFRACTIONf_plane_restr0.006255
X-RAY DIFFRACTIONf_dihedral_angle_d17.402519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63480.31311420.2822592273498
1.6348-1.67280.28961400.27092636277698
1.6728-1.71470.29771450.27052544268995
1.7147-1.7610.24951240.2352656278097
1.761-1.81290.23371270.20412572269995
1.8129-1.87140.24581250.19182672279798
1.8714-1.93830.22161450.18072626277198
1.9383-2.01590.22621480.15822638278698
2.0159-2.10760.19881400.15092558269896
2.1076-2.21870.17551540.15092520267494
2.2187-2.35770.15461630.14292514267795
2.3577-2.53970.13891370.14262648278598
2.5397-2.79530.18641390.15572590272996
2.7953-3.19960.17761400.16172432257291
3.1996-4.03060.17521280.15082564269295
4.0306-40.53260.16711310.15732582271395
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)
11.34950.19840.22821.49590.40070.96440.0143-0.01090.1057-0.00080.0222-0.2397-0.05980.1501-0.04340.1239-0.02280.0020.12910.00650.137813.820711.962113.517
22.5102-1.36480.80513.51130.47451.6887-0.07830.57130.5097-0.34040.0449-0.4039-0.11220.2957-0.00820.2079-0.06350.04690.21380.05030.168213.962316.04063.2898
32.8572-1.156-0.68545.31150.49431.18620.0109-0.01390.14010.1208-0.05640.0116-0.13280.0120.04790.0983-0.0064-0.030.0933-0.00220.03182.690110.315215.6921
42.46590.3879-0.25654.4651.31045.3431-0.0716-0.15170.33890.2334-0.05780.2596-0.0404-0.04550.09150.092-0.0084-0.02260.1025-0.02180.0959-1.442210.82320.3482
52.8033-0.86060.34383.4094-0.30062.65950.0354-0.23890.20520.1805-0.0311-0.0932-0.10970.0530.00130.1304-0.021-0.01510.1417-0.0160.10295.42512.773227.168
62.1173-0.12630.97344.5967-1.82163.9219-0.03830.00750.140.0501-0.0333-0.0755-0.3116-0.04740.03750.12750.00360.00050.1021-0.02590.11484.463215.995318.1982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq -3:77)A-3 - 77
2X-RAY DIFFRACTION2chain 'A' and (resseq 78:89)A78 - 89
3X-RAY DIFFRACTION3chain 'A' and (resseq 90:111)A90 - 111
4X-RAY DIFFRACTION4chain 'A' and (resseq 112:123)A112 - 123
5X-RAY DIFFRACTION5chain 'A' and (resseq 124:149)A124 - 149
6X-RAY DIFFRACTION6chain 'A' and (resseq 150:180)A150 - 180

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