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- PDB-4wmd: Crystal structure of catalytically inactive MERS-CoV 3CL protease... -

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Basic information

Entry
Database: PDB / ID: 4wmd
TitleCrystal structure of catalytically inactive MERS-CoV 3CL protease (C148A) in spacegroup C2221
ComponentsORF1a
KeywordsHYDROLASE / 3CL protease / MERS / coronavirus
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / endonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification ...host cell membrane / viral genome replication / methyltransferase activity / endonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / membrane
Similarity search - Function
Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 ...Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Thrombin, subunit H / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / ORF1a
Similarity search - Component
Biological speciesMiddle East respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.585 Å
AuthorsLountos, G.T. / Needle, D. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity.
Authors: Needle, D. / Lountos, G.T. / Waugh, D.S.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF1a
B: ORF1a
C: ORF1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,01810
Polymers99,9663
Non-polymers1,0517
Water5,116284
1
A: ORF1a
B: ORF1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2016
Polymers66,6442
Non-polymers5574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-1 kcal/mol
Surface area24580 Å2
MethodPISA
2
C: ORF1a
hetero molecules

C: ORF1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6338
Polymers66,6442
Non-polymers9896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5510 Å2
ΔGint-8 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.017, 168.518, 250.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein ORF1a


Mass: 33322.109 Da / Num. of mol.: 3 / Mutation: C148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Plasmid: pDN2551 / Production host: Escherichia coli (E. coli) / References: UniProt: W6A941

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Non-polymers , 5 types, 291 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.28 Å3/Da / Density % sol: 71.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20.3 mg/mL protein, well solution: 0.1M Tris-Bis Tris pH 8.5, 0.12M ethylene glycols, 30% (v/v) ethylene glycol-polyethylene glycol 8000, (Morpheus Screeen condition E10).
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 53763 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rsym value: 0.077 / Net I/σ(I): 23.5
Reflection shellResolution: 2.58→2.62 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1448) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2YNA chain A

2yna


Resolution: 2.585→46.162 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 39.84 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 1998 3.72 %Random selection
Rwork0.1764 ---
obs0.1779 53691 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.585→46.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6908 0 70 284 7262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097163
X-RAY DIFFRACTIONf_angle_d1.1749727
X-RAY DIFFRACTIONf_dihedral_angle_d14.8592529
X-RAY DIFFRACTIONf_chiral_restr0.0441104
X-RAY DIFFRACTIONf_plane_restr0.0051239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5854-2.65010.30141310.26823387X-RAY DIFFRACTION92
2.6501-2.72170.31281410.2443665X-RAY DIFFRACTION100
2.7217-2.80180.29521420.23883659X-RAY DIFFRACTION100
2.8018-2.89220.27291430.2363702X-RAY DIFFRACTION100
2.8922-2.99560.2841430.24263677X-RAY DIFFRACTION100
2.9956-3.11550.29741440.24513714X-RAY DIFFRACTION100
3.1155-3.25730.26151410.22333667X-RAY DIFFRACTION100
3.2573-3.42890.23341430.20193690X-RAY DIFFRACTION100
3.4289-3.64370.24321410.20653671X-RAY DIFFRACTION100
3.6437-3.92490.20391460.1743738X-RAY DIFFRACTION100
3.9249-4.31960.18131440.14423722X-RAY DIFFRACTION100
4.3196-4.9440.18051440.12453743X-RAY DIFFRACTION100
4.944-6.22650.17151470.13463784X-RAY DIFFRACTION100
6.2265-46.16970.16911480.13353874X-RAY DIFFRACTION99

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