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- PDB-4rna: Crystal structure of PLpro from Middle East Respiratory Syndrome ... -

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Basic information

Entry
Database: PDB / ID: 4rna
TitleCrystal structure of PLpro from Middle East Respiratory Syndrome (MERS) coronavirus
Componentspapain-like protease
KeywordsHYDROLASE / MERS / coronavirus / papain-like protease / PLpro
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / membrane
Similarity search - Function
Papain-like viral protease, N-terminal domain / Jelly Rolls - #1680 / Papain-like viral protease, thumb domain / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus ...Papain-like viral protease, N-terminal domain / Jelly Rolls - #1680 / Papain-like viral protease, thumb domain / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Peptidase S1, PA clan / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / ORF1a
Similarity search - Component
Biological speciesHuman betacoronavirus 2c EMC/2012
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å
AuthorsLei, H. / Santarsiero, B.D. / Lee, H. / Johnson, M.E.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Inhibitor Recognition Specificity of MERS-CoV Papain-like Protease May Differ from That of SARS-CoV.
Authors: Lee, H. / Lei, H. / Santarsiero, B.D. / Gatuz, J.L. / Cao, S. / Rice, A.J. / Patel, K. / Szypulinski, M.Z. / Ojeda, I. / Ghosh, A.K. / Johnson, M.E.
History
DepositionOct 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: papain-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4976
Polymers36,0511
Non-polymers4455
Water3,675204
1
A: papain-like protease
hetero molecules

A: papain-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,99412
Polymers72,1032
Non-polymers89110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5590 Å2
ΔGint-84 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.899, 48.780, 87.464
Angle α, β, γ (deg.)90.00, 121.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein papain-like protease


Mass: 36051.457 Da / Num. of mol.: 1 / Fragment: UNP residues 1482-1803
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betacoronavirus 2c EMC/2012 / Gene: orf1ab / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 star
References: UniProt: K4LC41, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.056 M sodium phosphate monobasic monohydrate, 1.344 M potassium phosphate, pH 8.0, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.794→19.731 Å / Num. all: 33609 / Num. obs: 33172 / % possible obs: 98.7 % / Observed criterion σ(I): 1.27 / Redundancy: 5 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 6.714
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.794-1.894.81.3480.6194.1
1.89-2.0150.8370.71100
2.01-2.145.10.4391.71100
2.14-2.325.10.272.71100
2.32-2.545.10.1654.41100
2.54-2.845.10.1027.11100
2.84-3.285.10.06510.11100
3.28-4.015.10.04812.51100
4.01-5.6750.04115.51100
5.67-19.7314.80.04115.3197.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PT5

4pt5


Resolution: 1.794→19.731 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.127 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 1681 5.1 %RANDOM
Rwork0.18853 ---
obs0.1912 31482 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.631 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å2-1.67 Å2
2--3.51 Å20 Å2
3----2.71 Å2
Refinement stepCycle: LAST / Resolution: 1.794→19.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 21 204 2729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022590
X-RAY DIFFRACTIONr_angle_refined_deg2.2091.9613520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49823.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16715440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9391514
X-RAY DIFFRACTIONr_chiral_restr0.1360.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211914
LS refinement shellResolution: 1.794→1.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 108 -
Rwork0.407 1955 -
obs--86.72 %

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