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- PDB-4rez: Crystal structure of the Middle-East respiratory syndrome coronav... -

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Basic information

Entry
Database: PDB / ID: 4rez
TitleCrystal structure of the Middle-East respiratory syndrome coronavirus papain-like protease
ComponentsORF1ab protein
KeywordsVIRAL PROTEIN / zinc ribbon / deubiquitinase / papain-like protease
Function / homology
Function and homology information


: / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host gene expression / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity ...: / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host gene expression / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / zinc ion binding / ATP binding / membrane
Similarity search - Function
Papain-like viral protease, N-terminal domain / Jelly Rolls - #1680 / Papain-like viral protease, thumb domain / RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / Nonstructural protein 14, betacoronavirus ...Papain-like viral protease, N-terminal domain / Jelly Rolls - #1680 / Papain-like viral protease, thumb domain / RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / Nonstructural protein 14, betacoronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / : / 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 (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
Similarity search - Domain/homology
S-1,2-PROPANEDIOL / ORF1ab polyprotein
Similarity search - Component
Biological speciesHuman betacoronavirus 2c Jordan-N3/2012
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsBailey-Elkin, B.A. / Johnson, G.G. / Mark, B.L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to ...Title: Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression.
Authors: Bailey-Elkin, B.A. / Knaap, R.C. / Johnson, G.G. / Dalebout, T.J. / Ninaber, D.K. / van Kasteren, P.B. / Bredenbeek, P.J. / Snijder, E.J. / Kikkert, M. / Mark, B.L.
History
DepositionSep 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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: ORF1ab protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3405
Polymers36,0461
Non-polymers2944
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.938, 137.938, 57.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein ORF1ab protein /


Mass: 36046.461 Da / Num. of mol.: 1 / Fragment: UNP residues 1480-1803
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betacoronavirus 2c Jordan-N3/2012
Gene: ORF1ab / Production host: Escherichia coli (E. coli) / References: UniProt: M4STU1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 4.4 Å3/Da / Density % sol: 72.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 18% PEG 4000, 0.1 M trisodium citrate, 16% isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.28294 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28294 Å / Relative weight: 1
ReflectionResolution: 2.6→45.15 Å / Num. all: 19517 / Num. obs: 19513 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
MxDCdata collection
SOLVEphasing
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→45.15 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 31.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 1570 10.01 %
Rwork0.2314 --
obs0.2357 15679 99.97 %
all-19517 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 16 23 2423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022449
X-RAY DIFFRACTIONf_angle_d0.6043319
X-RAY DIFFRACTIONf_dihedral_angle_d11.8845
X-RAY DIFFRACTIONf_chiral_restr0.023390
X-RAY DIFFRACTIONf_plane_restr0.003418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.89040.36411410.31281278X-RAY DIFFRACTION100
2.8904-2.99370.42651440.32121273X-RAY DIFFRACTION100
2.9937-3.11350.37421360.31051270X-RAY DIFFRACTION100
3.1135-3.25520.29441400.29491273X-RAY DIFFRACTION100
3.2552-3.42670.36981390.28331264X-RAY DIFFRACTION100
3.4267-3.64130.37431440.27951288X-RAY DIFFRACTION100
3.6413-3.92230.31461420.24311272X-RAY DIFFRACTION100
3.9223-4.31680.23251420.21791271X-RAY DIFFRACTION100
4.3168-4.94080.25051470.18851286X-RAY DIFFRACTION100
4.9408-6.22230.2231410.21731299X-RAY DIFFRACTION100
6.2223-45.15670.22251540.19321335X-RAY DIFFRACTION100

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