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- PDB-4ylu: X-ray structure of MERS-CoV nsp5 protease bound with a non-covale... -

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Basic information

Entry
Database: PDB / ID: 4ylu
TitleX-ray structure of MERS-CoV nsp5 protease bound with a non-covalent inhibitor
ComponentsORF1a proteinORF1ab
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / methylation / 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 / cysteine-type deubiquitinase activity ...host cell membrane / viral genome replication / methyltransferase activity / methylation / 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 / cysteine-type deubiquitinase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / membrane / identical protein binding
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 / : / 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 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / : / 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 / 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 / Trypsin-like serine proteases / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Chem-R30 / 1A polyprotein / Orf1a
Similarity search - Component
Biological speciesMiddle East respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsTomar, S. / Mesecar, A.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI08508 to ADM United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI026603 to ADM and MRD United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS.
Authors: Tomar, S. / Johnston, M.L. / St John, S.E. / Osswald, H.L. / Nyalapatla, P.R. / Paul, L.N. / Ghosh, A.K. / Denison, M.R. / Mesecar, A.D.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)135,44914
Polymers133,4174
Non-polymers2,03210
Water17,925995
1
A: ORF1a protein
B: ORF1a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7848
Polymers66,7082
Non-polymers1,0756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-19 kcal/mol
Surface area24670 Å2
MethodPISA
2
C: ORF1a protein
D: ORF1a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6656
Polymers66,7082
Non-polymers9574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-20 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.439, 114.930, 92.341
Angle α, β, γ (deg.)90.00, 90.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ORF1a protein / ORF1ab


Mass: 33354.172 Da / Num. of mol.: 4 / Fragment: residues 3248-3553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Gene: orf1ab / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: A0A0A7E693, UniProt: V9TU12*PLUS
#2: Chemical
ChemComp-R30 / N-{4-[(1H-benzotriazol-1-ylacetyl)(thiophen-3-ylmethyl)amino]phenyl}propanamide


Mass: 419.499 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H21N5O2S
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 995 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris pH-5.5, 12% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 12, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 76865 / % possible obs: 96.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 25.55 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.054 / Rrim(I) all: 0.114 / Χ2: 0.95 / Net I/σ(I): 11.17 / Num. measured all: 322955
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.144.10.5861.8337950.8440.3530.7360.81393.8
2.14-2.184.10.55538290.8720.3050.6350.80599.6
2.18-2.224.20.50438060.8750.2760.5760.81199.6
2.22-2.264.10.47638210.8870.2610.5440.80899.5
2.26-2.314.20.41637970.9220.2280.4750.82599.6
2.31-2.374.20.35438230.9320.1930.4040.82799.5
2.37-2.424.20.3338030.9410.1810.3780.82799.7
2.42-2.494.20.27137980.9580.1480.310.81999.7
2.49-2.564.20.24838320.9640.1360.2840.85199.7
2.56-2.654.20.20538310.9730.1120.2350.87399.9
2.65-2.744.30.17738510.9790.0970.2020.88999.9
2.74-2.854.30.14938300.9840.0810.170.986100
2.85-2.984.30.12838390.9860.070.1461.117100
2.98-3.144.30.10638410.990.0580.1211.117100
3.14-3.334.30.08338470.9930.0450.0951.13100
3.33-3.594.30.06838350.9950.0370.0781.158100
3.59-3.954.30.05338670.9970.0290.061.088100
3.95-4.524.20.04338400.9980.0240.0491.03499.6
4.52-5.74.20.03938790.9980.0210.0450.91999.8
5.7-504.10.04638970.9960.0250.0521.26299.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.1→42.587 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 2019 2.63 %RANDOM
Rwork0.1591 ---
obs0.1606 76623 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→42.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9220 0 144 995 10359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139781
X-RAY DIFFRACTIONf_angle_d1.28813351
X-RAY DIFFRACTIONf_dihedral_angle_d14.7453466
X-RAY DIFFRACTIONf_chiral_restr0.0531503
X-RAY DIFFRACTIONf_plane_restr0.0071713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.15270.28881350.21315003X-RAY DIFFRACTION94
2.1527-2.21090.24291380.20465337X-RAY DIFFRACTION100
2.2109-2.27590.29731470.20195309X-RAY DIFFRACTION100
2.2759-2.34940.2991450.19345339X-RAY DIFFRACTION99
2.3494-2.43330.25271410.1885327X-RAY DIFFRACTION100
2.4333-2.53080.25461480.185332X-RAY DIFFRACTION100
2.5308-2.64590.22121460.16925339X-RAY DIFFRACTION100
2.6459-2.78540.21121410.17025364X-RAY DIFFRACTION100
2.7854-2.95990.25571460.16935330X-RAY DIFFRACTION100
2.9599-3.18830.27081430.16965388X-RAY DIFFRACTION100
3.1883-3.5090.1881470.15175368X-RAY DIFFRACTION100
3.509-4.01650.21581470.13545362X-RAY DIFFRACTION100
4.0165-5.0590.14031440.11825376X-RAY DIFFRACTION100
5.059-42.59610.18321510.1525430X-RAY DIFFRACTION99

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