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- PDB-7ldx: SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fr... -

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Basic information

Entry
Database: PDB / ID: 7ldx
TitleSARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment
Components3C-like proteinase
KeywordsHYDROLASE / 3cl / protease / sars / sars-cov-2 / covid / main protease
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / G-quadruplex RNA binding / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host ISG15-protein conjugation / protein K48-linked deubiquitination / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / viral transcription / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host TRAF activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / thiol-dependent deubiquitinase / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / suppression by virus of host type I interferon-mediated signaling pathway / transcription, DNA-templated / host cell cytoplasm / protein dimerization activity / : / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, middle domain superfamily / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / RNA polymerase, N-terminal, coronavirus / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP1 superfamily, betacoronavirus / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Non-structural protein NSP1, betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3c-C domain profile. / Non-structural protein 6, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / Lipocalin signature. / Papain-like viral protease, palm and finger domains, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP8 / Coronavirus replicase NSP4, N-terminal / Coronavirus papain-like peptidase / Coronavirus endopeptidase C30 / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Coronavirus replicase NSP4, N-terminal / Peptidase C30, domain 3, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus-like / 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 NSP8 superfamily, coronavirus
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / (3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsNoske, G.D. / Nakamura, A.M. / Gawriljuk, V.O. / Lima, G.M.A. / Zeri, A.C.M. / Nascimento, A.F.Z. / Oliva, G. / Godoy, A.S.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/07600-3 Brazil
CitationJournal: J.Mol.Biol. / Year: 2021
Title: A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process.
Authors: Noske, G.D. / Nakamura, A.M. / Gawriljuk, V.O. / Fernandes, R.S. / Lima, G.M.A. / Rosa, H.V.D. / Pereira, H.D. / Zeri, A.C.M. / Nascimento, A.F.Z. / Freire, M.C.L.C. / Fearon, D. / ...Authors: Noske, G.D. / Nakamura, A.M. / Gawriljuk, V.O. / Fernandes, R.S. / Lima, G.M.A. / Rosa, H.V.D. / Pereira, H.D. / Zeri, A.C.M. / Nascimento, A.F.Z. / Freire, M.C.L.C. / Fearon, D. / Douangamath, A. / von Delft, F. / Oliva, G. / Godoy, A.S.
History
DepositionJan 14, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJan 20, 2021ID: 7KW5
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 28, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,39213
Polymers68,1702
Non-polymers1,22211
Water2,360131
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint11 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.389, 101.679, 101.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 34084.871 Da / Num. of mol.: 2 / Fragment: UNP residues 3264-3569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-R9V / (3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol


Mass: 217.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M MES, pH 6.7, 5% DMSO, 8% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRUS / Beamline: MANACA / Wavelength: 1.35502 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 3, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.35502 Å / Relative weight: 1
ReflectionResolution: 2.23→56.21 Å / Num. obs: 21562 / % possible obs: 61.5 % / Redundancy: 1.9 % / CC1/2: 0.649 / Rmerge(I) obs: 0.318 / Rpim(I) all: 0.318 / Rrim(I) all: 0.449 / Net I/σ(I): 5.1 / Num. measured all: 40531
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.23-2.31.90.6643922110.2670.6640.9391.36.4
8.92-56.211.60.08810286240.8980.0880.12411.999.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7KFI
Resolution: 2.23→56.21 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 1992 9.26 %
Rwork0.2417 19518 -
obs0.2446 21510 61.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.66 Å2 / Biso mean: 29.1637 Å2 / Biso min: 6.27 Å2
Refinement stepCycle: final / Resolution: 2.23→56.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4657 0 77 132 4866
Biso mean--45.08 23.86 -
Num. residues----603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.290.3007110.35661111225
2.29-2.350.3346360.325235639216
2.35-2.420.3577550.323256061525
2.42-2.50.3835730.330372079332
2.5-2.580.376880.294781089837
2.58-2.690.34951080.30231072118048
2.69-2.810.31881350.29371367150261
2.81-2.960.29561590.2831580173971
2.96-3.140.30781840.26681819200381
3.14-3.390.29212100.25452021223189
3.39-3.730.25892250.23622165239097
3.73-4.270.24332270.21782241246898
4.27-5.380.24562350.19262287252299
5.38-56.210.22442460.21492409265599
Refinement TLS params.Method: refined / Origin x: -1.8918 Å / Origin y: -3.4803 Å / Origin z: 16.4708 Å
111213212223313233
T0.0291 Å2-0.0093 Å2-0.0021 Å2-0.0839 Å2-0.057 Å2--0.0304 Å2
L0.5479 °20.2686 °2-0.0539 °2-0.2653 °2-0.1707 °2--0.8086 °2
S0.0141 Å °-0.0622 Å °-0.0343 Å °-0.0485 Å °-0.0165 Å °-0.07 Å °0.0189 Å °0.0402 Å °-0.0122 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 301
2X-RAY DIFFRACTION1allA501 - 701
3X-RAY DIFFRACTION1allB2 - 300
4X-RAY DIFFRACTION1allB403 - 601

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