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- PDB-6m03: The crystal structure of COVID-19 main protease in apo form -

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Entry
Database: PDB / ID: 6m03
TitleThe crystal structure of COVID-19 main protease in apo form
Components3C-like proteinase
KeywordsBIOSYNTHETIC PROTEIN / Coronavirus / COVID-19 / viral protease
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / Transcription of SARS-CoV-2 sgRNAs / 5'-3' RNA helicase activity / mRNA cap binding complex / Lyases; Phosphorus-oxygen lyases / Translation of Replicase and Assembly of the Replication Transcription Complex / positive regulation of RNA biosynthetic process / Replication of the SARS-CoV-2 genome / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific peptidase activity / SARS coronavirus main proteinase / suppression by virus of host type I interferon production / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endosome / induction by virus of catabolism of host mRNA / host cell endoplasmic reticulum-Golgi intermediate compartment / cytoplasmic viral factory / protein K48-linked deubiquitination / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / 7-methylguanosine mRNA capping / viral transcription / RNA-templated transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell endoplasmic reticulum / suppression by virus of host toll-like receptor signaling pathway / host cell Golgi apparatus / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive stranded viral RNA replication / positive regulation of viral genome replication / suppression by virus of host TRAF-mediated signal transduction => GO:0039527 / helicase activity / protein autoprocessing / cysteine-type peptidase activity / ubiquitinyl hydrolase 1 / DNA helicase / cysteine-type deubiquitinase activity / DNA helicase activity / single-stranded RNA binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / integral to membrane of host cell / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / host cell cytoplasm / DNA-templated transcription / protein dimerization activity / suppression by virus of host type I interferon-mediated signaling pathway / host cell nucleus / ATP hydrolysis activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 14, betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 14, betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Viral (Superfamily 1) RNA helicase / Coronavirus replicase NSP15, N-terminal oligomerization / Non-structural protein NSP16, coronavirus-like / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Non-structural protein 14, coronavirus / Nonstructural protein 15, middle domain, coronavirus / Non-structural protein NSP15, middle domain superfamily / RNA polymerase, N-terminal, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Coronaviridae zinc-binding (CV ZBD) domain profile. / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus SUD-C domain / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / NSP1 globular domain superfamily, betacoronavirus / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Carbamoyl-phosphate synthase subdomain signature 2. / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Lipocalin signature. / : / : / : / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-M domain profile. / : / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Betacoronavirus replicase NSP1 / 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. / Non-structural protein NSP3, SUD-M domain, betacoronavirus / 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 NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / 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. / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / 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 / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus endopeptidase C30 / RNA synthesis protein NSP10, coronavirus / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus papain-like peptidase
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, B. / Zhao, Y. / Jin, Z. / Liu, X. / Yang, H. / Rao, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of Sciences2017YFC0840300 China
National Natural Science Foundation of China (NSFC)81520108019 China
CitationJournal: To be published
Title: The crystal structure of COVID-19 main protease in apo form
Authors: Zhang, B. / Zhao, Y. / Jin, Z. / Liu, X. / Yang, H. / Rao, Z.
History
DepositionFeb 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_ec / _entity_src_gen.gene_src_common_name ..._entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Jun 10, 2020Group: Database references / Structure summary / Category: entity / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.3Mar 10, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase


Theoretical massNumber of molelcules
Total (without water)33,8261
Polymers33,8261
Non-polymers00
Water1,56787
1
A: 3C-like proteinase

A: 3C-like proteinase


Theoretical massNumber of molelcules
Total (without water)67,6512
Polymers67,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3100 Å2
ΔGint-19 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.964, 53.450, 45.029
Angle α, β, γ (deg.)90.000, 101.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-471-

HOH

21A-475-

HOH

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Components

#1: Protein 3C-like proteinase / pp1a / ORF1a polyprotein / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 ...pp1a / ORF1a polyprotein / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.1
Details: 10% polyethylene glycol (PEG) 3000, 0.2M LiSO4, 1mM DTT, 0.1M imidazole buffer (pH 8.1), protein concentration 5mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→38.648 Å / Num. obs: 35505 / % possible obs: 99.5 % / Redundancy: 3.47 % / Biso Wilson estimate: 41.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.046 / Χ2: 1.104 / Net I/σ(I): 16.29 / Num. measured all: 123190 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.043.4830.6251.8725890.7520.73997.8
2.04-2.13.5430.4582.5625480.8280.54299.8
2.1-2.163.5150.3563.324900.870.42199.8
2.16-2.233.4570.2943.9824440.9220.34997.8
2.23-2.33.2840.225.1923030.9520.26399.7
2.3-2.383.4790.1866.1723160.9710.22100
2.38-2.473.5950.1527.9921900.9750.17999.5
2.47-2.573.550.11710.0621070.9840.138100
2.57-2.683.4570.09811.9520480.9880.11799.6
2.68-2.813.30.07514.6119510.9940.08999.7
2.81-2.973.4940.05619.5317950.9960.06699.3
2.97-3.153.5740.04525.0317640.9970.05399.3
3.15-3.363.5240.03729.1516160.9980.04499.9
3.36-3.633.3310.0334.3315100.9980.03699.7
3.63-3.983.4870.02640.0113970.9990.0399.1
3.98-4.453.5920.02444.212830.9990.028100.2
4.45-5.143.40.02344.210920.9990.02799.4
5.14-6.293.3680.02342.349530.9990.02898.2
6.29-8.93.4590.02145.777260.9990.02599.6
8.9-38.6483.2430.01948.013830.9990.02396

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LU7
Resolution: 2→38.648 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 3494 9.97 %
Rwork0.1962 31552 -
obs0.2011 35046 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.54 Å2 / Biso mean: 52.3756 Å2 / Biso min: 26.05 Å2
Refinement stepCycle: final / Resolution: 2→38.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 0 87 2454
Biso mean---54.88 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032420
X-RAY DIFFRACTIONf_angle_d0.5953289
X-RAY DIFFRACTIONf_chiral_restr0.042371
X-RAY DIFFRACTIONf_plane_restr0.004428
X-RAY DIFFRACTIONf_dihedral_angle_d8.7481424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02740.38311420.32781261100
2.0274-2.05640.28021430.28021291100
2.0564-2.08710.3241410.27121230100
2.0871-2.11970.31121390.27041261100
2.1197-2.15450.31821410.28421253100
2.1545-2.19160.31971420.2721285100
2.1916-2.23150.33951370.26221266100
2.2315-2.27440.29651430.26511261100
2.2744-2.32080.30221370.26081274100
2.3208-2.37120.30741350.25721240100
2.3712-2.42640.30081440.25161286100
2.4264-2.48710.40051340.24891250100
2.4871-2.55430.28251420.24561272100
2.5543-2.62940.33431380.22741260100
2.6294-2.71430.35511450.25391277100
2.7143-2.81130.27021430.24051263100
2.8113-2.92380.24321390.2284123799
2.9238-3.05680.24031410.21651276100
3.0568-3.21790.32521430.2231263100
3.2179-3.41940.24241360.19981221100
3.4194-3.68320.20061350.17421302100
3.6832-4.05350.20921410.16271246100
4.0535-4.63920.18291350.1445125699
4.6392-5.84170.22021400.1667127999
5.8417-38.6480.18131380.1369124299
Refinement TLS params.Method: refined / Origin x: 12.2137 Å / Origin y: -11.5109 Å / Origin z: 4.7846 Å
111213212223313233
T0.2353 Å2-0.0257 Å20.0376 Å2-0.2997 Å20.0322 Å2--0.2903 Å2
L2.0897 °2-0.2354 °21.0786 °2-1.9549 °2-0.8848 °2--2.7591 °2
S0.0433 Å °0.0264 Å °0.1604 Å °-0.0642 Å °-0.1258 Å °-0.0541 Å °0.1419 Å °0.0675 Å °0.0541 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 306
2X-RAY DIFFRACTION1allS1 - 87

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