[English] 日本語
Yorodumi
- PDB-7vk6: Crystal Structure of SARS-CoV-2 Mpro at 2.25 A resolution-13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vk6
TitleCrystal Structure of SARS-CoV-2 Mpro at 2.25 A resolution-13
Components3C-like proteinase
KeywordsVIRAL PROTEIN / SARS-CoV-2 / main protease / SFX
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / methylation / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane
Similarity search - Function
Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. ...Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / 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 / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) 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, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto 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. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, 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 / Papain-like protease, thumb domain 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDeMirci, H. / Yuksel, B.
Funding support United States, Turkey, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-1231306 United States
Other government118C270 Turkey
CitationJournal: Crystals / Year: 2021
Title: Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Authors: Guven, O. / Gul, M. / Ayan, E. / Johnson, J.A. / Cakilkaya, B. / Usta, G. / Ertem, F.B. / Tokay, N. / Yuksel, B. / Gocenler, O. / Buyukdag, C. / Botha, S. / Ketawala, G. / Su, Z. / Hayes, B. ...Authors: Guven, O. / Gul, M. / Ayan, E. / Johnson, J.A. / Cakilkaya, B. / Usta, G. / Ertem, F.B. / Tokay, N. / Yuksel, B. / Gocenler, O. / Buyukdag, C. / Botha, S. / Ketawala, G. / Su, Z. / Hayes, B. / Poitevin, F. / Batyuk, A. / Yoon, C.H. / Kupitz, C. / Durdagi, S. / Sierra, R.G. / DeMirci, H.
History
DepositionSep 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,6512
Polymers67,6512
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-11 kcal/mol
Surface area26950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.300, 105.500, 69.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 3C-like proteinase / main protease


Mass: 33825.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 294 K / Method: batch mode / pH: 8.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Tris 8.5, 30% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 294 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.25 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Aug 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 2.2→41.93 Å / Num. obs: 39491 / % possible obs: 100 % / Redundancy: 1 % / Biso Wilson estimate: 26.18 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
2.2-2.27133770.9931100
2.25-16.8116540.993199.1

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CWC

7cwc


Resolution: 2.25→16.82 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 833 2.27 %
Rwork0.2329 35935 -
obs0.2336 36768 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.07 Å2 / Biso mean: 60.3596 Å2 / Biso min: 25.97 Å2
Refinement stepCycle: final / Resolution: 2.25→16.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 0 103 4745
Biso mean---56.41 -
Num. residues----599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.25-2.390.3841390.367159026041
2.39-2.570.42341340.383759106044
2.57-2.830.33631340.302159196053
2.83-3.240.28071410.245759646105
3.24-4.070.22581380.201260376175
4.07-16.820.21471470.175162036350
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0298-1.11560.98413.1207-2.05392.2517-0.1842-0.18010.06180.15250.0095-0.04580.09780.19940.18020.3934-0.0372-0.00320.33910.01340.2974-8.1721-19.1218.193
20.714-1.0251.21569.7963-3.72332.0481-0.1901-0.20820.22240.98220.1473-0.5089-0.50860.01070.28710.6316-0.00470.01690.484-0.01470.373-3.2054-28.757734.3527
31.5314-0.84460.18653.0833-0.09994.6238-0.0713-0.27240.03120.6815-0.07870.0798-0.25930.0760.14810.3467-0.04620.04120.3225-0.03420.3461-12.5114-20.938221.3624
43.5720.9458-2.40985.16643.45326.41410.34890.02280.4362-0.2264-0.2474-0.2635-0.02720.2851-0.28810.42550.0284-0.00650.37180.01670.3756-5.848-23.66459.5888
50.18760.91780.4171.3550.14014.906-0.02050.4150.0022-0.19780.055-0.4330.66320.2233-0.13240.43290.05740.0450.3892-0.02820.3034-4.3932-32.947514.3359
64.8526-0.1377-2.28364.11451.36086.61160.1870.2884-0.06550.0782-0.08480.1044-0.1024-0.4608-0.12370.43020.0056-0.02130.4506-0.08080.2636-9.5579-37.0656-14.6922
79.42934.3688-5.2984.6692-3.0989.146-0.0812-0.62950.0687-0.2253-0.06810.0038-1.05660.02450.1710.5366-0.0553-0.13640.337-0.07920.2703-6.2782-26.0564-10.3991
81.79820.6172-0.85083.803-2.123.2254-0.1650.5312-0.1311-0.06730.13440.2564-0.0001-0.42180.02430.21270.0020.01490.34620.03950.3002-11.4295-0.6415-0.6725
95.8317-0.1345-2.57587.1542-2.55963.61830.14721.4040.7559-1.65330.2530.86250.3909-0.4929-0.07770.6510.0886-0.22850.99120.17980.6559-17.767810.3499-14.7702
101.8588-1.2344-1.38215.6018-0.1283.4646-0.04630.2057-0.0197-0.15880.09180.3850.0425-0.0790.10350.2072-0.0608-0.02440.3316-0.01510.3236-9.23534.45290.7199
116.1657-2.8298-5.12896.7265-0.02685.9884-0.54970.0553-0.27060.04320.36510.34720.1816-0.53470.02810.29170.0822-0.00510.36440.09190.3432-3.1029-7.2175-3.1076
123.5785-0.0846-0.98494.1448-0.34845.95910.25470.6966-0.2646-0.59620.03320.24370.56350.1252-0.22670.39320.08930.03770.3952-0.00730.2677-1.2986-1.4259-11.7368
139.1355-7.15550.98176.24771.06584.70480.0932-0.01021.199-0.3667-0.2019-1.4258-0.34740.24420.0440.39480.04690.08960.41190.08170.59222.3777-17.1892-3.8023
143.6887-4.2878-0.09534.87541.3853.334-0.4707-0.2161-1.69710.87010.23181.93040.6107-1.14060.08920.63110.07880.00450.6680.0410.966211.4551-20.1891-0.2318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )A1 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 70 )A44 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 120 )A71 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 155 )A121 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 200 )A156 - 200
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 274 )A201 - 274
7X-RAY DIFFRACTION7chain 'A' and (resid 275 through 300 )A275 - 300
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 43 )B3 - 43
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 70 )B44 - 70
10X-RAY DIFFRACTION10chain 'B' and (resid 71 through 120 )B71 - 120
11X-RAY DIFFRACTION11chain 'B' and (resid 121 through 155 )B121 - 155
12X-RAY DIFFRACTION12chain 'B' and (resid 156 through 200 )B156 - 200
13X-RAY DIFFRACTION13chain 'B' and (resid 201 through 274 )B201 - 274
14X-RAY DIFFRACTION14chain 'B' and (resid 275 through 301 )B275 - 301

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more