[English] 日本語
Yorodumi
- PDB-9eus: Mpro from SARS-CoV-2 with R298A mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eus
TitleMpro from SARS-CoV-2 with R298A mutation
ComponentsReplicase polyprotein 1a
KeywordsVIRAL PROTEIN / SARS-CoV-2 / main protease / oligomerization
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / 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 / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification ...host cell membrane / viral genome replication / methyltransferase activity / 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 / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / 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 / : ...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 / : / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPlewka, J. / Lis, K. / Czarna, A. / Pyrc, K. / Kantyka, T. / Chykunova, Y.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2017/27/B/NZ6/02488 Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: SARS-CoV-2 M pro oligomerization as a potential target for therapy.
Authors: Lis, K. / Plewka, J. / Menezes, F. / Bielecka, E. / Chykunova, Y. / Pustelny, K. / Niebling, S. / Garcia, A.S. / Garcia-Alai, M. / Popowicz, G.M. / Czarna, A. / Kantyka, T. / Pyrc, K.
History
DepositionMar 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Replicase polyprotein 1a
B: Replicase polyprotein 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9425
Polymers66,6662
Non-polymers2763
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-15 kcal/mol
Surface area25730 Å2
Unit cell
Length a, b, c (Å)44.825, 53.392, 114.514
Angle α, β, γ (deg.)90, 101.046, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 302 / Label seq-ID: 2 - 302

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Replicase polyprotein 1a / ORF1a polyprotein


Mass: 33333.004 Da / Num. of mol.: 2 / Mutation: R298A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8B6REU6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.18 mM benzamidine hydrochloride, 200 mM potassium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03323 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 2→48.23 Å / Num. obs: 245946 / % possible obs: 97.7 % / Redundancy: 7 % / CC1/2: 0.994 / Net I/σ(I): 6
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 17804 / CC1/2: 0.579

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.227 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.741 / SU ML: 0.199 / Cross valid method: FREE R-VALUE / ESU R: 0.264 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2773 1739 4.93 %
Rwork0.2279 33536 -
all0.23 --
obs-35275 97.404 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.615 Å2
Baniso -1Baniso -2Baniso -3
1--1.888 Å20 Å2-0.71 Å2
2---0.925 Å2-0 Å2
3---2.872 Å2
Refinement stepCycle: LAST / Resolution: 2→48.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 18 26 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124777
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164435
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.86491
X-RAY DIFFRACTIONr_angle_other_deg0.691.73210191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0585603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.56520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00410757
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.06710214
X-RAY DIFFRACTIONr_chiral_restr0.0820.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025663
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021125
X-RAY DIFFRACTIONr_nbd_refined0.1880.2843
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1560.24038
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22319
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3060.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0980.218
X-RAY DIFFRACTIONr_nbd_other0.1230.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.25
X-RAY DIFFRACTIONr_mcbond_it3.1993.762418
X-RAY DIFFRACTIONr_mcbond_other3.1953.762418
X-RAY DIFFRACTIONr_mcangle_it4.7036.773019
X-RAY DIFFRACTIONr_mcangle_other4.7036.773020
X-RAY DIFFRACTIONr_scbond_it3.7854.1512359
X-RAY DIFFRACTIONr_scbond_other3.7844.1512360
X-RAY DIFFRACTIONr_scangle_it5.7647.4663472
X-RAY DIFFRACTIONr_scangle_other5.7637.4673473
X-RAY DIFFRACTIONr_lrange_it7.6238.775036
X-RAY DIFFRACTIONr_lrange_other7.62238.7715037
X-RAY DIFFRACTIONr_ncsr_local_group_10.0830.059372
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.082710.05009
12AX-RAY DIFFRACTIONLocal ncs0.082710.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3761460.3824780.3826940.8910.88797.40160.361
2.052-2.1080.3591280.34723930.34725690.9040.91198.13160.326
2.108-2.1690.3141450.31822970.31824990.9220.92797.71910.3
2.169-2.2360.2931160.28322960.28424690.9180.94197.69140.261
2.236-2.3090.3331190.27521880.27823570.9220.94497.87870.252
2.309-2.390.3261010.27221010.27522810.9370.94796.53660.253
2.39-2.480.305880.25219280.25422570.9330.95889.32210.231
2.48-2.5810.2951050.23819800.24121120.9420.96298.72160.221
2.581-2.6950.295980.23619240.23920440.950.96598.92370.221
2.695-2.8260.255840.24618540.24619610.9610.96598.82710.235
2.826-2.9780.35810.22617660.23118690.9190.9798.82290.219
2.978-3.1580.243880.21316660.21517680.9640.97399.20810.212
3.158-3.3750.288660.21315780.21616600.9490.97399.03610.219
3.375-3.6440.252880.19814450.20115530.9650.97698.71220.213
3.644-3.990.243710.19313390.19514350.9510.97998.25780.215
3.99-4.4570.222690.17111910.17313120.9710.98496.03660.203
4.457-5.1390.221530.199790.19111410.9790.98390.4470.231
5.139-6.2760.264430.29490.2039930.9610.98499.89930.253
6.276-8.8020.263320.1957560.1987880.9810.9841000.249
8.802-48.2270.283180.2024280.2054510.9680.98698.89140.26

+
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://pdbjlvh1.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