[English] 日本語
Yorodumi
- PDB-7ene: Crystal structure of MERS-CoV 3CLpro in complex with the non-cova... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ene
TitleCrystal structure of MERS-CoV 3CLpro in complex with the non-covalent inhibitor WU-04
ComponentsORF1a protein
KeywordsVIRAL PROTEIN / Non-covalent / Inhibitor / 3CLpro / Coronavirus
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / endonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification ...host cell membrane / viral genome replication / methyltransferase activity / endonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / membrane
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 / Trypsin-like serine proteases / 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 ...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 / Trypsin-like serine proteases / 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 / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / 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 / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / 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. / Coronavirus main protease (M-pro) 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 replicase NSP9 / Thrombin, subunit H / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-J7R / 1A polyprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsHou, N. / Peng, C. / Hu, Q.
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro.
Authors: Hou, N. / Shuai, L. / Zhang, L. / Xie, X. / Tang, K. / Zhu, Y. / Yu, Y. / Zhang, W. / Tan, Q. / Zhong, G. / Wen, Z. / Wang, C. / He, X. / Huo, H. / Gao, H. / Xu, Y. / Xue, J. / Peng, C. / ...Authors: Hou, N. / Shuai, L. / Zhang, L. / Xie, X. / Tang, K. / Zhu, Y. / Yu, Y. / Zhang, W. / Tan, Q. / Zhong, G. / Wen, Z. / Wang, C. / He, X. / Huo, H. / Gao, H. / Xu, Y. / Xue, J. / Peng, C. / Zou, J. / Schindewolf, C. / Menachery, V. / Su, W. / Yuan, Y. / Shen, Z. / Zhang, R. / Yuan, S. / Yu, H. / Shi, P.Y. / Bu, Z. / Huang, J. / Hu, Q.
History
DepositionApr 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.3Nov 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: ORF1a protein
B: ORF1a protein
C: ORF1a protein
D: ORF1a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5228
Polymers133,4174
Non-polymers2,1064
Water00
1
A: ORF1a protein
B: ORF1a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7614
Polymers66,7082
Non-polymers1,0532
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-19 kcal/mol
Surface area24710 Å2
MethodPISA
2
C: ORF1a protein
D: ORF1a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7614
Polymers66,7082
Non-polymers1,0532
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-18 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.755, 112.952, 92.355
Angle α, β, γ (deg.)90.000, 91.316, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
ORF1a protein


Mass: 33354.172 Da / Num. of mol.: 4 / Fragment: UNP residues 3248-3553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Gene: orf1ab / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7E693
#2: Chemical
ChemComp-J7R / ~{N}-[(1~{S},2~{R})-2-[[4-bromanyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]isoquinoline-4-carboxamide


Mass: 526.382 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H24BrN5O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 4% v/v Tacsimate pH 5.0, 0.1M sodium citrate tribasic pH 5.4, 12% v/v PEG 3,350, 8 mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.541 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.98→29.18 Å / Num. obs: 25971 / % possible obs: 98.42 % / Redundancy: 4.8 % / Biso Wilson estimate: 36.42 Å2 / CC1/2: 0.947 / Rpim(I) all: 0.1235 / Rrim(I) all: 0.2769 / Net I/σ(I): 10.58
Reflection shellResolution: 2.98→3.086 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.72 / Num. unique obs: 2568 / CC1/2: 0.866 / Rpim(I) all: 0.2094 / Rrim(I) all: 0.4803 / % possible all: 99.38

-
Processing

Software
NameVersionClassification
CrysalisPro1.171.40.73adata collection
PHENIX1.17.1_3660refinement
CrysalisPro1.171.40.73adata reduction
CrysalisPro1.171.40.73adata scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ylu

4ylu


Resolution: 2.98→29.18 Å / SU ML: 0.3898 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 1182 4.55 %
Rwork0.2349 24777 -
obs0.2367 25959 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.32 Å2
Refinement stepCycle: LAST / Resolution: 2.98→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9248 0 136 0 9384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00559612
X-RAY DIFFRACTIONf_angle_d1.01613092
X-RAY DIFFRACTIONf_chiral_restr0.05841484
X-RAY DIFFRACTIONf_plane_restr0.00611664
X-RAY DIFFRACTIONf_dihedral_angle_d16.99413320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.120.36141470.30343073X-RAY DIFFRACTION99.35
3.12-3.280.37541540.30243113X-RAY DIFFRACTION99.15
3.28-3.480.33121420.28213116X-RAY DIFFRACTION99.24
3.48-3.750.28241510.25833087X-RAY DIFFRACTION98.87
3.75-4.130.30661440.2383076X-RAY DIFFRACTION98.35
4.13-4.720.24351500.20323105X-RAY DIFFRACTION98.46
4.73-5.950.21681500.20043115X-RAY DIFFRACTION98.61
5.95-29.180.20341440.17733092X-RAY DIFFRACTION96.28
Refinement TLS params.Method: refined / Origin x: 25.6357041015 Å / Origin y: -25.978363762 Å / Origin z: 69.0568660854 Å
111213212223313233
T0.0948121366754 Å2-0.0657299839582 Å20.0347361883533 Å2-0.139172949936 Å20.00541385707454 Å2--0.148226788028 Å2
L0.267354162663 °2-0.210980795746 °20.243294714112 °2-0.316156067835 °2-0.225877908558 °2--1.31567228853 °2
S-0.0213126079689 Å °0.0513978185782 Å °-0.0106199766638 Å °0.0699056559514 Å °0.000491459764364 Å °0.00991471181918 Å °-0.102037634472 Å °0.146148629845 Å °0.00263475646521 Å °
Refinement TLS groupSelection details: all

+
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