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- PDB-9jj7: The crystal structure of SARS-CoV-2 NSP5 in complex with eIF4G2 -

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Entry
Database: PDB / ID: 9jj7
TitleThe crystal structure of SARS-CoV-2 NSP5 in complex with eIF4G2
Components
  • 3C-like proteinase nsp5
  • Eukaryotic translation initiation factor 4 gamma 2
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


macromolecule biosynthetic process / cell death / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / regulation of translational initiation / positive regulation of dendritic spine development / positive regulation of axon extension / translation initiation factor activity / negative regulation of autophagy / positive regulation of translation ...macromolecule biosynthetic process / cell death / eukaryotic translation initiation factor 4F complex / translation factor activity, RNA binding / regulation of translational initiation / positive regulation of dendritic spine development / positive regulation of axon extension / translation initiation factor activity / negative regulation of autophagy / positive regulation of translation / adherens junction / translational initiation / ISG15 antiviral mechanism / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / heart development / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / positive regulation of cell growth / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of cell cycle / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / cadherin binding / symbiont-mediated suppression of host gene expression / copper ion binding / axon / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / mRNA binding / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / cytosol
Similarity search - Function
eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) ...eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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 / 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
Similarity search - Domain/homology
Replicase polyprotein 1ab / Eukaryotic translation initiation factor 4 gamma 2
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYan, X. / Jin, Z. / Wang, Y. / Zhang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Coronavirus NSP5 is an Evolutionarily Conserved Inhibitor of Host Translation
Authors: Cao, W. / Yan, X. / Liu, S. / Zheng, N. / Wang, Y. / Chen, J. / Zhang, J. / Cao, H. / Zhong, Y. / Yuan, S. / Cao, Y. / Jin, Z. / Zhang, G.
History
DepositionSep 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase nsp5
C: Eukaryotic translation initiation factor 4 gamma 2


Theoretical massNumber of molelcules
Total (without water)34,8612
Polymers34,8612
Non-polymers00
Water3,513195
1
A: 3C-like proteinase nsp5
C: Eukaryotic translation initiation factor 4 gamma 2

A: 3C-like proteinase nsp5
C: Eukaryotic translation initiation factor 4 gamma 2


Theoretical massNumber of molelcules
Total (without water)69,7214
Polymers69,7214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5500 Å2
ΔGint-22 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.001, 81.980, 51.649
Angle α, β, γ (deg.)90.00, 114.99, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-446-

HOH

21A-517-

HOH

31A-521-

HOH

41A-551-

HOH

51A-582-

HOH

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Components

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


Mass: 33758.477 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Protein/peptide Eukaryotic translation initiation factor 4 gamma 2 / eIF-4-gamma 2 / eIF-4G 2 / eIF4G 2 / Death-associated protein 5 / DAP-5 / p97


Mass: 1102.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78344
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 5.6, 7% PEG 6000, and 6% dimethyl sulfoxide (DMSO)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→43.96 Å / Num. obs: 66581 / % possible obs: 99.64 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 17.24
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 33873 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.96 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 3934 5.91 %
Rwork0.194 --
obs0.1951 66581 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 0 195 2624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112484
X-RAY DIFFRACTIONf_angle_d2.0163375
X-RAY DIFFRACTIONf_dihedral_angle_d10.144337
X-RAY DIFFRACTIONf_chiral_restr0.074383
X-RAY DIFFRACTIONf_plane_restr0.014439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.27291360.25242142X-RAY DIFFRACTION94
1.82-1.840.23121350.22622187X-RAY DIFFRACTION99
1.84-1.870.28171360.24022251X-RAY DIFFRACTION99
1.87-1.890.25511390.22842219X-RAY DIFFRACTION100
1.89-1.920.25691420.23582271X-RAY DIFFRACTION99
1.92-1.950.31351360.22462183X-RAY DIFFRACTION99
1.95-1.980.31421460.22672314X-RAY DIFFRACTION100
1.98-2.010.2181350.21552171X-RAY DIFFRACTION99
2.01-2.050.30951440.22292314X-RAY DIFFRACTION100
2.05-2.080.22541350.21572191X-RAY DIFFRACTION100
2.08-2.120.23861400.22032262X-RAY DIFFRACTION99
2.12-2.170.27251430.20922236X-RAY DIFFRACTION99
2.17-2.210.23931400.21162191X-RAY DIFFRACTION100
2.21-2.270.25361430.21542305X-RAY DIFFRACTION100
2.27-2.320.26231420.21482217X-RAY DIFFRACTION100
2.32-2.390.23641380.20412223X-RAY DIFFRACTION100
2.39-2.460.22681410.22612272X-RAY DIFFRACTION99
2.46-2.530.24331430.20812273X-RAY DIFFRACTION100
2.53-2.630.23391450.20762225X-RAY DIFFRACTION99
2.63-2.730.2491370.20492222X-RAY DIFFRACTION100
2.73-2.850.24511440.21922259X-RAY DIFFRACTION100
2.85-30.19151422247X-RAY DIFFRACTION100
3-3.190.23541410.19532255X-RAY DIFFRACTION100
3.19-3.440.1691462247X-RAY DIFFRACTION100
3.44-3.790.18891390.1722241X-RAY DIFFRACTION100
3.79-4.330.19671430.16322249X-RAY DIFFRACTION100
4.33-5.460.16571410.15822250X-RAY DIFFRACTION100
5.46-43.960.16071422230X-RAY DIFFRACTION99

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