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- PDB-6yva: PLpro-C111S with mISG15 -

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Basic information

Entry
Database: PDB / ID: 6yva
TitlePLpro-C111S with mISG15
Components
  • Replicase polyprotein 1a
  • Ubiquitin-like protein ISG15
KeywordsCELL INVASION / Deubiquitinase / papain-like-protease / SARS-CoV-2 / ISG15 / complex
Function / homology
Function and homology information


positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication ...positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / viral genome replication / positive regulation of erythrocyte differentiation / methyltransferase activity / integrin-mediated signaling pathway / response to bacterium / response to virus / modification-dependent protein catabolic process / protein tag activity / positive regulation of type II interferon production / integrin binding / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 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 / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / methylation / defense response to virus / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / defense response to bacterium / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / ubiquitin protein ligase binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / extracellular region / ATP binding / membrane / cytoplasm
Similarity search - Function
Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / : / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / RNA-dependent RNA polymerase, SARS-CoV-like / Ubiquitin family / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : ...Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / : / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / RNA-dependent RNA polymerase, SARS-CoV-like / Ubiquitin family / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / : / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Ubiquitin homologues / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Lipocalin signature. / Ubiquitin domain profile. / Ubiquitin-like 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 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 3Ecto domain profile. / : / 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
Similarity search - Domain/homology
Replicase polyprotein 1a / Replicase polyprotein 1ab / Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsShin, D. / Dikic, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1177 Germany
Citation
Journal: Nature / Year: 2020
Title: Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.
Authors: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / Wilhelm, A. / van der Heden van ...Authors: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / Wilhelm, A. / van der Heden van Noort, G.J. / Ovaa, H. / Muller, S. / Knobeloch, K.P. / Rajalingam, K. / Schulman, B.A. / Cinatl, J. / Hummer, G. / Ciesek, S. / Dikic, I.
#1: Journal: Nature / Year: 2020
Title: Inhibition of papain-like protease PLpro blocks SARS-CoV-2 spread and promotes anti-viral immunity
Authors: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / van der Heden van Noort, G.J. / ...Authors: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / van der Heden van Noort, G.J. / Ovaa, H. / Knobeloch, K.P. / Rajalingam, K. / Schulman, B.A. / Cinatl, J. / Hummer, G. / Ciesek, S. / Dikic, I.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 15, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / struct_asym / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns.B_iso_Wilson_estimate / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Real space R-factor
Details: We have refined the structure to have a better R-free value.
Provider: author / Type: Coordinate replacement
Revision 2.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Revision 2.2Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.3Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase polyprotein 1a
C: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6403
Polymers53,5752
Non-polymers651
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Based on previously known structure, the complex exists as a monomer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-10 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.047, 157.047, 83.633
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein Replicase polyprotein 1a / pp1a / ORF1a polyprotein


Mass: 35655.438 Da / Num. of mol.: 1
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, UniProt: P0DTD1*PLUS, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase
#2: Protein Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein


Mass: 17919.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Isg15, G1p2, Ucrp / Production host: Escherichia coli (E. coli) / References: UniProt: Q64339
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG4450, 100 mM bis-tris propane pH 6.5, 200 mM Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 3.18→45.34 Å / Num. obs: 10590 / % possible obs: 99.61 % / Redundancy: 2 % / Biso Wilson estimate: 88.46 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05751 / Net I/σ(I): 8.58
Reflection shellResolution: 3.185→3.298 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5689 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 1008 / CC1/2: 0.594 / CC star: 0.863 / % possible all: 97.77

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W9C, 5TLA

6w9c

5tla


Resolution: 3.18→45.34 Å / SU ML: 0.5141 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.5098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2902 515 4.86 %
Rwork0.2496 10075 -
obs0.2515 10590 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.6 Å2
Refinement stepCycle: LAST / Resolution: 3.18→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 1 23 3401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383456
X-RAY DIFFRACTIONf_angle_d0.63414697
X-RAY DIFFRACTIONf_chiral_restr0.0422535
X-RAY DIFFRACTIONf_plane_restr0.0044602
X-RAY DIFFRACTIONf_dihedral_angle_d12.3995472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.50.39531250.31572432X-RAY DIFFRACTION99.07
3.51-4.010.37771190.27042484X-RAY DIFFRACTION99.88
4.01-5.050.24311260.22542506X-RAY DIFFRACTION99.96
5.05-45.340.26411450.24012653X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: 38.6251045464 Å / Origin y: -33.7660531 Å / Origin z: 2.62099956023 Å
111213212223313233
T0.657994987802 Å2-0.114530781987 Å2-0.088385130238 Å2-0.646781237677 Å2-0.0544067901059 Å2--0.503217448178 Å2
L0.669908209242 °20.789793815271 °2-0.651669736489 °2-3.78940815833 °2-0.509026579538 °2--1.69721425608 °2
S0.436621956809 Å °-0.259169652037 Å °-0.0326552401393 Å °0.551926008285 Å °-0.570374312226 Å °-0.228821498369 Å °-0.169622258273 Å °0.20217262926 Å °0.131548412746 Å °
Refinement TLS groupSelection details: all

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