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- PDB-6m71: SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors -

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Entry
Database: PDB / ID: 6m71
TitleSARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors
Components
  • Non-structural protein 7
  • Non-structural protein 8
  • RNA-directed RNA polymeraseRNA-dependent RNA polymerase
KeywordsVIRAL PROTEIN / COVID-19 / 2019-nCoV / SARS-CoV-2 / Virus / RdRp / nsp12 / nsp7 / nsp8 / RTC / cryo-EM / RNA polymerase / drug target / antiviral / replication transcription complex
Function / homology
Function and homology information


Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation ...Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / G-quadruplex RNA binding / 3'-5'-exoribonuclease activity / suppression by virus of host ISG15-protein conjugation / host cell endoplasmic reticulum-Golgi intermediate compartment / protein K48-linked deubiquitination / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / viral genome replication / suppression by virus of host TRAF activity / helicase activity / viral transcription / Transferases; Transferring one-carbon groups; Methyltransferases / ubiquitinyl hydrolase 1 / methyltransferase activity / DNA helicase / thiol-dependent deubiquitinase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / DNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / methylation / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral protein processing / suppression by virus of host type I interferon-mediated signaling pathway / Hydrolases; Acting on ester bonds / transcription, DNA-templated / host cell cytoplasm / protein dimerization activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Non-structural protein 14, coronavirus / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP16, coronavirus-like / Coronavirus proofreading exoribonuclease / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, middle domain superfamily / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP15, middle domain / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein 2, SARS-CoV-like / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Non-structural protein NSP1, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Coronavirus (CoV) Nsp1 globular domain profile. / Non-structural protein 6, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Lipocalin signature. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Coronavirus replicase NSP7 / Coronavirus papain-like peptidase / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus RNA synthesis protein NSP10 / Coronavirus endopeptidase C30 / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP8 / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Coronavirus replicase NSP4, N-terminal / RNA synthesis protein NSP10, coronavirus / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Coronavirus replicase NSP4, N-terminal / Peptidase C30, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein 6, coronavirus / Peptidase C30, domain 3, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGao, Y. / Yan, L. / Huang, Y. / Liu, F. / Cao, L. / Wang, T. / Wang, Q. / Lou, Z. / Rao, Z.
Funding support China, 4items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020200 China
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
CitationJournal: Science / Year: 2020
Title: Structure of the RNA-dependent RNA polymerase from COVID-19 virus.
Authors: Yan Gao / Liming Yan / Yucen Huang / Fengjiang Liu / Yao Zhao / Lin Cao / Tao Wang / Qianqian Sun / Zhenhua Ming / Lianqi Zhang / Ji Ge / Litao Zheng / Ying Zhang / Haofeng Wang / Yan Zhu / ...Authors: Yan Gao / Liming Yan / Yucen Huang / Fengjiang Liu / Yao Zhao / Lin Cao / Tao Wang / Qianqian Sun / Zhenhua Ming / Lianqi Zhang / Ji Ge / Litao Zheng / Ying Zhang / Haofeng Wang / Yan Zhu / Chen Zhu / Tianyu Hu / Tian Hua / Bing Zhang / Xiuna Yang / Jun Li / Haitao Yang / Zhijie Liu / Wenqing Xu / Luke W Guddat / Quan Wang / Zhiyong Lou / Zihe Rao /
Abstract: A novel coronavirus [severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2)] outbreak has caused a global coronavirus disease 2019 (COVID-19) pandemic, resulting in tens of thousands of ...A novel coronavirus [severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2)] outbreak has caused a global coronavirus disease 2019 (COVID-19) pandemic, resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase [(RdRp), also named nsp12] is the central component of coronaviral replication and transcription machinery, and it appears to be a primary target for the antiviral drug remdesivir. We report the cryo-electron microscopy structure of COVID-19 virus full-length nsp12 in complex with cofactors nsp7 and nsp8 at 2.9-angstrom resolution. In addition to the conserved architecture of the polymerase core of the viral polymerase family, nsp12 possesses a newly identified β-hairpin domain at its N terminus. A comparative analysis model shows how remdesivir binds to this polymerase. The structure provides a basis for the design of new antiviral therapeutics that target viral RdRp.
History
DepositionMar 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 15, 2020Group: Database references / Category: citation / citation_author
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_DOI / _citation.title / _citation.year
Revision 2.0May 27, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / computing / em_software / entity / entity_name_com / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine_ls_restr / software / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_software.fitting_id / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 2.1Jul 29, 2020Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 2.2Mar 10, 2021Group: Structure summary / Category: entity / entity_name_com
Item: _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name

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Structure visualization

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Assembly

Deposited unit
A: RNA-directed RNA polymerase
C: Non-structural protein 7
D: Non-structural protein 8
B: Non-structural protein 8


Theoretical massNumber of molelcules
Total (without water)161,2174
Polymers161,2174
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9100 Å2
ΔGint-91 kcal/mol
Surface area43870 Å2

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Components

#1: Protein RNA-directed RNA polymerase / RNA-dependent RNA polymerase / pp1ab / ORF1ab polyprotein / Pol / RdRp / Non-structural protein 12 / nsp12 / SARS-Cov-2 NSP 12


Mass: 108162.461 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 / Plasmid: pET-22a / Details (production host): none / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DTD1, RNA-directed RNA polymerase
#2: Protein Non-structural protein 7 / pp1ab / ORF1ab polyprotein / nsp7 / SARS-Cov-2 NSP 7


Mass: 9248.804 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) / Strain (production host): BL21(DE3) / References: UniProt: P0DTD1
#3: Protein Non-structural protein 8 / pp1ab / ORF1ab polyprotein / nsp8 / SARS-Cov-2 NSP 8


Mass: 21903.047 Da / Num. of mol.: 2
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) / Strain (production host): BL21(DE3) / References: UniProt: P0DTD1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SARS-CoV-2 RNA-dependent RNA polymerase in complex with cofactors
Type: COMPLEX
Details: The bacterially expressed full-length SARS-CoV-2 nsp12 (residues S1-Q932) was incubated with nsp7 (residues S1-Q83) and nsp8 (residues A1-Q198), and the complex was then purified
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.155 MDa / Experimental value: YES
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Plasmid: pET-22a
Buffer solutionpH: 7.5
Details: Solutions were made fresh from concentrated to avoid microbial contamination.
Buffer component
IDConc.NameFormulaBuffer-ID
1250 mMsodium chlorideNaClSodium chloride1
220 mMTris (hydroxymethyl) aminomethaneTris-HClTris1
34 mMmagnesium chlorideMgCl21
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono disperse.
Specimen supportDetails: None. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: blot for 3 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Preliminary grid screening was performed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78.6 K / Temperature (min): 78.5 K / Residual tilt: 10 mradians
Image recordingAverage exposure time: 5 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 7994
Details: Images were collected in movie-mode at 8 frames per second.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Chromatic aberration corrector: NONE / Energyfilter slit width: 30 eV / Phase plate: VOLTA PHASE PLATE / Spherical aberration corrector: NONE
Image scansSampling size: 2.5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 2-40

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2SerialEM3-7-3image acquisitionSerialEM was used to automatically data collection
4cryoSPARC2.9.1CTF correctioncryoSPARC was used to determine CTF correction.
7UCSF Chimera1.14model fittingUCSF chimera was used to do model fitting
9PHENIX1.16model refinementPHENIX was used to do model refinement
10cryoSPARC2.9.1initial Euler assignmentcryoSPARC was used to do initial angular assignment
11cryoSPARC2.9.1final Euler assignmentcryoSPARC was used to do final angular assignment.
12cryoSPARC2.9.1classificationcryoSPARC was used to do final classification
13cryoSPARC2.9.13D reconstructioncryoSPARC was used to do final reconstruction
Image processingDetails: The selected images were normalized.
CTF correctionDetails: The CTF correction was done by patch CTF correction.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2334248
Details: The particles were automatically selected using blob pickier (diameter range from 100 angstroms to 150 angstroms)
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110176 / Algorithm: FOURIER SPACE
Details: The particle set was used to perform homogeneous refinement, yielding a resolution of 3.1-angstrom. After local refinement, the final resolution reached 2.9-angstrom.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 65 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient
Details: After the corresponding amino acids were replaced with those from 2019-nCoV, the model was manually built in Coot with the guidance of the cryo-EM map, and in combination with real space refinement with Phenix.
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDPdb chain residue range
16NURA1117-903
26NURB177-191
36NURC12-71
46NURD184-192
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 64.82 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038736
ELECTRON MICROSCOPYf_angle_d0.48211859
ELECTRON MICROSCOPYf_dihedral_angle_d2.4855198
ELECTRON MICROSCOPYf_chiral_restr0.0411344
ELECTRON MICROSCOPYf_plane_restr0.0041511

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