[English] 日本語
Yorodumi
- PDB-6y2f: Crystal structure (monoclinic form) of the complex resulting from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y2f
TitleCrystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Novel coronavirus / alpha-ketoamide / antiviral / drug design
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 / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy ...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 / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / 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 / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / G-quadruplex RNA binding / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host ISG15-protein conjugation / 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 / viral transcription / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host TRAF activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / thiol-dependent deubiquitinase / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / suppression by virus of host type I interferon-mediated signaling pathway / 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
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus replicase NSP15, middle domain / Coronavirus RNA-dependent RNA polymerase, N-terminal / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, middle domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / Betacoronavirus SUD-C domain / Non-structural protein 2, SARS-CoV-like / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Betacoronavirus Nsp3c-M domain profile. / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Non-structural protein NSP1, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-C domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Non-structural protein 6, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / 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. / Papain-like protease, N-terminal domain superfamily, coronavirus / Lipocalin signature. / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP9, coronavirus / Peptidase C16, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Non-structural protein NSP8 superfamily, coronavirus / Coronavirus replicase NSP8 / Peptidase C30, coronavirus / 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 RNA synthesis protein NSP10 / Non-structural protein NSP7 superfamily, coronavirus / Coronavirus replicase NSP4, N-terminal / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein 6, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / Non-structural protein NSP8, coronavirus-like
Similarity search - Domain/homology
Chem-O6K / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhang, L. / Lin, D. / Sun, X. / Hilgenfeld, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchDZIF-TTU01 grant 8011801806 Germany
CitationJournal: Science / Year: 2020
Title: Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.
Authors: Zhang, L. / Lin, D. / Sun, X. / Curth, U. / Drosten, C. / Sauerhering, L. / Becker, S. / Rox, K. / Hilgenfeld, R.
History
DepositionFeb 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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
Revision 1.2Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Apr 8, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Structure summary
Category: atom_site / entity_poly ...atom_site / entity_poly / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_conn / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_asym_id / _entity_poly.pdbx_strand_id ..._atom_site.auth_asym_id / _entity_poly.pdbx_strand_id / _pdbx_database_status.pdb_format_compatible / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_ref_seq.pdbx_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Revision 2.1May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _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_db_accession
Revision 2.2Apr 28, 2021Group: Source and taxonomy / Structure summary / Category: entity / entity_name_com / entity_src_gen
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4993
Polymers33,8261
Non-polymers6742
Water3,189177
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9996
Polymers67,6512
Non-polymers1,3484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3640 Å2
ΔGint-5 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)98.085, 80.926, 51.659
Angle α, β, γ (deg.)90.000, 114.838, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

21A-690-

HOH

31A-709-

HOH

-
Components

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


Mass: 33825.547 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 (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-O6K / ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate


Mass: 595.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H41N5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10% PEG 200, 0.1 M bis-tris propane, pH 9.0, 18% PEG 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→43.369 Å / Num. obs: 26757 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Net I/σ(I): 15.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7 % / Rmerge(I) obs: 0.826 / Num. unique obs: 3919 / CC1/2: 0.809 / Rpim(I) all: 0.335 / Rrim(I) all: 0.892 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BX4
Resolution: 1.95→43.369 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.284 / SU ML: 0.116 / Cross valid method: FREE R-VALUE / ESU R: 0.145 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 1293 4.833 %4.83
Rwork0.1779 ---
all0.18 ---
obs-26755 99.955 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.377 Å2
Baniso -1Baniso -2Baniso -3
1-1.854 Å2-0 Å2-0.302 Å2
2--1.848 Å2-0 Å2
3----2.396 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 47 177 2565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132443
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172207
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.6653319
X-RAY DIFFRACTIONr_angle_other_deg1.4341.5945118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2215301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24223.051118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04915383
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.836151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9461511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022741
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
X-RAY DIFFRACTIONr_nbd_refined0.2050.2447
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.22117
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21179
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2123
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.216
X-RAY DIFFRACTIONr_nbd_other0.180.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.220
X-RAY DIFFRACTIONr_mcbond_it3.2513.6611210
X-RAY DIFFRACTIONr_mcbond_other3.2523.6581209
X-RAY DIFFRACTIONr_mcangle_it4.7365.4661509
X-RAY DIFFRACTIONr_mcangle_other4.7355.4691510
X-RAY DIFFRACTIONr_scbond_it4.0764.061233
X-RAY DIFFRACTIONr_scbond_other4.0754.0621234
X-RAY DIFFRACTIONr_scangle_it6.0085.9411807
X-RAY DIFFRACTIONr_scangle_other6.0075.9431808
X-RAY DIFFRACTIONr_lrange_it8.08343.7252649
X-RAY DIFFRACTIONr_lrange_other8.05543.5452627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.341110.2731878X-RAY DIFFRACTION100
2.001-2.0550.2851090.2571815X-RAY DIFFRACTION100
2.115-2.180.245760.2271758X-RAY DIFFRACTION99.9455
2.18-2.2510.27770.2291657X-RAY DIFFRACTION99.9424
2.251-2.330.258780.2071630X-RAY DIFFRACTION100
2.33-2.4180.237860.2021556X-RAY DIFFRACTION100
2.418-2.5170.274820.1871487X-RAY DIFFRACTION100
2.517-2.6280.221770.1811444X-RAY DIFFRACTION100
2.628-2.7560.204760.181377X-RAY DIFFRACTION100
2.756-2.9050.208700.1851313X-RAY DIFFRACTION100
2.905-3.0810.25670.1831237X-RAY DIFFRACTION100
3.081-3.2930.213570.1751167X-RAY DIFFRACTION100
3.293-3.5560.212620.171103X-RAY DIFFRACTION100
3.556-3.8940.192440.1561000X-RAY DIFFRACTION99.9043
3.894-4.3510.202450.141916X-RAY DIFFRACTION100
4.351-5.020.13410.126801X-RAY DIFFRACTION99.5272
5.02-6.1370.21300.153697X-RAY DIFFRACTION100
6.137-8.6340.195170.161553X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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