[English] 日本語
Yorodumi
- PDB-7nfv: Structure of SARS-CoV-2 Papain-like protease PLpro -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nfv
TitleStructure of SARS-CoV-2 Papain-like protease PLpro
ComponentsPapain-like protease nsp3
KeywordsHYDROLASE / Papain-like protease SARS-CoV-2 Hydrolase Zinc binding protein
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / 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 ...viral genome replication / methyltransferase activity / 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 / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / 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 / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / methylation / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral translational frameshifting / 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 / 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
Similarity search - Function
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 / : ...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 Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface 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 / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
PHOSPHATE ION / Replicase polyprotein 1a / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsSrinivasan, V. / Gunther, S. / Reinke, P. / Werner, N. / Falke, S. / Brognaro, H. / Ullah, N. / Andaleeb, H. / Perbandt, M. / Alves Franca, B. ...Srinivasan, V. / Gunther, S. / Reinke, P. / Werner, N. / Falke, S. / Brognaro, H. / Ullah, N. / Andaleeb, H. / Perbandt, M. / Alves Franca, B. / Schwinzer, M. / Wang, M. / Sprenger, J. / Lieske, J. / Ginn, H. / Lane, T.J. / Yefanov, O. / Gelisio, L. / Koua, F. / Saouane, S. / Tolstikova, A. / Groessler, M. / Fleckenstein, H. / Ewert, W. / Trost, F. / Lorenzen, K. / Schubert, R. / Han, H. / Schmidt, C. / Brings, L. / Ehrt, C. / Rarey, M. / Galchenkova, M. / Gevorkov, Y. / Li, C. / Perk, A. / Awel, S. / Hinrichs, W. / Meents, A. / Betzel, C.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2056 - project ID 390715994 Germany
European CommissionEU project 101003551 - EXSCALATE4CoV (E4C)European Union
CitationJournal: Commun Biol / Year: 2022
Title: Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.
Authors: Srinivasan, V. / Brognaro, H. / Prabhu, P.R. / de Souza, E.E. / Gunther, S. / Reinke, P.Y.A. / Lane, T.J. / Ginn, H. / Han, H. / Ewert, W. / Sprenger, J. / Koua, F.H.M. / Falke, S. / Werner, ...Authors: Srinivasan, V. / Brognaro, H. / Prabhu, P.R. / de Souza, E.E. / Gunther, S. / Reinke, P.Y.A. / Lane, T.J. / Ginn, H. / Han, H. / Ewert, W. / Sprenger, J. / Koua, F.H.M. / Falke, S. / Werner, N. / Andaleeb, H. / Ullah, N. / Franca, B.A. / Wang, M. / Barra, A.L.C. / Perbandt, M. / Schwinzer, M. / Schmidt, C. / Brings, L. / Lorenzen, K. / Schubert, R. / Machado, R.R.G. / Candido, E.D. / Oliveira, D.B.L. / Durigon, E.L. / Niebling, S. / Garcia, A.S. / Yefanov, O. / Lieske, J. / Gelisio, L. / Domaracky, M. / Middendorf, P. / Groessler, M. / Trost, F. / Galchenkova, M. / Mashhour, A.R. / Saouane, S. / Hakanpaa, J. / Wolf, M. / Alai, M.G. / Turk, D. / Pearson, A.R. / Chapman, H.N. / Hinrichs, W. / Wrenger, C. / Meents, A. / Betzel, C.
History
DepositionFeb 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.2Sep 7, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_type / citation ...atom_type / citation / citation_author / database_2 / entity / entity_name_com / entity_src_gen
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name
Revision 1.3Jan 31, 2024Group: 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
AAA: Papain-like protease nsp3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9956
Polymers35,6721
Non-polymers3235
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-27 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.330, 82.330, 134.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Papain-like protease nsp3 / Non-structural protein 3 / nsp3 / PL2-PRO / Papain-like proteinase / PL-PRO


Mass: 35671.500 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 BL21(DE3) (bacteria)
References: UniProt: P0DTC1, UniProt: P0DTD1*PLUS, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

-
Non-polymers , 5 types, 535 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 1.0M NaH2PO4/1.0MKH2PO4 100mM Tris_HCl pH=7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.42→48.89 Å / Num. obs: 99793 / % possible obs: 100 % / Redundancy: 52.9 % / CC1/2: 0.97 / Net I/σ(I): 28.3
Reflection shellResolution: 1.42→1.44 Å / Num. unique obs: 4864 / CC1/2: 0.36

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7jrn
Resolution: 1.42→48.89 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.331 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1714 4919 4.929 %
Rwork0.1538 94872 -
all0.155 --
obs-99791 99.989 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.299 Å20.15 Å20 Å2
2--0.299 Å2-0 Å2
3----0.972 Å2
Refinement stepCycle: LAST / Resolution: 1.42→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 14 530 3046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0132769
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172516
X-RAY DIFFRACTIONr_angle_refined_deg2.3081.6553780
X-RAY DIFFRACTIONr_angle_other_deg1.6091.585839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.59924.296135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27115474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.021157
X-RAY DIFFRACTIONr_chiral_restr0.1190.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023252
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02642
X-RAY DIFFRACTIONr_nbd_refined0.2440.2455
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22246
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21263
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21324
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.2395
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0910.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3140.219
X-RAY DIFFRACTIONr_nbd_other0.2130.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2660.241
X-RAY DIFFRACTIONr_mcbond_it1.942.6851358
X-RAY DIFFRACTIONr_mcbond_other1.9392.6831357
X-RAY DIFFRACTIONr_mcangle_it2.6074.0221729
X-RAY DIFFRACTIONr_mcangle_other2.6064.0251730
X-RAY DIFFRACTIONr_scbond_it3.8923.0791409
X-RAY DIFFRACTIONr_scbond_other3.893.081406
X-RAY DIFFRACTIONr_scangle_it5.6364.4632051
X-RAY DIFFRACTIONr_scangle_other5.6314.4632046
X-RAY DIFFRACTIONr_lrange_it7.26134.0583228
X-RAY DIFFRACTIONr_lrange_other6.90731.9473028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.4570.3513660.3346893X-RAY DIFFRACTION99.9725
1.457-1.4970.2853460.2776812X-RAY DIFFRACTION99.9581
1.497-1.540.2583350.2536556X-RAY DIFFRACTION100
1.54-1.5880.2433380.2236412X-RAY DIFFRACTION99.9852
1.588-1.640.2153530.2046169X-RAY DIFFRACTION99.9693
1.64-1.6970.2093050.186009X-RAY DIFFRACTION100
1.697-1.7610.1893330.1695752X-RAY DIFFRACTION100
1.761-1.8330.1953030.1615624X-RAY DIFFRACTION100
1.833-1.9140.1733090.155335X-RAY DIFFRACTION100
1.914-2.0080.1492790.1415125X-RAY DIFFRACTION100
2.008-2.1160.1622490.1434892X-RAY DIFFRACTION100
2.116-2.2450.1582370.1414649X-RAY DIFFRACTION100
2.245-2.3990.1732000.1414386X-RAY DIFFRACTION100
2.399-2.5910.1552150.1374093X-RAY DIFFRACTION100
2.591-2.8380.1681780.1423804X-RAY DIFFRACTION100
2.838-3.1730.1671560.1583429X-RAY DIFFRACTION100
3.173-3.6620.1521520.1483053X-RAY DIFFRACTION100
3.662-4.4820.1411120.122616X-RAY DIFFRACTION100
4.482-6.3270.159930.1562061X-RAY DIFFRACTION100
6.327-70.235600.1921202X-RAY DIFFRACTION99.7628
Refinement TLS params.Method: refined / Origin x: 36.9797 Å / Origin y: 9.5722 Å / Origin z: 16.052 Å
111213212223313233
T0.0222 Å2-0.0072 Å20.0026 Å2-0.0263 Å20.0023 Å2--0.0047 Å2
L0.1039 °2-0.0375 °2-0.0352 °2-0.1466 °20.1024 °2--0.1079 °2
S0.0058 Å °0.004 Å °0.0181 Å °-0.0133 Å °-0.0117 Å °0.0033 Å °0.0095 Å °0.0042 Å °0.0058 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 315
2X-RAY DIFFRACTION1ALLAAA401
3X-RAY DIFFRACTION1ALLAAA402
4X-RAY DIFFRACTION1ALLAAA403
5X-RAY DIFFRACTION1ALLAAA404

+
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