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- PDB-7pxz: Reduced form of SARS-CoV-2 Main Protease determined by XFEL radiation -

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Entry
Database: PDB / ID: 7pxz
TitleReduced form of SARS-CoV-2 Main Protease determined by XFEL radiation
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / 3C-like protease / Main-Protease / Viral replication / Polyprotein maturation
Function / homology
Function and homology information


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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / 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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease 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 / mRNA (guanine-N7)-methyltransferase / SARS-CoV-2 modulates host translation machinery / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / 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 / symbiont-mediated suppression of host gene expression / copper ion binding / 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 / 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
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 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. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 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 / Trypsin-like serine proteases / 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 / 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 / Peptidase family C16 domain profile. / : / :
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSchubert, R. / Reinke, P. / Galchenkova, M. / Oberthuer, D. / Murillo, G.E.P. / Kim, C. / Bean, R. / Turk, D. / Hinrichs, W. / Middendorf, P. ...Schubert, R. / Reinke, P. / Galchenkova, M. / Oberthuer, D. / Murillo, G.E.P. / Kim, C. / Bean, R. / Turk, D. / Hinrichs, W. / Middendorf, P. / Round, A. / Schmidt, C. / Mills, G. / Kirkwood, H. / Han, H. / Koliyadu, J. / Bielecki, J. / Gelisio, L. / Sikorski, M. / Kloos, M. / Vakilii, M. / Yefanov, O.N. / Vagovic, P. / de-Wijn, R. / Letrun, R. / Guenther, S. / White, T.A. / Sato, T. / Srinivasan, V. / Kim, Y. / Chretien, A. / Han, S. / Brognaro, H. / Maracke, J. / Knoska, J. / Seychell, B.C. / Brings, L. / Norton-Baker, B. / Geng, T. / Dore, A.S. / Uetrecht, C. / Redecke, L. / Beck, T. / Lorenzen, K. / Betzel, C. / Mancuso, A.P. / Bajt, S. / Chapman, H.N. / Meents, A. / Lane, T.J.
Funding support Germany, European Union, 4items
OrganizationGrant numberCountry
Helmholtz Association Germany
German Research Foundation (DFG) Germany
European CommissionEuropean Union
German Federal Ministry for Education and Research Germany
CitationJournal: Nat Commun / Year: 2024
Title: SARS-CoV-2 M pro responds to oxidation by forming disulfide and NOS/SONOS bonds.
Authors: Reinke, P.Y.A. / Schubert, R. / Oberthur, D. / Galchenkova, M. / Rahmani Mashhour, A. / Gunther, S. / Chretien, A. / Round, A. / Seychell, B.C. / Norton-Baker, B. / Kim, C. / Schmidt, C. / ...Authors: Reinke, P.Y.A. / Schubert, R. / Oberthur, D. / Galchenkova, M. / Rahmani Mashhour, A. / Gunther, S. / Chretien, A. / Round, A. / Seychell, B.C. / Norton-Baker, B. / Kim, C. / Schmidt, C. / Koua, F.H.M. / Tolstikova, A. / Ewert, W. / Pena Murillo, G.E. / Mills, G. / Kirkwood, H. / Brognaro, H. / Han, H. / Koliyadu, J. / Schulz, J. / Bielecki, J. / Lieske, J. / Maracke, J. / Knoska, J. / Lorenzen, K. / Brings, L. / Sikorski, M. / Kloos, M. / Vakili, M. / Vagovic, P. / Middendorf, P. / de Wijn, R. / Bean, R. / Letrun, R. / Han, S. / Falke, S. / Geng, T. / Sato, T. / Srinivasan, V. / Kim, Y. / Yefanov, O.M. / Gelisio, L. / Beck, T. / Dore, A.S. / Mancuso, A.P. / Betzel, C. / Bajt, S. / Redecke, L. / Chapman, H.N. / Meents, A. / Turk, D. / Hinrichs, W. / Lane, T.J.
History
DepositionOct 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Feb 14, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_sheet_range / symmetry
Item: _cell.angle_alpha / _cell.angle_beta ..._cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.length_a / _cell.length_b / _cell.length_c / _cell.volume / _entity.pdbx_number_of_molecules / _pdbx_audit_support.country / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_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_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_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_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _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 / _symmetry.space_group_name_Hall
Description: Model orientation/position
Details: * consistent treatment of hydrogens in refinement for a single series of structures * rotamer model for catalytic His41
Provider: author / Type: Coordinate replacement
Revision 2.1May 1, 2024Group: Database references / Category: pdbx_related_exp_data_set
Revision 2.2Jul 31, 2024Group: Database references / Structure summary / Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._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 / _entity.pdbx_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8612
Polymers33,8261
Non-polymers351
Water4,197233
1
A: 3C-like proteinase nsp5
hetero molecules

A: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7224
Polymers67,6512
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area3380 Å2
ΔGint-31 kcal/mol
Surface area24790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115, 54, 45
Angle α, β, γ (deg.)90, 102, 90
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-401-

CL

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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: 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 BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.99 Å3/Da / Density % sol: 38.1 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 7.5
Details: Vapor diffusion was set up with 2 uL MPro (35 mg/mL) and 2 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO. Seedstock was prepared by 100 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO and 4 uL seeds ...Details: Vapor diffusion was set up with 2 uL MPro (35 mg/mL) and 2 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO. Seedstock was prepared by 100 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO and 4 uL seeds from plate, vortex 5 times for 5 seconds, add 12.5 uL of MPro (35 mg/mL) and incubate at 18 deg overnight. Final sample was prepared in batch mode by adding 900 uL 25% PEG1500, 0.1 M MIB pH 7.5, 5% DMSO and 100 uL seedstock and 100 uL MPro (35 mg per mL). Add seedbeads (250 uL volume in 1.5 mL Eppi) and incubate overnight at 900 rpm and 18 deg.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Apr 16, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.75→31.81 Å / Num. obs: 27995 / % possible obs: 100 % / Redundancy: 946 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.9961933 / CC star: 0.9990461 / R split: 0.0707 / Net I/σ(I): 11.443052
Reflection shellResolution: 1.75→1.79 Å / Mean I/σ(I) obs: 0.72 / Num. unique obs: 1380 / CC1/2: 0.207 / CC star: 0.586 / R split: 1.195 / % possible all: 99.56
Serial crystallography sample deliveryDescription: GDVN / Method: injection
Serial crystallography sample delivery injectionDescription: GDVN

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487: ???refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YNQ

6ynq


Resolution: 1.75→31.62 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.212 1496 -
Rwork0.1635 --
obs0.1662 26365 96.35 %
Refinement stepCycle: LAST / Resolution: 1.75→31.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 1 233 2598

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