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- PDB-7ali: Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-... -

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Basic information

Entry
Database: PDB / ID: 7ali
TitleCrystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 at 1.65A resolution (spacegroup P2(1)).
Components3C-like proteinase
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Mpro / 3CLpro / EXSCALATE4COV / drug discovery / Elettra
Function / homology
Function and homology information


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 ...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 / 5'-3' DNA helicase activity / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / 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 / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent 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
RNA-dependent RNA polymerase, SARS-CoV-like / 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. ...RNA-dependent RNA polymerase, SARS-CoV-like / 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 / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Lipocalin signature. / (+) 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) / Coronavirus 3Ecto domain profile. / 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 (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 / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCostanzi, E. / Demitri, N. / Giabbai, B. / Heroux, A. / Storici, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission101003551European Union
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L.
Authors: Costanzi, E. / Kuzikov, M. / Esposito, F. / Albani, S. / Demitri, N. / Giabbai, B. / Camasta, M. / Tramontano, E. / Rossetti, G. / Zaliani, A. / Storici, P.
History
DepositionOct 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _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 / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase


Theoretical massNumber of molelcules
Total (without water)67,6512
Polymers67,6512
Non-polymers00
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-14 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.776, 53.698, 114.550
Angle α, β, γ (deg.)90.000, 101.172, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPRO(chain 'A' and (resid 1 through 109 or resid 111...AA1 - 1081 - 108
12THRTHRHISHIS(chain 'A' and (resid 1 through 109 or resid 111...AA111 - 164111 - 164
13GLUGLULEULEU(chain 'A' and (resid 1 through 109 or resid 111...AA166 - 253166 - 253
14ALAALALEULEU(chain 'A' and (resid 1 through 109 or resid 111...AA255 - 287255 - 287
15ASPASPPHEPHE(chain 'A' and (resid 1 through 109 or resid 111...AA289 - 305289 - 305
26SERSERPROPRO(chain 'B' and (resid 1 through 109 or resid 111...BB1 - 1081 - 108
27THRTHRHISHIS(chain 'B' and (resid 1 through 109 or resid 111...BB111 - 164111 - 164
28GLUGLULEULEU(chain 'B' and (resid 1 through 109 or resid 111...BB166 - 253166 - 253
29ALAALALEULEU(chain 'B' and (resid 1 through 109 or resid 111...BB255 - 287255 - 287
210ASPASPPHEPHE(chain 'B' and (resid 1 through 109 or resid 111...BB289 - 305289 - 305

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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.: 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 (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Na Acetate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2020
RadiationMonochromator: SI(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.45 Å / Num. obs: 63251 / % possible obs: 98.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.078 / Net I/σ(I): 9.8
Reflection shellResolution: 1.65→1.68 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3121 / CC1/2: 0.657

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y2E
Resolution: 1.65→38.46 Å / SU ML: 0.1812 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2167 3142 4.98 %
Rwork0.1888 59941 -
obs0.1901 63083 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.16 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4725 0 0 490 5215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524879
X-RAY DIFFRACTIONf_angle_d0.84936642
X-RAY DIFFRACTIONf_chiral_restr0.0484749
X-RAY DIFFRACTIONf_plane_restr0.0057866
X-RAY DIFFRACTIONf_dihedral_angle_d17.91551760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.32561410.30222716X-RAY DIFFRACTION97.24
1.68-1.70.27711320.29212693X-RAY DIFFRACTION96.85
1.7-1.730.28431380.27282684X-RAY DIFFRACTION97.21
1.73-1.760.2811460.2622667X-RAY DIFFRACTION97.27
1.76-1.80.23851560.25522697X-RAY DIFFRACTION97.31
1.8-1.830.25321460.25812660X-RAY DIFFRACTION97.3
1.83-1.870.2941780.23642649X-RAY DIFFRACTION97.15
1.87-1.920.28211430.2272709X-RAY DIFFRACTION97.4
1.92-1.970.28211390.21372717X-RAY DIFFRACTION97.77
1.97-2.020.21621460.21262701X-RAY DIFFRACTION98.07
2.02-2.080.22011300.20612733X-RAY DIFFRACTION97.95
2.08-2.150.23661530.19962744X-RAY DIFFRACTION98.3
2.15-2.220.23061350.192716X-RAY DIFFRACTION97.97
2.22-2.310.23881570.18972682X-RAY DIFFRACTION98.24
2.31-2.420.23341290.18692770X-RAY DIFFRACTION98.4
2.42-2.540.22041540.18652728X-RAY DIFFRACTION98.77
2.54-2.70.2041560.1862756X-RAY DIFFRACTION98.71
2.7-2.910.22381170.18172773X-RAY DIFFRACTION98.74
2.91-3.210.18551590.17272764X-RAY DIFFRACTION98.82
3.21-3.670.20411180.16432792X-RAY DIFFRACTION98.98
3.67-4.620.15721180.15062812X-RAY DIFFRACTION98.55
4.62-38.460.20171510.17882778X-RAY DIFFRACTION95.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.235175487390.581410862557-0.5262847754452.18843598831-0.3802229085171.50977013958-0.02466549432090.0400361743548-0.0328846916959-0.1172187499620.0667642069932-0.01438455742950.0292302622491-0.015281608507-0.02656259296030.129532399003-0.0121075550076-0.02042577601860.150800439902-0.01528713376850.149006176395-3.85907423397-9.743138383141.9067823164
21.970798810441.36282179798-0.8395775756891.1570271198-0.7707408314680.9993068156080.216370163434-0.0853303188030.3334654422150.0660142275538-0.03266875655710.256588451199-0.148662280140.173031491818-0.1606601226890.167719948141-0.0101918114825-0.009684731089110.178799306633-0.04539772629540.2095492927724.470861771388.3142201605143.1082895916
32.57471140655-0.7453147474780.8549720883671.94323500389-0.1045500024322.09993326843-0.1713206308230.06149642780320.1725031843180.1353189953790.0200597563357-0.177731245094-0.2838090945950.259146466260.1220558124250.230802085295-0.0730579628606-0.02091968064140.241502690842-0.02142883911420.20848512946519.89791154118.578378221541.3021271984
42.60226353736-0.5015349791640.670405587113.172742689890.02920508018642.805480174140.03650872312380.481411959846-0.338717136999-0.270273586398-0.1205732976090.1109646571980.2351132502440.1591314105080.1038160840750.228101734707-0.06717880983870.01281125397850.370663852565-0.08687587978940.24845864860914.44168513927.6525066529532.1663560611
51.89639210288-1.77981919852-0.4449362704562.917238843750.4998452342842.21782444163-0.1200564247750.128561955433-0.03294880773950.337015198872-0.0622142318291-0.2031809588910.340942892390.04804642324890.1432415894990.25357487508-0.00197515770720.02843133366630.2221624403670.03092577812120.1986074946917.84388051198-8.4515833173123.8375594849
61.310238416111.22232375696-1.94208385581.67569951731-0.3983337535913.34915773949-0.37877084111-0.316407689285-0.507961986052-0.0808155743029-0.019058381107-0.3215513103230.6729068979580.513578462870.2250103881270.3210425777820.09571019805530.06507760708460.2258499281690.03498443802120.27791055371718.8126113595-14.484493430911.7817226164
71.01188540569-0.02518336963080.3478055845471.73530350295-2.328903454543.706792396250.141924390980.01883685405510.1070048831760.0793536114172-0.0913007436203-0.0644862103538-0.1139005226010.297446768768-0.1129754769270.2369505579940.02550623060940.02397993178460.2078774895830.0004493172023720.25403796112810.35191570051.6146355147417.9301012993
81.90939230175-1.12769808112-1.099245912391.764530266640.6443325813611.62191505550.041683545734-0.01169491687340.0124675438686-0.0695483304803-0.0188705722201-0.06042557931120.03402015056280.069060710784-0.02998035251770.165116389759-0.0150631259331-0.01790807934190.1843282516290.00335061835380.1619318492629.75134496530.74304857503113.8343889776
93.223439072861.26982658271-0.5430219415471.57779478165-0.192140142492.679826364760.1195416478110.1493833125550.958330988685-0.07576238096550.07596111531530.303938069933-0.545939778464-0.394725947087-0.119829109140.2791308378310.07913335490770.05704009655790.2700449596030.04463015022290.412174564875-6.8745923817817.434849223616.8845845773
103.055138190110.158591127916-0.2488785490877.29969866694-2.245890113621.94676206473-0.00865090982718-0.735081213742-1.00233857966-0.1788549052730.1994109541120.03024771771340.450613605785-0.509337324189-0.263508269970.34231947743-0.02129597229550.001124884216590.4554136614920.1203558381040.403369953154-7.61396071984-1.7262806029622.4227154368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 214 )
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 274 )
4X-RAY DIFFRACTION4chain 'A' and (resid 275 through 306 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 22 )
6X-RAY DIFFRACTION6chain 'B' and (resid 23 through 120 )
7X-RAY DIFFRACTION7chain 'B' and (resid 121 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 214 )
9X-RAY DIFFRACTION9chain 'B' and (resid 215 through 292 )
10X-RAY DIFFRACTION10chain 'B' and (resid 293 through 306 )

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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

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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

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