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- PDB-7ju7: The crystal structure of SARS-CoV-2 Main Protease in complex with... -

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Basic information

Entry
Database: PDB / ID: 7ju7
TitleThe crystal structure of SARS-CoV-2 Main Protease in complex with masitinib
Components3C-like proteinase
KeywordsHYDROLASE / SARS-CoV-2 / COVID-19 / 3CL / main protease / masitinib / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / endopeptidase complex / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / endopeptidase complex / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / positive regulation of RNA biosynthetic process / 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 peptidase activity / SARS coronavirus main proteinase / suppression by virus of host type I interferon production / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endosome / 3'-5'-exoribonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / protein K48-linked deubiquitination / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / 7-methylguanosine mRNA capping / transcription, RNA-templated / viral transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / suppression by virus of host toll-like receptor signaling pathway / host cell Golgi apparatus / host cell endoplasmic reticulum / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive regulation of viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive stranded viral RNA replication / suppression by virus of host TRAF activity / protein autoprocessing / cysteine-type peptidase activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / DNA helicase activity / cysteine-type deubiquitinase activity / single-stranded RNA binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / suppression by virus of host type I interferon-mediated signaling pathway / host cell cytoplasm / protein dimerization activity / host cell nucleus / ATP hydrolysis 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 / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 14, betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 14, betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) 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 proofreading exoribonuclease / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP16, coronavirus-like / Coronavirus RNA-dependent RNA polymerase, N-terminal / Non-structural protein 14, coronavirus / Nonstructural protein 15, middle domain, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerisation / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein NSP3, N-terminal, betacoronavirus / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Lipocalin signature. / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-M 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 / Non-structural protein NSP1, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Non-structural protein 6, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3d Ubl domain profile. / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp3a Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP8 / Coronavirus endopeptidase C30 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP3, C-terminal / Coronavirus papain-like peptidase / Coronavirus replicase NSP4, N-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Non-structural protein NSP7 superfamily, coronavirus / Coronavirus replicase NSP3, C-terminal / Peptidase C30, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP8, coronavirus / Non-structural protein 6, coronavirus
Similarity search - Domain/homology
Masitinib / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTan, K. / Maltseva, N.I. / Welk, L.F. / Jedrzejczak, R.P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201 700060C United States
Citation
Journal: Science / Year: 2021
Title: Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2.
Authors: Drayman, N. / DeMarco, J.K. / Jones, K.A. / Azizi, S.A. / Froggatt, H.M. / Tan, K. / Maltseva, N.I. / Chen, S. / Nicolaescu, V. / Dvorkin, S. / Furlong, K. / Kathayat, R.S. / Firpo, M.R. / ...Authors: Drayman, N. / DeMarco, J.K. / Jones, K.A. / Azizi, S.A. / Froggatt, H.M. / Tan, K. / Maltseva, N.I. / Chen, S. / Nicolaescu, V. / Dvorkin, S. / Furlong, K. / Kathayat, R.S. / Firpo, M.R. / Mastrodomenico, V. / Bruce, E.A. / Schmidt, M.M. / Jedrzejczak, R. / Munoz-Alia, M.A. / Schuster, B. / Nair, V. / Han, K.Y. / O'Brien, A. / Tomatsidou, A. / Meyer, B. / Vignuzzi, M. / Missiakas, D. / Botten, J.W. / Brooke, C.B. / Lee, H. / Baker, S.C. / Mounce, B.C. / Heaton, N.S. / Severson, W.E. / Palmer, K.E. / Dickinson, B.C. / Joachimiak, A. / Randall, G. / Tay, S.
#1: Journal: Biorxiv / Year: 2020
Title: Drug repurposing screen identifies masitinib as a 3CLpro inhibitor that blocks replication of SARS-CoV-2 in vitro .
Authors: Drayman, N. / Jones, K.A. / Azizi, S.A. / Froggatt, H.M. / Tan, K. / Maltseva, N.I. / Chen, S. / Nicolaescu, V. / Dvorkin, S. / Furlong, K. / Kathayat, R.S. / Firpo, M.R. / Mastrodomenico, V. ...Authors: Drayman, N. / Jones, K.A. / Azizi, S.A. / Froggatt, H.M. / Tan, K. / Maltseva, N.I. / Chen, S. / Nicolaescu, V. / Dvorkin, S. / Furlong, K. / Kathayat, R.S. / Firpo, M.R. / Mastrodomenico, V. / Bruce, E.A. / Schmidt, M.M. / Jedrzejczak, R. / Munoz-Alia, M.A. / Schuster, B. / Nair, V. / Botten, J.W. / Brooke, C.B. / Baker, S.C. / Mounce, B.C. / Heaton, N.S. / Dickinson, B.C. / Jaochimiak, A. / Randall, G. / Tay, S.
History
DepositionAug 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: 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 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.id / _citation.journal_abbrev ..._citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.citation_id / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Sep 1, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5875
Polymers33,8261
Non-polymers7614
Water3,549197
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,17310
Polymers67,6512
Non-polymers1,5228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4030 Å2
ΔGint-6 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.591, 81.299, 51.859
Angle α, β, γ (deg.)90.000, 114.620, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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-532-

HOH

21A-620-

HOH

31A-655-

HOH

41A-693-

HOH

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Components

#1: Protein 3C-like proteinase / SARS-CoV-2 3CL protease


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 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-G65 / Masitinib / Masitinib


Mass: 498.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30N6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M NaCl, 0.1 M MES, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 12, 2020 / Details: Mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→43.5 Å / Num. obs: 48121 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 23.98 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.05 / Rrim(I) all: 0.098 / Χ2: 1.357 / Net I/σ(I): 26.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2341 / CC1/2: 0.354 / CC star: 0.723 / Rpim(I) all: 0.672 / Rrim(I) all: 1.111 / Χ2: 0.678 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JFQ
Resolution: 1.6→43.5 Å / SU ML: 0.1703 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6957
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 2338 4.92 %random
Rwork0.1686 45227 --
obs0.1698 47565 97.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.49 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 52 197 2583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01562472
X-RAY DIFFRACTIONf_angle_d1.42853365
X-RAY DIFFRACTIONf_chiral_restr0.096374
X-RAY DIFFRACTIONf_plane_restr0.0093437
X-RAY DIFFRACTIONf_dihedral_angle_d20.5532900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.29691370.28512478X-RAY DIFFRACTION90.74
1.63-1.670.28291350.26262598X-RAY DIFFRACTION95.56
1.67-1.710.29261420.23122637X-RAY DIFFRACTION97.1
1.71-1.750.2421550.21362636X-RAY DIFFRACTION97.32
1.75-1.80.23091190.19682667X-RAY DIFFRACTION97.01
1.8-1.850.18911290.18022655X-RAY DIFFRACTION96.07
1.85-1.910.2211370.17812633X-RAY DIFFRACTION98.26
1.91-1.980.20681530.16582709X-RAY DIFFRACTION98.45
1.98-2.060.20341140.16982724X-RAY DIFFRACTION98.1
2.06-2.150.20611330.16792648X-RAY DIFFRACTION97.58
2.15-2.260.19051290.16092670X-RAY DIFFRACTION97.19
2.26-2.410.1911410.17042691X-RAY DIFFRACTION98.81
2.41-2.590.22591330.17322726X-RAY DIFFRACTION98.76
2.59-2.850.19081430.18242659X-RAY DIFFRACTION97.09
2.85-3.270.22141460.17552712X-RAY DIFFRACTION98.65
3.27-4.110.15971470.15932660X-RAY DIFFRACTION97.09
4.11-43.50.16121450.14282724X-RAY DIFFRACTION97.09
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)
11.390499061480.8743088847811.212073633682.24114980711.960380674465.38056389450.0967973724154-0.02837479731850.0436503991793-0.1166628454270.103678514935-0.27803178668-0.374302691870.286891603427-0.1523661759350.204734333751-0.04638019720570.03666637522670.155340532368-0.02430863685340.2308195874132.3140147957910.70172254512.3942219787
21.623219653691.149825113170.3838627112862.238002011740.9758482635874.400654796890.157730872172-0.121781847780.07775403228030.18242290409-0.0586781119281-0.441726960265-0.4848781231720.613565106546-0.1607627700490.348887716623-0.09637086110230.01271268509590.279246024849-0.07496532396280.3212236014495.4479875565517.026940668624.3117249418
31.370137033740.00437048501329-0.9500119442753.511519842560.1339984855913.029033023080.0158857175906-0.02107019159560.0140280748461-0.086032977610.0457181585381-0.0346391573043-0.09251570237670.011994453527-0.04164885261110.164793845257-0.0269213643912-0.02170226781140.148944198059-0.01746588529890.154082129-2.027443752482.5295757373113.3616254066
41.997972321181.116360987471.270371043242.551018187151.785929667974.583741393470.208356440744-0.0839168447034-0.2530013219430.3021997062510.0327261916274-0.2429477530170.4840425068380.0308115907787-0.1333128941810.191588632581-0.021373090724-0.01505628531250.1617991638440.0003973870333970.228048489883-6.16666698389-9.2344183609614.6294607168
52.191368248910.9202295298121.288942004891.975684934381.70080310543.68150077275-0.0051921183569-0.167903808811-0.2231972912010.235575177287-0.04169083802110.1558587290420.598640980069-0.7282975497610.07590913850890.373213997708-0.1323721915350.006946809793040.365319835948-0.0303653388910.275568445688-19.1031610294-19.55063864084.12113022353
63.099277673730.7396593748160.8696622564614.487640202971.990575562345.18022122256-0.09144490423850.445718221763-0.0566276056422-0.33793683332-0.0269236196979-0.0635144531587-0.1977029058750.015757378142-0.03007860582870.249241300991-0.07616874496130.00559705072360.299784249144-0.04020742120890.227302732843-10.2724909305-11.5276506397-1.46011214486
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )1 - 431 - 43
22chain 'A' and (resid 44 through 100 )44 - 10044 - 101
33chain 'A' and (resid 101 through 180 )101 - 180102 - 182
44chain 'A' and (resid 181 through 213 )181 - 213183 - 215
55chain 'A' and (resid 214 through 274 )214 - 274216 - 276
66chain 'A' and (resid 275 through 304 )275 - 304277 - 308

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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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