[English] 日本語
Yorodumi
- PDB-7ju7: The crystal structure of SARS-CoV-2 Main Protease in complex with... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5875
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)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

+
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