[English] 日本語
Yorodumi
- PDB-8okm: Crystal structure of F2F-2020197-00X bound to the main protease (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8okm
TitleCrystal structure of F2F-2020197-00X bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.
Components3C-like proteinase nsp5
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, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...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) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / 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 / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase 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 / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase 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 / 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. / : / : / Coronavirus replicase NSP7
Similarity search - Domain/homology
Chem-84C / BROMIDE ION / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsCostanzi, E. / Demitri, N. / Storici, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission101003551European Union
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination.
Authors: Stefanelli, I. / Corona, A. / Cerchia, C. / Cassese, E. / Improta, S. / Costanzi, E. / Pelliccia, S. / Morasso, S. / Esposito, F. / Paulis, A. / Scognamiglio, S. / Di Leva, F.S. / Storici, P. ...Authors: Stefanelli, I. / Corona, A. / Cerchia, C. / Cassese, E. / Improta, S. / Costanzi, E. / Pelliccia, S. / Morasso, S. / Esposito, F. / Paulis, A. / Scognamiglio, S. / Di Leva, F.S. / Storici, P. / Brindisi, M. / Tramontano, E. / Cannalire, R. / Summa, V.
History
DepositionMar 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,22314
Polymers67,6512
Non-polymers1,57212
Water9,134507
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-50 kcal/mol
Surface area25300 Å2
Unit cell
Length a, b, c (Å)68.025, 100.036, 104.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#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.: 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 BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase

-
Non-polymers , 8 types, 519 molecules

#2: Chemical ChemComp-84C / tert-butyl-N-[(2S)-1-[(3S,3aS,6aR)-3-[[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]-3,3a,4,5,6,6a-hexahydro-1H-cyclopenta[c]pyrrol-2-yl]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate / tert-butyl N-[(2S)-1-[(3S,3aS,6aR)-3-[[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]-3,3a,4,5,6,6a-hexahydro-1H-cyclopenta[c]pyrrol-2-yl]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate


Mass: 494.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.09M Sodium fluoride 0.09M Sodium bromide 0.09M Sodium iodide, 0.1M Hepes/MOPS pH 7.5, 0.1 M Hepes/Mops pH 7.5, 12.5% v/v MPD; 12.5% PEG 1000, 12.5% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.66→104.07 Å / Num. obs: 84525 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 22.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.6
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 4072 / CC1/2: 0.625

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BB2

7bb2


Resolution: 1.66→41.33 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5913
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1867 4365 5.17 %
Rwork0.1633 80064 -
obs0.1645 84429 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.52 Å2
Refinement stepCycle: LAST / Resolution: 1.66→41.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 0 93 507 5287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944922
X-RAY DIFFRACTIONf_angle_d1.0456702
X-RAY DIFFRACTIONf_chiral_restr0.0587757
X-RAY DIFFRACTIONf_plane_restr0.0093870
X-RAY DIFFRACTIONf_dihedral_angle_d14.92131790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.680.35951450.29732612X-RAY DIFFRACTION100
1.68-1.70.29411450.27772650X-RAY DIFFRACTION99.96
1.7-1.720.26081440.26542599X-RAY DIFFRACTION99.93
1.72-1.740.25931400.24152643X-RAY DIFFRACTION99.93
1.74-1.760.24511630.23742617X-RAY DIFFRACTION100
1.76-1.790.26781420.23382657X-RAY DIFFRACTION100
1.79-1.810.26351470.21672611X-RAY DIFFRACTION100
1.81-1.840.28361340.22412671X-RAY DIFFRACTION100
1.84-1.870.24051570.21252615X-RAY DIFFRACTION99.96
1.87-1.90.20231220.21172690X-RAY DIFFRACTION100
1.9-1.930.21571280.19092630X-RAY DIFFRACTION99.96
1.93-1.970.19371540.17942649X-RAY DIFFRACTION100
1.97-2.010.22591360.17022688X-RAY DIFFRACTION100
2.01-2.050.18731460.16662634X-RAY DIFFRACTION99.96
2.05-2.090.23171320.15862655X-RAY DIFFRACTION100
2.09-2.140.17241340.15772661X-RAY DIFFRACTION100
2.14-2.190.19051410.14852667X-RAY DIFFRACTION100
2.19-2.250.18081340.15112683X-RAY DIFFRACTION100
2.25-2.320.15831500.14862641X-RAY DIFFRACTION100
2.32-2.390.1781530.15462649X-RAY DIFFRACTION100
2.39-2.480.18951670.15332663X-RAY DIFFRACTION100
2.48-2.580.18991380.15272693X-RAY DIFFRACTION100
2.58-2.70.16021460.15762651X-RAY DIFFRACTION100
2.7-2.840.18491390.15942706X-RAY DIFFRACTION100
2.84-3.020.17941380.16712697X-RAY DIFFRACTION100
3.02-3.250.19811620.16392687X-RAY DIFFRACTION100
3.25-3.580.16661480.15162711X-RAY DIFFRACTION100
3.58-4.090.14671460.13572706X-RAY DIFFRACTION100
4.09-5.150.14641760.12352747X-RAY DIFFRACTION99.97
5.16-41.330.21391580.17752881X-RAY DIFFRACTION99.97
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)
12.94854223425-0.186324184379-1.158949817121.09105818915-0.1275794587792.77635266699-0.0359498473659-0.03405747386010.03125568611840.02854566527540.0122079645689-0.08989657138930.0463371625820.4248883996470.02975839421080.1792778585270.024686951621-0.003832499981010.2305641811960.006899048358110.16759829853818.1826857535-6.85027568802-18.4769889015
22.497607493580.316203570299-0.480783984650.706351565556-0.580086458613.55399329772-0.068222260456-0.2730192105090.2082333426360.0594662926848-0.0266405825957-0.129779055613-0.2145980373580.5899360771650.1024807296290.2107854031130.06914395988610.006642438388460.498589664230.02586922682450.30060242409133.0369849025-5.58911617159-24.8909135861
33.19655676993-1.604864876622.301035104641.90172077637-1.284417342644.761620688880.0240725097302-0.0142693791041-0.2919588029250.009042484395990.004719898943940.02844098687030.351077039060.422963556721-0.04859400461170.2360353380530.06749573231030.02344201850520.228874350220.012658521860.25007571951315.9332813086-15.8668117419-21.341312088
42.926104723680.272372996698-0.02652740827221.04229548490.02396440863583.090957452530.02467406864390.0535037707558-0.0189796707955-0.00175786815329-0.0286943568799-0.0186797562719-0.006174232386640.1675646635530.0154840128510.154504154950.007014999282290.002707560356610.1717963284040.001882095219830.17808843691412.0863797453-4.32155941316-24.7322669839
53.986656964240.265902097499-0.1874976374240.586208579289-0.2051443165931.03024069995-0.008166330824590.4180579059360.234851430237-0.05437287219290.00939672466856-0.00095796097245-0.02080522533650.147967747953-0.02274442377240.1689615393430.0112482205098-0.01341626269010.2247102278750.01477673584450.1748719935254.03566504444-3.13726154022-34.3930479985
61.63794601453-0.1423921557420.5685022172.09292883569-0.361800568632.70898459288-0.016980042687-0.05200528682890.01190147185930.03323001330790.03022188557350.153075432121-0.0336759425269-0.0799456555124-0.01478406305420.1681100565990.00916383409124-0.0006681620027630.206264916179-0.01258577092790.227283833855-12.7499607273-7.02700534224-33.839997469
72.25818619012-0.387914773282-0.4212924001540.882778514229-0.2741769972643.08237575683-0.098198683853-0.188743764363-0.2900603230890.030639971773-0.03897703618440.06645095711520.4620537426960.1272482384820.126980458730.2309954211670.01880615355750.03391240496920.132054811757-0.004292238935090.184911029291-0.105406725654-10.701367807-1.69813607774
86.17361100271-0.9552583753181.403394567364.746168479760.1964415827964.016679664310.00580158035796-0.467971245956-0.337425796780.3760693204370.01438633147070.9226517060630.507588034148-1.08911789891-0.1062030596430.527659522158-0.2051805776010.1366519285930.7041170346230.06862769856110.540549271277-19.4617306509-15.19936478919.88343939592
98.679013810371.59675868269-2.623786613453.02762222272-1.175858737825.102799205670.171049191298-0.341315848337-1.496189126250.289903785347-0.06802074588660.2320117179981.38125085046-0.1215429330570.1931966298360.762239986088-0.000132971206750.009908816183610.3112557555590.1696505363630.535857006841-2.55254058581-23.90591577277.98713545513
106.04806726408-6.064791504591.524607182317.7151085803-2.204507231391.92884863563-0.316060925239-0.756831602214-0.2667037538620.2884679433520.3397408123050.03780565725360.477877619584-0.122868482871-0.03782522963460.3568978412770.0574034707950.07049845389480.3432791425440.0812114604510.226078001989-4.33891769921-13.088993382712.3946298098
114.63720870157-2.236909920610.868208845053.76315460376-1.713887700144.40494451353-0.122904710931-0.3858024021930.01868166701230.2013096689610.0486250086492-0.0463426065112-0.02458842007730.4340933625320.1068718140130.191817335385-0.001166768894010.02193470551580.267583219827-0.01436384616060.161465274484.35556900666-3.664598103173.710613374
122.65912149199-1.06284944772-0.5244801062251.3052290119-0.1905358529822.94317155632-0.00187932133212-0.0191512080575-0.0310413795214-0.00595673593562-0.0696612255079-0.07112763818490.08943609073160.006229694918510.06790152402330.189590332314-0.01438891594810.02195461321170.1371573621540.007135235131390.180460645056-4.70094475846-3.9297359339-5.02512781624
130.8427048241880.313052783006-0.431821523791.01737735387-0.7796789268912.28172601258-0.03176949104380.03994134869560.0329220566634-0.01157241962560.1248034465610.101343161476-0.00663958104113-0.284345875725-0.1046633830940.1859972496040.0068498749920.02595059749270.1936965398950.00136178804020.220010476212-11.21791556856.32427162389-7.38014934911
141.989517551571.506006563610.297351406922.57211835191-1.29197318021.68602430795-0.0299746711069-0.0760918960680.3684969188660.3110694701810.166992970040.15567823707-0.286582224167-0.143545299306-0.1074317126450.342827450120.05249439402080.04132596205530.1863077500240.01571202766230.228254297867-7.2113722577724.9548057512-18.7316987532
152.810658431340.735011006861-0.1914218876112.697733199710.2097684325052.972844398330.102354721738-0.03536983380060.2727740153290.1884458132810.012151821316-0.0204142578271-0.5703111221560.229063181886-0.06992275953730.371911314244-0.009895263862180.03280945297120.184699550568-0.02238323488830.268791907499-3.4805873164722.6625393359-14.1174361798
163.082642537930.496132110997-0.6474680340291.668179033660.2927619518542.55612028601-0.120252395120.00295650939052-0.148936886621-0.0463626331818-0.0113448864397-0.0746945191254-0.1200962323920.2601417541380.1169479325850.270454864746-0.01569489065460.02827247646860.179273237869-0.003030554558460.2814201164710.71842310237110.5267021294-18.2081960907
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )AA1 - 431 - 43
22chain 'A' and (resid 44 through 91 )AA44 - 9144 - 91
33chain 'A' and (resid 92 through 110 )AA92 - 11092 - 110
44chain 'A' and (resid 111 through 180 )AA111 - 180111 - 180
55chain 'A' and (resid 181 through 213 )AA181 - 213181 - 213
66chain 'A' and (resid 214 through 301 )AA214 - 301214 - 301
77chain 'B' and (resid 1 through 43 )BC1 - 431 - 43
88chain 'B' and (resid 44 through 59 )BC44 - 5944 - 59
99chain 'B' and (resid 60 through 76 )BC60 - 7660 - 76
1010chain 'B' and (resid 77 through 91 )BC77 - 9177 - 91
1111chain 'B' and (resid 92 through 110 )BC92 - 11092 - 110
1212chain 'B' and (resid 111 through 180 )BC111 - 180111 - 180
1313chain 'B' and (resid 181 through 213 )BC181 - 213181 - 213
1414chain 'B' and (resid 214 through 237 )BC214 - 237214 - 237
1515chain 'B' and (resid 238 through 274 )BC238 - 274238 - 274
1616chain 'B' and (resid 275 through 305 )BC275 - 305275 - 305

+
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