[English] 日本語
Yorodumi
- PDB-8drs: Product structure of SARS-CoV-2 Mpro C145A mutant in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8drs
TitleProduct structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp6-nsp7 (C6) cut site sequence
Components3C-like proteinase nsp5
KeywordsHYDROLASE / Viral protease / SARS-CoV-2
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / 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 / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Lipocalin signature. / 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. / Coronavirus 3Ecto domain profile. / : / 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) / 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 / NSP3, second 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: 1.8 Å
AuthorsLee, J. / Kenward, C. / Worrall, L.J. / Vuckovic, M. / Paetzel, M. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2022
Title: X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.
Authors: Lee, J. / Kenward, C. / Worrall, L.J. / Vuckovic, M. / Gentile, F. / Ton, A.T. / Ng, M. / Cherkasov, A. / Strynadka, N.C.J. / Paetzel, M.
History
DepositionJul 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,4053
Polymers101,4053
Non-polymers00
Water9,476526
1
A: 3C-like proteinase nsp5
B: 3C-like proteinase nsp5


Theoretical massNumber of molelcules
Total (without water)67,6032
Polymers67,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-11 kcal/mol
Surface area25520 Å2
MethodPISA
2
C: 3C-like proteinase nsp5

C: 3C-like proteinase nsp5


Theoretical massNumber of molelcules
Total (without water)67,6032
Polymers67,6032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area2590 Å2
ΔGint-13 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.090, 108.530, 137.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein 3C-like proteinase nsp5 / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33801.566 Da / Num. of mol.: 3 / Fragment: UNP residues 3264-3563 / Mutation: C145A
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.: 526 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.1 M HEPES, 20% PEG6000, 0.2 M ammonium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2021
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→68.87 Å / Num. obs: 93855 / % possible obs: 99.8 % / Redundancy: 11.7 % / Biso Wilson estimate: 26.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.057 / Rrim(I) all: 0.198 / Net I/σ(I): 7
Reflection shellResolution: 1.8→60.32 Å / Redundancy: 12 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 14.1 / Num. unique obs: 93822 / CC1/2: 0.999 / Rpim(I) all: 0.043 / % possible all: 99.95

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7JOY

7joy


Resolution: 1.8→60.32 Å / SU ML: 0.2071 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 4638 4.94 %
Rwork0.1797 89173 -
obs0.1816 93811 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.27 Å2
Refinement stepCycle: LAST / Resolution: 1.8→60.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7029 0 0 526 7555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01567281
X-RAY DIFFRACTIONf_angle_d1.399918
X-RAY DIFFRACTIONf_chiral_restr0.08971121
X-RAY DIFFRACTIONf_plane_restr0.01221293
X-RAY DIFFRACTIONf_dihedral_angle_d15.8672625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.33031390.31532960X-RAY DIFFRACTION99.97
1.82-1.840.34321460.30932945X-RAY DIFFRACTION99.97
1.84-1.860.25141440.27832965X-RAY DIFFRACTION100
1.86-1.890.30211510.27312900X-RAY DIFFRACTION99.77
1.89-1.910.28821520.26462945X-RAY DIFFRACTION99.77
1.91-1.940.28481790.24312918X-RAY DIFFRACTION100
1.94-1.970.23011570.22442938X-RAY DIFFRACTION100
1.97-20.24451530.21412924X-RAY DIFFRACTION100
2-2.030.26581520.21452966X-RAY DIFFRACTION99.68
2.03-2.060.27351660.2192894X-RAY DIFFRACTION100
2.06-2.10.25871510.22322969X-RAY DIFFRACTION100
2.1-2.130.26311490.21882934X-RAY DIFFRACTION99.9
2.13-2.180.26951730.19632923X-RAY DIFFRACTION100
2.18-2.220.23921520.19192964X-RAY DIFFRACTION100
2.22-2.270.23681520.20392953X-RAY DIFFRACTION99.94
2.27-2.320.23551730.18032967X-RAY DIFFRACTION100
2.32-2.380.231480.18852942X-RAY DIFFRACTION100
2.38-2.440.24321550.19242933X-RAY DIFFRACTION100
2.44-2.510.24441410.1862995X-RAY DIFFRACTION100
2.51-2.60.22681420.18972991X-RAY DIFFRACTION100
2.6-2.690.23031680.18962956X-RAY DIFFRACTION100
2.69-2.80.2461440.18542993X-RAY DIFFRACTION100
2.8-2.920.23011560.18542976X-RAY DIFFRACTION100
2.92-3.080.20731550.1732976X-RAY DIFFRACTION100
3.08-3.270.21741290.17883010X-RAY DIFFRACTION100
3.27-3.520.19731770.17222995X-RAY DIFFRACTION100
3.52-3.880.21491790.15942995X-RAY DIFFRACTION100
3.88-4.440.17391590.13763032X-RAY DIFFRACTION100
4.44-5.590.17841490.13693083X-RAY DIFFRACTION99.91
5.59-60.320.16821470.16073231X-RAY DIFFRACTION99.82
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)
18.79245033777-2.592243940012.083877120.786766960393-0.6545286910835.27300482973-0.995639525914-0.67921202033-2.081789361811.219256026460.6070872233930.1039279886952.18794463730.820382369122-0.3002726822681.219823695680.5259706630190.2736954174680.6513516818250.2181189362540.50865190520114.397-26.756-4.086
20.66947930656-0.3283588871550.3632184034811.682954115610.6621912361331.01822383862-0.612798080102-0.435978876725-0.1698048217970.6175090370180.6354883779360.0006165805043161.338074909191.496304043060.07124046860570.8887643354750.4241217948170.07898671588860.8856619567620.01278268384540.22991284638913.983-14.4261.643
32.11322236376-0.0853024477784-1.665250804064.479507875261.16433223762.37274195975-1.06851846409-0.423062571205-0.891113642361.43903561117-0.08033408338361.770744720831.711380609150.07429271756910.02419904952760.9919278736130.02770660659610.5425903995250.4046808936080.1067416644070.6164946268270.938-16.7673.606
41.49499752619-0.1015517235481.952016890170.0197699169813-0.1299340034522.57953658073-0.70283425316-0.4502448109511.776330125960.477797435807-0.05678865136071.39889975216-0.301291682538-0.7089946829350.3504976802970.5887699992450.03689413959150.1535236558640.542525841016-0.1431372236851.5016810957-16.743.31117.323
59.121478596575.89880487651-2.334565609854.21022847631-1.19005784443.17481262798-0.479458112865-0.4295832509910.1508460546740.520513731559-0.0209581743581.673299740140.439178117987-0.3373304971570.4117930485560.689811220586-0.02028758220570.3925301646520.552766008525-0.0366923562491.17699773457-16.984-5.48220.431
61.16759566208-0.308516541483-2.408950324162.130248914711.395920933015.59769354016-0.6156450585490.577359803342-0.315605196485-0.4657579018030.5075247495270.6650889291990.1683434892650.01261044061790.1117379251210.345613057239-0.0818178333728-0.1065088030920.3589421252390.0518143890140.534911233778-10.2373.45612.121
71.60125181444-0.6291271945191.560256610021.780786615220.3409973403315.41342645021-0.262997747515-0.1639448016240.1360900485530.3390842826250.0223090746853-0.0742150255623-0.549611830251-0.03448830251020.226764798250.2726028723290.00438323930996-0.02199207691720.167607093585-0.0004112688304530.16340800339918.45814.12359.079
82.18512465718-1.5866144710.7419627880973.943346342550.581508297395.43121291283-0.331519466512-0.4255452015410.5123216800670.7987341425680.20085179733-0.546605947699-0.6216622453620.2347028316460.06381248306320.519378924894-0.0255181746383-0.08424482439440.3380291783520.002376559357410.23547930721224.51414.0471.387
92.62194933677-0.8626699750590.6131759757093.20547493285-0.1293653121454.37065612830.07157315997520.0989266290107-0.04591738283320.0844075885571-0.222208730858-0.000363480085540.0004909657785910.08530261680910.1243809358580.157438121827-0.00480521333392-0.01905307023630.1494801386440.009659666944230.11526673408521.6328.07352.655
101.11686830933-1.02334081217-0.3443396510881.607719406590.07598632981752.417713356290.118377753780.279310769109-0.2117072851550.0221612395866-0.0176561687384-0.136989072330.2118108349720.969116219746-0.0629612817050.1636410738230.0475337467328-0.008954908844740.3100596608640.0005553053855770.21121007743827.3150.95244.277
112.94270277874-0.772440014050.7478981787743.768112024270.2314959954482.527267143040.3210982497760.425329643-0.152138351372-0.553292186123-0.3350942571260.1538775905380.1075579733970.1103776624840.01663020788840.2986187637140.13080575112-0.07804457327940.26662931371-0.06449655511050.24865043191719.337-4.90130.247
121.217927722940.0174927327620.08633219264821.8060129315-0.2498206459332.10936408595-0.153072540194-0.337550766190.2021758172640.1313747998930.01134544072550.342334148166-0.150785281037-0.4480799380240.09300493419440.1682479264020.0740334529706-0.01200191151320.247990570494-0.06126024202170.260403259232-0.75819.54842.999
133.92706308703-0.3394821342670.2255845871231.28605847588-0.8595661828051.92325363899-0.158224858843-0.3096316498110.1299731497620.05509998023850.1420515767180.442459678103-0.0781723891146-0.838452785768-0.01116791765850.235004582590.119513042518-0.0003898447664990.542185376732-0.1039159118750.491759679539-13.88422.19639.761
142.995820195540.124671843535-0.5618582342861.73295500727-0.7978124544762.93354063842-0.0811887861108-0.1450213962330.362788729580.106566493213-0.05006789123230.0357930572894-0.2414301997890.04323752840870.09895932057760.1360196374770.042139272226-0.06416611445160.135939737181-0.04542098776590.2426319298616.93121.51137.921
153.401139123571.258710655320.8560979346981.36853466418-0.03863083070971.60846918331-0.225585907430.6170354770460.144255636886-0.1900008956070.0307159459112-0.0482112415389-0.2018284435750.2387516642980.1122629750220.1921691092050.00399615780574-0.05435426393460.2095881209780.06408688679730.25052881005716.4924.4427.818
166.285904187881.936407332750.4678835741273.504819521410.07066897775216.10007485053-0.1100524087360.309029402403-0.202574514302-0.03610217930.0213477113313-0.125717406218-0.04822618296560.3623799645590.06413242417590.14045944447-0.0341022497403-0.03832948955890.2152935829140.06115744370510.29076148191228.79725.56431.216
172.59752983169-1.27973737582-1.386493100797.837078353243.228524997435.32668967596-0.379480999834-0.5002420974820.1617713674380.3310070751570.5530855140390.05758808207550.2503613123430.888581492005-0.2024271491350.3719068432340.05486438822470.005365216843130.4158786833490.06429052725370.1161400890358.6-4.8350.8
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 23:66 )C23 - 66
2X-RAY DIFFRACTION2( CHAIN C AND RESID 67:129 )C67 - 129
3X-RAY DIFFRACTION3( CHAIN C AND RESID 130:200 )C130 - 200
4X-RAY DIFFRACTION4( CHAIN C AND RESID 201:226 )C201 - 226
5X-RAY DIFFRACTION5( CHAIN C AND RESID 227:273 )C227 - 273
6X-RAY DIFFRACTION6( CHAIN C AND RESID 274:306 )C274 - 306
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1:43 )A1 - 43
8X-RAY DIFFRACTION8( CHAIN A AND RESID 44:100 )A44 - 100
9X-RAY DIFFRACTION9( CHAIN A AND RESID 101:180 )A101 - 180
10X-RAY DIFFRACTION10( CHAIN A AND RESID 181:213 )A181 - 213
11X-RAY DIFFRACTION11( CHAIN A AND RESID 214:302 )A214 - 302
12X-RAY DIFFRACTION12( CHAIN B AND RESID 1:43 )B1 - 43
13X-RAY DIFFRACTION13( CHAIN B AND RESID 44:100 )B44 - 100
14X-RAY DIFFRACTION14( CHAIN B AND RESID 101:155 )B101 - 155
15X-RAY DIFFRACTION15( CHAIN B AND RESID 156:237 )B156 - 237
16X-RAY DIFFRACTION16( CHAIN B AND RESID 238:302 )B238 - 302
17X-RAY DIFFRACTION17( CHAIN C AND RESID 1:22 )C1 - 22

+
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