[English] 日本語
Yorodumi
- PDB-7be7: Crystal structure of MG-132 covalently bound to the main protease... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7be7
TitleCrystal structure of MG-132 covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.
Components3C-like proteinase
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Mpro / 3CLpro / EXSCALATE4COV / drug discovery / Elettra / MG-132
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / G-quadruplex RNA binding / 3'-5'-exoribonuclease activity / suppression by virus of host ISG15-protein conjugation / suppression by virus of host toll-like receptor signaling pathway / host cell endoplasmic reticulum-Golgi intermediate compartment / protein K48-linked deubiquitination / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / viral genome replication / suppression by virus of host TRAF activity / helicase activity / viral transcription / Transferases; Transferring one-carbon groups; Methyltransferases / ubiquitinyl hydrolase 1 / DNA helicase / methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / thiol-dependent deubiquitinase / DNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / methylation / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / endonuclease activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / viral RNA genome replication / RNA helicase activity / suppression by virus of host type I interferon-mediated signaling pathway / viral protein processing / Hydrolases; Acting on ester bonds / transcription, DNA-templated / host cell cytoplasm / protein dimerization 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 / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 14, betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 14, betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) 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 / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus replicase NSP15, middle domain / RNA polymerase, N-terminal, coronavirus / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / Coronavirus replicase NSP15, N-terminal oligomerisation / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP1 superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / Betacoronavirus SUD-C domain / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP3, N-terminal, betacoronavirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Betacoronavirus single-stranded poly(A) binding domain / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Non-structural protein NSP1, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Coronavirus (CoV) Nsp1 globular domain profile. / 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 / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Lipocalin signature. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Peptidase family C16 domain profile. / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP7 / RNA synthesis protein NSP10, coronavirus / Coronavirus papain-like peptidase / Non-structural protein NSP8, coronavirus-like / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP4, N-terminal / Coronavirus endopeptidase C30 / Coronavirus replicase NSP4, N-terminal / Peptidase C30, domain 3, coronavirus / Non-structural protein NSP9, coronavirus / Peptidase C16, coronavirus / Peptidase C30, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Coronavirus replicase NSP3, C-terminal
Similarity search - Domain/homology
PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form / Chem-ALD / DI(HYDROXYETHYL)ETHER / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsCostanzi, E. / Demitri, N. / Giabbai, B. / Storici, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission101003551European Union
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L.
Authors: Costanzi, E. / Kuzikov, M. / Esposito, F. / Albani, S. / Demitri, N. / Giabbai, B. / Camasta, M. / Tramontano, E. / Rossetti, G. / Zaliani, A. / Storici, P.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,57820
Polymers67,6512
Non-polymers1,92718
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint21 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.898, 99.240, 103.375
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 / 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 , 6 types, 417 molecules

#2: Chemical ChemComp-ALD / N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide


Type: Peptide-like / Class: Inhibitor / Mass: 477.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H43N3O5 / Feature type: SUBJECT OF INVESTIGATION / References: PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12M Ethylene glycols (Diethylene glycol; Triethylene glycol; Tetraethylene glycol; Pentaethylene glycol) 0.1M Tris/BICINE pH 8.5, 20% v/v PEG 500 MME; 10 % w/v PEG 20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→99.24 Å / Num. obs: 80180 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 21.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.9
Reflection shellResolution: 1.68→1.71 Å / Num. unique obs: 4066 / CC1/2: 0.619

-
Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
PHENIX1.19_4085refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BB2
Resolution: 1.68→45.84 Å / SU ML: 0.1821 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2013 3972 4.96 %
Rwork0.1766 76115 -
obs0.1778 80087 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.53 Å2
Refinement stepCycle: LAST / Resolution: 1.68→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 129 399 5219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00554968
X-RAY DIFFRACTIONf_angle_d0.90136726
X-RAY DIFFRACTIONf_chiral_restr0.0479754
X-RAY DIFFRACTIONf_plane_restr0.0065872
X-RAY DIFFRACTIONf_dihedral_angle_d14.74341794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.70.33341600.30912687X-RAY DIFFRACTION99.68
1.7-1.720.3341440.29512691X-RAY DIFFRACTION99.96
1.72-1.740.30331620.28382676X-RAY DIFFRACTION99.82
1.74-1.770.28471240.27782696X-RAY DIFFRACTION99.93
1.77-1.790.27851330.26472695X-RAY DIFFRACTION99.93
1.79-1.820.2571350.24732673X-RAY DIFFRACTION99.96
1.82-1.850.2571340.23672718X-RAY DIFFRACTION99.93
1.85-1.880.25061630.2242657X-RAY DIFFRACTION99.93
1.88-1.910.25441490.20952694X-RAY DIFFRACTION99.96
1.91-1.950.2121390.20322676X-RAY DIFFRACTION99.96
1.95-1.980.23591520.19072689X-RAY DIFFRACTION99.96
1.98-2.020.21141390.18942709X-RAY DIFFRACTION99.93
2.02-2.070.21571540.18472694X-RAY DIFFRACTION99.93
2.07-2.120.19371500.17852700X-RAY DIFFRACTION99.96
2.12-2.170.19961480.17032691X-RAY DIFFRACTION99.96
2.17-2.230.21411410.17312692X-RAY DIFFRACTION100
2.23-2.290.18161340.16682728X-RAY DIFFRACTION99.97
2.29-2.370.18051580.16542697X-RAY DIFFRACTION99.96
2.37-2.450.17391020.16312734X-RAY DIFFRACTION100
2.45-2.550.20731430.16932732X-RAY DIFFRACTION99.97
2.55-2.670.21241210.17592759X-RAY DIFFRACTION99.9
2.67-2.810.1991500.1762726X-RAY DIFFRACTION99.93
2.81-2.980.20131350.18382735X-RAY DIFFRACTION99.86
2.98-3.210.20031520.17062724X-RAY DIFFRACTION99.9
3.21-3.540.20181590.16492766X-RAY DIFFRACTION99.86
3.54-4.050.18321260.14822752X-RAY DIFFRACTION98.97
4.05-5.10.14531520.13092793X-RAY DIFFRACTION99.49
5.1-45.840.19041130.18072931X-RAY DIFFRACTION98.26
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)
11.72031521033-0.052247418745-0.2302482618640.74600155723-0.05277720419292.35453556280.00813438369019-0.1281007434320.000540490192629-0.00846661670712-0.0341300769932-0.03224045060610.05477744955950.2766399154340.03006663473290.1893054112830.0243367199698-0.001511339641540.1581819452130.008677353174380.19341648764618.4227484432-6.70182535977-18.6269627469
21.805983836040.159915180329-0.4187067631070.611387861248-0.6479093654642.2678137277-0.0526181287686-0.2291296459670.07495417299130.0694277529234-0.147364222079-0.177379176391-0.0674235867180.7337242174440.1722267198260.2048488374320.00969336123295-0.00324908639250.3989956115090.04953181269730.27242797630233.2805067505-5.3982041726-24.9445119517
31.4970334363-0.6877507116091.244367917361.36728253982-0.893317970653.30172820256-0.0488116840674-0.0298327185427-0.1347568508750.00723139111873-0.039189429128-0.04252418657880.2229912334010.3313519882340.03210474883430.2081019668730.04672681739470.01594970365560.1475729686150.02701333868180.2258676277616.196631205-15.7318969548-21.421689436
41.988140178640.08914276772750.1359985368880.3982202999210.2538142346182.571521644530.00191813306353-0.05946601045240.00997602540161-0.02649275643750.005417195011730.05097778431740.05446534351170.0560435760208-0.009147074047750.177799483765-0.00151316656221-0.002134161738190.1291599315550.003592912517120.19529654492211.7258195371-4.56696585285-23.4221140599
52.398946773680.479867981313-0.3259962997980.2106414862650.09106484389580.434776306465-0.01779992145720.2701240128810.157172162265-0.03674240258480.04706052336280.0310492739474-0.0579855207548-0.0275946837192-0.03733996819330.187030540921-0.00202154836882-0.005831683790870.1653821045040.02583486934090.1861291882397.37089275895-3.03647622999-33.6980809865
62.29496754112-0.2947623318650.175785323661.62381681667-0.4657901327161.6918711-0.02247801375990.164363162445-0.01624538603420.004261395122620.007514006044360.119850505919-0.0191636416609-0.162902296553-0.001222729680490.163411684922-0.00248305888932-0.005469175754630.22563127888-0.008185388621990.201683142269-12.4193927592-6.76973359407-34.0860618509
70.996404029920.2723214598080.01265891022971.68747232336-0.9323194596522.247426997410.05817443484890.03003130685030.0668128567658-0.1661056066120.002708688314620.1850670394350.302203569327-0.2024449654640.008434574814510.245983145449-0.01138781204920.01950340170390.1950554401660.0181804052060.2450133543264.01425620646-6.81649615978-8.36434140568
82.17241522927-0.7388507062361.274202334651.71699145485-0.6167038747143.915974550410.0376622291154-0.361813751181-0.1797464287260.030437269870.08510736613870.1721776857060.304977645386-0.690411653545-0.02001226901650.177516806246-0.07597110917480.02818179163290.2764380815670.02991404880280.179762912043-4.70846968223-9.87340223161.79042590513
90.751945820821-0.3982606094250.2163525121351.29651106582-1.226803233951.86813298735-0.0468576158170.0979035130440.01988717305060.101486785780.1542342343060.00355887918026-0.3386190545-0.593450610238-0.008878098774180.2387412745360.05791825068880.005384312377420.229544606223-0.03780962083390.179052439548-7.8165210061212.2176086642-12.9842207975
101.73581731283-0.180916067175-0.5721828472221.91864446455-1.131397151632.98805792847-0.06500186203370.02692545989480.07048980702940.3152466930930.04542114370530.128135833337-0.849673253596-0.1902227418190.02806067722220.4461900300220.05024764106570.01101787098740.218549927182-0.02945554941660.241537331375-3.5097639069818.0129078987-15.2582059979
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 166 )AA111 - 166111 - 166
55chain 'A' and (resid 167 through 213 )AA167 - 213167 - 213
66chain 'A' and (resid 214 through 301 )AA214 - 301214 - 301
77chain 'B' and (resid 1 through 22 )BL1 - 221 - 22
88chain 'B' and (resid 23 through 180 )BL23 - 18023 - 180
99chain 'B' and (resid 181 through 226 )BL181 - 226181 - 226
1010chain 'B' and (resid 227 through 305 )BL227 - 305227 - 305

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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