[English] 日本語
Yorodumi
- PDB-6qm7: Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qm7
TitleLeishmania tarentolae proteasome 20S subunit complexed with GSK3494245
Components
  • Proteasome alpha1 chain
  • Proteasome alpha2 chain
  • Proteasome alpha3 chain
  • Proteasome alpha4 chain
  • Proteasome alpha5 chain
  • Proteasome alpha6 chain
  • Proteasome alpha7 chain
  • Proteasome beta1 chain
  • Proteasome beta2 chain
  • Proteasome beta3 chain
  • Proteasome beta4 chain
  • Proteasome beta5 chain
  • Proteasome beta6 chain
  • Proteasome beta7 chain
KeywordsHYDROLASE / Proteasome 20S subunit
Function / homology
Function and homology information


proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / hydrolase activity ...proteasome core complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / hydrolase activity / nucleus / cytoplasm
Similarity search - Function
Proteasome subunit alpha 3 / Proteasome subunit beta Pre3 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit beta 1 / Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome subunit beta 4 / Proteasome subunit beta 2 ...Proteasome subunit alpha 3 / Proteasome subunit beta Pre3 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit beta 1 / Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J6E / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Putative proteasome alpha 7 subunit / Proteasome subunit beta ...Chem-J6E / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type / Putative proteasome alpha 7 subunit / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit beta / Proteasome subunit alpha type / Proteasome subunit alpha type
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRowland, P. / Goswami, P.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Preclinical candidate for the treatment of visceral leishmaniasis that acts through proteasome inhibition.
Authors: Susan Wyllie / Stephen Brand / Michael Thomas / Manu De Rycker / Chun-Wa Chung / Imanol Pena / Ryan P Bingham / Juan A Bueren-Calabuig / Juan Cantizani / David Cebrian / Peter D Craggs / ...Authors: Susan Wyllie / Stephen Brand / Michael Thomas / Manu De Rycker / Chun-Wa Chung / Imanol Pena / Ryan P Bingham / Juan A Bueren-Calabuig / Juan Cantizani / David Cebrian / Peter D Craggs / Liam Ferguson / Panchali Goswami / Judith Hobrath / Jonathan Howe / Laura Jeacock / Eun-Jung Ko / Justyna Korczynska / Lorna MacLean / Sujatha Manthri / Maria S Martinez / Lydia Mata-Cantero / Sonia Moniz / Andrea Nühs / Maria Osuna-Cabello / Erika Pinto / Jennifer Riley / Sharon Robinson / Paul Rowland / Frederick R C Simeons / Yoko Shishikura / Daniel Spinks / Laste Stojanovski / John Thomas / Stephen Thompson / Elisabet Viayna Gaza / Richard J Wall / Fabio Zuccotto / David Horn / Michael A J Ferguson / Alan H Fairlamb / Jose M Fiandor / Julio Martin / David W Gray / Timothy J Miles / Ian H Gilbert / Kevin D Read / Maria Marco / Paul G Wyatt /
Abstract: Visceral leishmaniasis (VL), caused by the protozoan parasites and , is one of the major parasitic diseases worldwide. There is an urgent need for new drugs to treat VL, because current therapies ...Visceral leishmaniasis (VL), caused by the protozoan parasites and , is one of the major parasitic diseases worldwide. There is an urgent need for new drugs to treat VL, because current therapies are unfit for purpose in a resource-poor setting. Here, we describe the development of a preclinical drug candidate, GSK3494245/DDD01305143/compound 8, with potential to treat this neglected tropical disease. The compound series was discovered by repurposing hits from a screen against the related parasite Subsequent optimization of the chemical series resulted in the development of a potent cidal compound with activity against a range of clinically relevant and isolates. Compound 8 demonstrates promising pharmacokinetic properties and impressive in vivo efficacy in our mouse model of infection comparable with those of the current oral antileishmanial miltefosine. Detailed mode of action studies confirm that this compound acts principally by inhibition of the chymotrypsin-like activity catalyzed by the β5 subunit of the proteasome. High-resolution cryo-EM structures of apo and compound 8-bound 20S proteasome reveal a previously undiscovered inhibitor site that lies between the β4 and β5 proteasome subunits. This induced pocket exploits β4 residues that are divergent between humans and kinetoplastid parasites and is consistent with all of our experimental and mutagenesis data. As a result of these comprehensive studies and due to a favorable developability and safety profile, compound 8 is being advanced toward human clinical trials.
History
DepositionFeb 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4590
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome alpha1 chain
B: Proteasome alpha2 chain
C: Proteasome alpha3 chain
D: Proteasome alpha4 chain
E: Proteasome alpha5 chain
F: Proteasome alpha6 chain
G: Proteasome alpha7 chain
H: Proteasome beta1 chain
I: Proteasome beta2 chain
J: Proteasome beta3 chain
K: Proteasome beta4 chain
L: Proteasome beta5 chain
M: Proteasome beta6 chain
N: Proteasome beta7 chain
O: Proteasome alpha1 chain
P: Proteasome alpha2 chain
Q: Proteasome alpha3 chain
R: Proteasome alpha4 chain
S: Proteasome alpha5 chain
T: Proteasome alpha6 chain
U: Proteasome alpha7 chain
V: Proteasome beta1 chain
W: Proteasome beta2 chain
X: Proteasome beta3 chain
Y: Proteasome beta4 chain
Z: Proteasome beta5 chain
a: Proteasome beta6 chain
b: Proteasome beta7 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)848,66530
Polymers847,84528
Non-polymers8212
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A6 - 249
2111O6 - 249
1121B3 - 231
2121P3 - 231
1131C2 - 277
2131Q2 - 277
1141D2 - 240
2141R2 - 240
1151E107 - 342
2151S107 - 342
1161F168 - 405
2161T168 - 405
1171G6 - 233
2171U6 - 233
1181H55 - 283
2181V55 - 283
1191I30 - 248
2191W30 - 248
11101J2 - 205
21101X2 - 205
11111K1 - 206
21111Y1 - 206
11121L100 - 301
21121Z100 - 301
11131M126 - 339
21131a126 - 339
11141N2 - 219
21141b2 - 219

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.665125, -0.004841, 0.746716), (-0.00577, -0.999916, -0.011623), (0.746709, -0.012039, 0.665041)75.13171, 203.50221, -32.23988
3given(1), (1), (1)
4given(-0.665345, -0.005685, 0.746514), (-0.004697, -0.999919, -0.011801), (0.746521, -0.011358, 0.665265)75.30414, 203.4167, -32.36692
5given(1), (1), (1)
6given(-0.665233, -0.0053, 0.746617), (-0.005422, -0.999914, -0.011928), (0.746616, -0.011983, 0.665147)75.2341, 203.49364, -32.26983
7given(1), (1), (1)
8given(-0.665721, -0.005036, 0.746184), (-0.005576, -0.999916, -0.011723), (0.74618, -0.011964, 0.665637)75.22888, 203.48132, -32.26265
9given(1), (1), (1)
10given(-0.664415, -0.005586, 0.747343), (-0.005056, -0.999916, -0.011968), (0.747346, -0.01173, 0.664331)75.20694, 203.48248, -32.27693
11given(1), (1), (1)
12given(-0.665377, -0.005478, 0.746488), (-0.005488, -0.99991, -0.01223), (0.746488, -0.012234, 0.665287)75.27681, 203.52753, -32.22129
13given(1), (1), (1)
14given(-0.666238, -0.005678, 0.745718), (-0.004818, -0.999917, -0.011919), (0.745724, -0.011534, 0.666155)75.43805, 203.46777, -32.36608
15given(1), (1), (1)
16given(-0.665092, -0.005363, 0.746742), (-0.004982, -0.99992, -0.011618), (0.746745, -0.011448, 0.665012)75.20097, 203.43146, -32.32114
17given(1), (1), (1)
18given(-0.665083, -0.00513, 0.746752), (-0.005613, -0.999914, -0.011868), (0.746748, -0.012085, 0.664997)75.16663, 203.52563, -32.25706
19given(1), (1), (1)
20given(-0.665447, -0.005983, 0.746421), (-0.004675, -0.999915, -0.012183), (0.746431, -0.011597, 0.665362)75.34206, 203.43799, -32.31695
21given(1), (1), (1)
22given(-0.664848, -0.005056, 0.746962), (-0.00541, -0.999918, -0.011584), (0.746959, -0.011742, 0.664766)75.17793, 203.4687, -32.31942
23given(1), (1), (1)
24given(-0.665401, -0.005594, 0.746465), (-0.004605, -0.999922, -0.011598), (0.746472, -0.011155, 0.665324)75.29401, 203.43518, -32.36393
25given(1), (1), (1)
26given(-0.665407, -0.004288, 0.746468), (-0.005449, -0.999929, -0.010601), (0.746461, -0.011122, 0.665336)75.13824, 203.3793, -32.37431
27given(1), (1), (1)
28given(-0.66567, -0.005346, 0.746227), (-0.005346, -0.999915, -0.011932), (0.746227, -0.011932, 0.665584)75.28982, 203.49944, -32.28619

-
Components

-
Protein , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZMaNb

#1: Protein Proteasome alpha1 chain


Mass: 27178.107 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q7JMX2*PLUS
#2: Protein Proteasome alpha2 chain


Mass: 25179.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q9GNZ8*PLUS
#3: Protein Proteasome alpha3 chain


Mass: 32321.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4HVX3*PLUS
#4: Protein Proteasome alpha4 chain


Mass: 27821.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4HUT6*PLUS
#5: Protein Proteasome alpha5 chain


Mass: 38312.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4HZI9*PLUS
#6: Protein Proteasome alpha6 chain


Mass: 47978.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4IDD0*PLUS
#7: Protein Proteasome alpha7 chain


Mass: 25591.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4I357*PLUS
#8: Protein Proteasome beta1 chain


Mass: 30280.010 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4HV47*PLUS
#9: Protein Proteasome beta2 chain


Mass: 27603.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4HN55*PLUS
#10: Protein Proteasome beta3 chain


Mass: 22470.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4I384*PLUS
#11: Protein Proteasome beta4 chain


Mass: 23065.291 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4ICV5*PLUS
#12: Protein Proteasome beta5 chain


Mass: 33704.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4IDD6*PLUS
#13: Protein Proteasome beta6 chain


Mass: 37676.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A4HSQ5*PLUS
#14: Protein Proteasome beta7 chain


Mass: 24737.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A381MU64*PLUS

-
Non-polymers , 2 types, 336 molecules

#15: Chemical ChemComp-J6E / ~{N}-[4-fluoranyl-3-(3-morpholin-4-ylimidazo[1,2-a]pyrimidin-7-yl)phenyl]pyrrolidine-1-carboxamide


Mass: 410.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#16: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Proteasome 20S subunit / Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

SoftwareName: REFMAC / Version: 5.8.0238 / Classification: refinement
EM software
IDNameVersionCategory
7Cootmodel fitting
9REFMACmodel refinement
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182775 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 4R3O

4r3o

RefinementResolution: 2.8→200.09 Å / Cor.coef. Fo:Fc: 0.893 / SU B: 10.057 / SU ML: 0.179 / ESU R: 0.363
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.25433 --
obs0.25433 388718 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.918 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.42 Å20.2 Å2
2--0.85 Å20.1 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Total: 49518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01350122
ELECTRON MICROSCOPYr_bond_other_d0.0020.01746240
ELECTRON MICROSCOPYr_angle_refined_deg1.4831.64367810
ELECTRON MICROSCOPYr_angle_other_deg1.2371.577107116
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.89756320
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.23521.942588
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.777158512
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.58615348
ELECTRON MICROSCOPYr_chiral_restr0.0630.26558
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.0256858
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0210682
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.7333.90325370
ELECTRON MICROSCOPYr_mcbond_other2.7333.90325369
ELECTRON MICROSCOPYr_mcangle_it4.5835.85431662
ELECTRON MICROSCOPYr_mcangle_other4.5835.85431663
ELECTRON MICROSCOPYr_scbond_it3.6784.6324752
ELECTRON MICROSCOPYr_scbond_other3.6784.6324753
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other6.4276.67436149
ELECTRON MICROSCOPYr_long_range_B_refined9.0445.15354290
ELECTRON MICROSCOPYr_long_range_B_other9.03945.15454288
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1010A1557tight positional0.030.05
1111A1612tight positional0.030.05
1212A1579tight positional0.030.05
1313A1702tight positional0.030.05
1414A1712tight positional0.030.05
11A1857tight thermal3.370.5
22B1754tight thermal2.830.5
33C2195tight thermal2.820.5
44D1873tight thermal3.420.5
55E1756tight thermal3.560.5
66F1869tight thermal30.5
77G1727tight thermal3.150.5
88H1710tight thermal1.870.5
99I1659tight thermal2.130.5
1010J1557tight thermal1.970.5
1111K1612tight thermal2.070.5
1212L1579tight thermal1.950.5
1313M1702tight thermal2.030.5
1414N1712tight thermal1.830.5
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.854 28902 -
obs--100 %

+
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