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- PDB-9ce8: 20S Proteasome core particle in complex with Ixazomib -

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Basic information

Entry
Database: PDB / ID: 9ce8
Title20S Proteasome core particle in complex with Ixazomib
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsANTIMICROBIAL PROTEIN / Proteasome / Proteolysis
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Chem-6V8 / Proteasome subunit beta / Proteasome subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsZeytuni, N. / Uday, A.B. / Vahidi, S. / Turner, M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT451412 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN/03031-2022 Canada
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for allosteric modulation of M. tuberculosis proteasome core particle.
Authors: Madison Turner / Adwaith B Uday / Algirdas Velyvis / Enrico Rennella / Natalie Zeytuni / Siavash Vahidi /
Abstract: The Mycobacterium tuberculosis (Mtb) proteasome system selectively degrades damaged or misfolded proteins and is crucial for the pathogen's survival within the host. Targeting the 20S core particle ...The Mycobacterium tuberculosis (Mtb) proteasome system selectively degrades damaged or misfolded proteins and is crucial for the pathogen's survival within the host. Targeting the 20S core particle (CP) offers a viable strategy for developing tuberculosis treatments. The activity of Mtb 20S CP, like that of its eukaryotic counterpart, is allosterically regulated, yet the specific conformations involved have not been captured in high-resolution structures to date. Here, we use single-particle electron cryomicroscopy and H/D exchange mass spectrometry to determine the Mtb 20S CP structure in an auto-inhibited state that is distinguished from the canonical resting state by the conformation of switch helices at the α/β interface. The rearrangement of these helices collapses the S1 pocket, effectively inhibiting substrate binding. Biochemical experiments show that the Mtb 20S CP activity can be altered through allosteric sites far from the active site. Our findings underscore the potential of targeting allostery to develop antituberculosis therapeutics.
History
DepositionJun 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit alpha
I: Proteasome subunit alpha
J: Proteasome subunit alpha
K: Proteasome subunit alpha
L: Proteasome subunit alpha
M: Proteasome subunit alpha
N: Proteasome subunit alpha
O: Proteasome subunit beta
P: Proteasome subunit beta
Q: Proteasome subunit beta
R: Proteasome subunit beta
S: Proteasome subunit beta
T: Proteasome subunit beta
U: Proteasome subunit beta
V: Proteasome subunit beta
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)724,04442
Polymers718,99028
Non-polymers5,05414
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "J"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "A"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "E"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_1ens_2chain "X"
d_2ens_2chain "P"
d_3ens_2chain "Q"
d_4ens_2chain "R"
d_5ens_2chain "S"
d_6ens_2chain "T"
d_7ens_2chain "U"
d_8ens_2chain "V"
d_9ens_2chain "W"
d_10ens_2chain "O"
d_11ens_2chain "Y"
d_12ens_2chain "Z"
d_13ens_2chain "a"
d_14ens_2chain "b"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERLEULEUJJ8 - 2348 - 234
d_21ens_1SERSERLEULEUBB8 - 2348 - 234
d_31ens_1SERSERLEULEUCC8 - 2348 - 234
d_41ens_1SERSERLEULEUDD8 - 2348 - 234
d_51ens_1SERSERLEULEUAA8 - 2348 - 234
d_61ens_1SERSERLEULEUFF8 - 2348 - 234
d_71ens_1SERSERLEULEUGG8 - 2348 - 234
d_81ens_1SERSERLEULEUHH8 - 2348 - 234
d_91ens_1SERSERLEULEUII8 - 2348 - 234
d_101ens_1SERSERLEULEUEE8 - 2348 - 234
d_111ens_1SERSERLEULEUKK8 - 2348 - 234
d_121ens_1SERSERLEULEULL8 - 2348 - 234
d_131ens_1SERSERLEULEUMM8 - 2348 - 234
d_141ens_1SERSERLEULEUNN8 - 2348 - 234
d_11ens_26V86V86V86V8XLA301
d_12ens_2THRTHRSERSERXX1 - 2221 - 222
d_21ens_26V86V86V86V8PDA301
d_22ens_2THRTHRSERSERPP1 - 2221 - 222
d_31ens_26V86V86V86V8QEA301
d_32ens_2THRTHRSERSERQQ1 - 2221 - 222
d_41ens_26V86V86V86V8RFA301
d_42ens_2THRTHRSERSERRR1 - 2221 - 222
d_51ens_26V86V86V86V8SGA301
d_52ens_2THRTHRSERSERSS1 - 2221 - 222
d_61ens_26V86V86V86V8THA301
d_62ens_2THRTHRSERSERTT1 - 2221 - 222
d_71ens_26V86V86V86V8UIA301
d_72ens_2THRTHRSERSERUU1 - 2221 - 222
d_81ens_26V86V86V86V8VJA301
d_82ens_2THRTHRSERSERVV1 - 2221 - 222
d_91ens_26V86V86V86V8WKA301
d_92ens_2THRTHRSERSERWW1 - 2221 - 222
d_101ens_26V86V86V86V8OCA301
d_102ens_2THRTHRSERSEROO1 - 2221 - 222
d_111ens_26V86V86V86V8YMA301
d_112ens_2THRTHRSERSERYY1 - 2221 - 222
d_121ens_26V86V86V86V8ZNA301
d_122ens_2THRTHRSERSERZZ1 - 2221 - 222
d_131ens_26V86V86V86V8aOA301
d_132ens_2THRTHRSERSERaAA1 - 2221 - 222
d_141ens_26V86V86V86V8bPA301
d_142ens_2THRTHRSERSERbBA1 - 2221 - 222

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.222508322455, -0.974930766413, 0.000217116264474), (0.974930766974, -0.222508262531, 0.000269654860841), (-0.000214584657371, 0.000271673776973, 0.999999940073)420.824667445, 47.375399372, -0.0271274243617
2given(0.222546301808, 0.974922106417, -0.000173122585195), (0.974922111222, -0.222546269743, 0.000186745429841), (0.000143534462281, -0.000210340541049, -0.999999967577)-37.7947220571, 47.3953331906, 383.065333373
3given(-0.623518813091, 0.781808295139, -0.000281733579321), (0.781808193892, 0.623518876092, 0.000398899535667), (0.000487529170647, 2.8459744214E-5, -0.999999880753)161.242763905, -77.6835990622, 382.957168237
4given(0.6232824711, -0.781996617029, 0.000502169620475), (0.781996182275, 0.623282660385, 0.000834368134095), (-0.000965466675233, -0.000127352306359, 0.999999525828)221.838131844, -77.7184192271, 0.194227679801
5given(-0.623013756652, -0.782210789936, -0.000373002562861), (-0.782210781438, 0.623013846223, -0.00020203152733), (0.000390417001924, 0.00016589820537, -0.999999910026)460.721415632, 222.036027818, 382.94581889
6given(0.222351032761, -0.974966649116, 0.000226586441348), (-0.974966623279, -0.222351090885, -0.000275454507856), (0.000318940700922, -0.000159666623301, -0.999999936392)335.623762675, 420.865532617, 383.01999697
7given(0.900984342016, -0.433851487958, 0.000319122496448), (-0.433851455327, -0.900984398428, -0.000168820241439), (0.000360767303433, 1.36526346403E-5, -0.99999993483)102.015163758, 447.191687251, 382.980916282
8given(0.901058784503, 0.433696836341, 0.000347875424887), (0.433696742295, -0.901058841836, 0.000315072653571), (0.000450102240523, -0.000133026543759, -0.999999889856)-64.1590591826, 280.98111728, 382.995470356
9given(-0.999999999839, -1.7699801096E-5, -3.07558670143E-6), (-1.76997972755E-5, 0.999999999843, -1.24219757269E-6), (3.0756086876E-6, -1.24214313523E-6, -0.999999999994)383.044515122, 0.00303866332996, 383.039699687
10given(0.623004051805, 0.782218523651, 0.000364270254332), (-0.782218517884, 0.62300413622, -0.000191133504569), (-0.000376450042915, -0.00016586199067, 0.999999915388)-77.6801483882, 222.037875907, 0.0919190706398
11given(-0.222358031301, 0.974965055215, -0.000216853678487), (-0.974965031822, -0.222358084402, -0.000262725205213), (-0.000304367062751, 0.000153005694143, 0.999999941975)47.416451027, 420.865146293, 0.0188389724765
12given(-0.900983526999, 0.433853159151, -0.000346946740013), (-0.433853124299, -0.900983593777, -0.000174013095511), (-0.000388089451887, -6.25900541799E-6, 0.999999924674)281.028282824, 447.192421851, 0.0617223246639
13given(-0.90106458419, -0.433684769721, -0.000368281050272), (0.433684665881, -0.901064648903, 0.000330268462845), (-0.000475077437516, 0.000137875370906, 0.999999877646)447.200144548, 280.982327337, 0.0476392132582
14given(0.900963711475, 0.433894444861, -3.63710776618E-5), (0.433894415816, -0.900963676298, -0.000299858449518), (-0.000162875935332, 0.000254380374101, -0.999999954381)-64.1177321234, 281.027369006, 383.008398048
15given(0.222102154343, 0.975023300531, 0.0004432355708), (0.975023396573, -0.222102085675, -0.000199180958277), (-9.5762530622E-5, 0.000476403571661, -0.999999881935)-37.8450035056, 47.3566596449, 382.953121393
16given(-0.623605041312, 0.781739478985, 0.000373426493677), (0.781739565404, 0.623605008177, 0.000213680351524), (-6.58282649731E-5, 0.000425174409317, -0.999999907447)161.166737682, -77.6678259653, 382.958383927
17given(-0.999999999861, -1.48778266271E-5, 7.47386313906E-6), (-1.48778826127E-5, 0.999999999861, -7.49085439408E-6), (-7.47375169039E-6, -7.4909655883E-6, -0.999999999944)383.041705132, 0.00369173211226, 383.042761203
18given(-0.623678576182, -0.781680876569, -0.000202033785865), (-0.781680895105, 0.623678513332, 0.000300392537815), (-0.000108806971063, 0.000345274340857, -0.999999934473)460.697927122, 221.73281959, 382.982783805
19given(0.222897412906, -0.974841889023, -0.0001863467238), (-0.974841878711, -0.22289744832, 0.000197594529642), (-0.000234159633774, 0.00013761528086, -0.999999963116)335.574085822, 420.883333731, 383.045226367
20given(0.901140836143, -0.433526277563, -0.000400123343919), (-0.433526261308, -0.90114092327, 0.000131008871878), (-0.000417363308114, 5.54065330052E-5, -0.999999911369)102.038855096, 447.124984125, 383.089062321
21given(0.623596838117, -0.781746013286, -0.000392684491297), (0.781746106741, 0.623596813094, 0.000198225790375), (8.99145759681E-5, -0.00043059254836, 0.999999903253)221.878763002, -77.6647123524, 0.0789307805478
22given(-0.222753867359, -0.974874573972, -0.000528772487846), (0.974874675115, -0.222753665228, -0.000415266815467), (0.000287047050073, -0.00060798919643, 0.999999773977)420.958442498, 47.5559117188, 0.0780484824074
23given(0.623666423925, 0.781690571943, 0.000203478834178), (-0.78169059062, 0.623666359779, 0.000303669914073), (0.00011047300501, -0.000348446219431, 0.99999993319)-77.6584248711, 221.736280445, 0.057672263773
24given(-0.222870683956, 0.974848000523, 0.000184687422325), (-0.974847989556, -0.222870719229, 0.000199421244914), (0.000235566820513, -0.000135597013101, 0.999999963061)47.4607368155, 420.87763313, -0.00583996920639
25given(-0.901131437263, 0.433545805321, 0.000409224110103), (-0.43354579005, -0.901131528162, 0.000129929324287), (0.000425095061231, -6.03339913846E-5, 0.999999907827)280.994047897, 447.126462173, -0.0492754701253
26given(-0.900967841195, -0.433885870294, 2.62925772439E-5), (0.433885843696, -0.900967804188, -0.00030076082999), (0.000154184640056, -0.000259567858652, 0.999999954426)447.158332044, 281.029664909, 0.0339010472214

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Components

#1: Protein
Proteasome subunit alpha / 20S proteasome alpha subunit / Proteasome core protein PrcA


Mass: 26911.039 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcA, Rv2109c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WHU1
#2: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PrcB


Mass: 24445.383 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcB, Rv2110c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WHT9, proteasome endopeptidase complex
#3: Chemical
ChemComp-6V8 / [(1~{R})-1-[2-[[2,5-bis(chloranyl)phenyl]carbonylamino]ethanoylamino]-3-methyl-butyl]boronic acid


Mass: 361.029 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C14H19BCl2N2O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: 20S Proteasome core particle in complex with Ixazomib / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium chlorideNaCl1
250 mMSodium phosphate monobasicNaH2PO41
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELD / Nominal defocus max: 2750 nm / Nominal defocus min: 1250 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
9PHENIXdev_5316model refinement
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 449574 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 39.64 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001947152
ELECTRON MICROSCOPYf_angle_d0.46863826
ELECTRON MICROSCOPYf_chiral_restr0.04277238
ELECTRON MICROSCOPYf_plane_restr0.00378400
ELECTRON MICROSCOPYf_dihedral_angle_d7.16076998
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2JJELECTRON MICROSCOPYNCS constraints5.29753199373E-12
ens_1d_3JJELECTRON MICROSCOPYNCS constraints2.20266893335E-10
ens_1d_4JJELECTRON MICROSCOPYNCS constraints2.74230043982E-12
ens_1d_5JJELECTRON MICROSCOPYNCS constraints7.02195006132E-13
ens_1d_6JJELECTRON MICROSCOPYNCS constraints1.1658036554E-10
ens_1d_7JJELECTRON MICROSCOPYNCS constraints4.76301197351E-13
ens_1d_8JJELECTRON MICROSCOPYNCS constraints5.37837812111E-13
ens_1d_9JJELECTRON MICROSCOPYNCS constraints2.38772321431E-11
ens_1d_10JJELECTRON MICROSCOPYNCS constraints7.71881307377E-11
ens_1d_11JJELECTRON MICROSCOPYNCS constraints3.91865958969E-12
ens_1d_12JJELECTRON MICROSCOPYNCS constraints1.6542102245E-11
ens_1d_13JJELECTRON MICROSCOPYNCS constraints3.66819216586E-13
ens_1d_14JJELECTRON MICROSCOPYNCS constraints1.34322846801E-12
ens_2d_2LAXELECTRON MICROSCOPYNCS constraints6.8950017235E-11
ens_2d_3LAXELECTRON MICROSCOPYNCS constraints4.74998322065E-13
ens_2d_4LAXELECTRON MICROSCOPYNCS constraints9.12829550353E-13
ens_2d_5LAXELECTRON MICROSCOPYNCS constraints3.05979499887E-12
ens_2d_6LAXELECTRON MICROSCOPYNCS constraints1.22122229266E-12
ens_2d_7LAXELECTRON MICROSCOPYNCS constraints1.5420943851E-11
ens_2d_8LAXELECTRON MICROSCOPYNCS constraints5.88913900861E-11
ens_2d_9LAXELECTRON MICROSCOPYNCS constraints7.35852868836E-13
ens_2d_10LAXELECTRON MICROSCOPYNCS constraints5.33557784323E-11
ens_2d_11LAXELECTRON MICROSCOPYNCS constraints3.36069234719E-12
ens_2d_12LAXELECTRON MICROSCOPYNCS constraints2.45841978091E-12
ens_2d_13LAXELECTRON MICROSCOPYNCS constraints8.74745899898E-13
ens_2d_14LAXELECTRON MICROSCOPYNCS constraints4.57829191864E-11

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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

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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

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