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- PDB-8teq: Tropomyosin-receptor kinase fused gene protein (TRK-fused gene pr... -

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Basic information

Entry
Database: PDB / ID: 8teq
TitleTropomyosin-receptor kinase fused gene protein (TRK-fused gene protein; TFG) Low Complexity Domain (residues 237-327) G269V mutant, amyloid fiber
ComponentsTRK-fused gene protein Low Complexity Domain G269V mutant
KeywordsPROTEIN FIBRIL / amyloid / mutation / Charcot-Marie-Tooth disease / Hereditary motor and sensory neuropathy with proximal dominant involvement
Function / homology
Function and homology information


COPII vesicle coating / COPII-mediated vesicle transport / Signaling by ALK fusions and activated point mutants / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / bioluminescence / generation of precursor metabolites and energy / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / identical protein binding ...COPII vesicle coating / COPII-mediated vesicle transport / Signaling by ALK fusions and activated point mutants / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / bioluminescence / generation of precursor metabolites and energy / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Protein TFG / TFG, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Uncharacterized protein / Protein TFG
Similarity search - Component
Biological speciesPurpureocillium lilacinum (fungus)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsRosenberg, G.M. / Sawaya, M.R. / Boyer, D.R. / Ge, P. / Abskharon, R. / Eisenberg, D.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG048120 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG07895 United States
National Institutes of Health/Office of the DirectorU24 GM129541 United States
CitationJournal: PNAS Nexus / Year: 2023
Title: Fibril structures of TFG protein mutants validate the identification of TFG as a disease-related amyloid protein by the IMPAcT method.
Authors: Gregory M Rosenberg / Romany Abskharon / David R Boyer / Peng Ge / Michael R Sawaya / David S Eisenberg /
Abstract: We previously presented a bioinformatic method for identifying diseases that arise from a mutation in a protein's low-complexity domain that drives the protein into pathogenic amyloid fibrils. One ...We previously presented a bioinformatic method for identifying diseases that arise from a mutation in a protein's low-complexity domain that drives the protein into pathogenic amyloid fibrils. One protein so identified was the tropomyosin-receptor kinase-fused gene protein (TRK-fused gene protein or TFG). Mutations in TFG are associated with degenerative neurological conditions. Here, we present experimental evidence that confirms our prediction that these conditions are amyloid-related. We find that the low-complexity domain of TFG containing the disease-related mutations G269V or P285L forms amyloid fibrils, and we determine their structures using cryo-electron microscopy (cryo-EM). These structures are unmistakably amyloid in nature and confirm the propensity of the mutant TFG low-complexity domain to form amyloid fibrils. Also, despite resulting from a pathogenic mutation, the fibril structures bear some similarities to other amyloid structures that are thought to be nonpathogenic and even functional, but there are other factors that support these structures' relevance to disease, including an increased propensity to form amyloid compared with the wild-type sequence, structure-stabilizing influence from the mutant residues themselves, and double-protofilament amyloid cores. Our findings elucidate two potentially disease-relevant structures of a previously unknown amyloid and also show how the structural features of pathogenic amyloid fibrils may not conform to the features commonly associated with pathogenicity.
History
DepositionJul 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRK-fused gene protein Low Complexity Domain G269V mutant
B: TRK-fused gene protein Low Complexity Domain G269V mutant
C: TRK-fused gene protein Low Complexity Domain G269V mutant
D: TRK-fused gene protein Low Complexity Domain G269V mutant
E: TRK-fused gene protein Low Complexity Domain G269V mutant
F: TRK-fused gene protein Low Complexity Domain G269V mutant
G: TRK-fused gene protein Low Complexity Domain G269V mutant
H: TRK-fused gene protein Low Complexity Domain G269V mutant
I: TRK-fused gene protein Low Complexity Domain G269V mutant
J: TRK-fused gene protein Low Complexity Domain G269V mutant
K: TRK-fused gene protein Low Complexity Domain G269V mutant
L: TRK-fused gene protein Low Complexity Domain G269V mutant
M: TRK-fused gene protein Low Complexity Domain G269V mutant
N: TRK-fused gene protein Low Complexity Domain G269V mutant
O: TRK-fused gene protein Low Complexity Domain G269V mutant
P: TRK-fused gene protein Low Complexity Domain G269V mutant
Q: TRK-fused gene protein Low Complexity Domain G269V mutant
R: TRK-fused gene protein Low Complexity Domain G269V mutant
S: TRK-fused gene protein Low Complexity Domain G269V mutant
T: TRK-fused gene protein Low Complexity Domain G269V mutant
U: TRK-fused gene protein Low Complexity Domain G269V mutant
V: TRK-fused gene protein Low Complexity Domain G269V mutant
W: TRK-fused gene protein Low Complexity Domain G269V mutant
X: TRK-fused gene protein Low Complexity Domain G269V mutant
Y: TRK-fused gene protein Low Complexity Domain G269V mutant
Z: TRK-fused gene protein Low Complexity Domain G269V mutant
0: TRK-fused gene protein Low Complexity Domain G269V mutant
1: TRK-fused gene protein Low Complexity Domain G269V mutant
2: TRK-fused gene protein Low Complexity Domain G269V mutant
3: TRK-fused gene protein Low Complexity Domain G269V mutant


Theoretical massNumber of molelcules
Total (without water)1,214,72430
Polymers1,214,72430
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "2"
d_2ens_1chain "C"
d_3ens_1chain "E"
d_4ens_1chain "G"
d_5ens_1chain "I"
d_6ens_1chain "K"
d_7ens_1chain "M"
d_8ens_1chain "O"
d_9ens_1chain "Q"
d_10ens_1chain "S"
d_11ens_1chain "U"
d_12ens_1chain "W"
d_13ens_1chain "Y"
d_14ens_1chain "0"
d_15ens_1chain "A"
d_1ens_2chain "1"
d_2ens_2chain "D"
d_3ens_2chain "F"
d_4ens_2chain "H"
d_5ens_2chain "J"
d_6ens_2chain "L"
d_7ens_2chain "N"
d_8ens_2chain "P"
d_9ens_2chain "R"
d_10ens_2chain "T"
d_11ens_2chain "V"
d_12ens_2chain "X"
d_13ens_2chain "Z"
d_14ens_2chain "B"
d_15ens_2chain "3"

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_12CA262 - 290293 - 321
d_2ens_1CC262 - 290293 - 321
d_3ens_1EE262 - 290293 - 321
d_4ens_1GG262 - 290293 - 321
d_5ens_1II262 - 290293 - 321
d_6ens_1KK262 - 290293 - 321
d_7ens_1MM262 - 290293 - 321
d_8ens_1OO262 - 290293 - 321
d_9ens_1QQ262 - 290293 - 321
d_10ens_1SS262 - 290293 - 321
d_11ens_1UU262 - 290293 - 321
d_12ens_1WW262 - 290293 - 321
d_13ens_1YY262 - 290293 - 321
d_14ens_10AA262 - 290293 - 321
d_15ens_1AA262 - 290293 - 321
d_1ens_21BA265 - 290296 - 321
d_2ens_2DD265 - 290296 - 321
d_3ens_2FF265 - 290296 - 321
d_4ens_2HH265 - 290296 - 321
d_5ens_2JJ265 - 290296 - 321
d_6ens_2LL265 - 290296 - 321
d_7ens_2NN265 - 290296 - 321
d_8ens_2PP265 - 290296 - 321
d_9ens_2RR265 - 290296 - 321
d_10ens_2TT265 - 290296 - 321
d_11ens_2VV265 - 290296 - 321
d_12ens_2XX265 - 290296 - 321
d_13ens_2ZZ265 - 290296 - 321
d_14ens_2BB265 - 290296 - 321
d_15ens_23DA265 - 290296 - 321

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.909272207545, 0.416201937269, 3.39580207463E-7), (-0.416201937268, 0.909272207543, -1.82553507532E-6), (-1.06856207978E-6, 1.51857436768E-6, 0.999999999998)-60.4600720944, 94.167549911, 39.4559074595
2given(0.948620641777, 0.3164156728, 9.4279517232E-7), (-0.3164156728, 0.948620641777, 5.07762330455E-7), (-7.33691002018E-7, -7.79988996549E-7, 0.999999999999)-49.2332663426, 68.3215837301, 29.5923003006
3given(0.885642888458, 0.46436696063, -2.27305002958E-7), (-0.46436696063, 0.885642888457, -1.24306228081E-6), (-3.75925993831E-7, 1.20646220227E-6, 0.999999999999)-65.0177419284, 107.503986755, 44.3878363808
4given(0.964224738496, 0.26508612501, 1.95996437891E-7), (-0.26508612501, 0.964224738495, -1.59236147734E-6), (-6.11097547715E-7, 1.48343839284E-6, 0.999999999999)-42.596801398, 55.8883275055, 24.6598271735
5given(0.859460093167, 0.511202844527, -2.10484415496E-7), (-0.511202844527, 0.859460093166, -1.61443262727E-6), (-6.44399596004E-7, 1.49514064817E-6, 0.999999999999)-68.8543658233, 121.068045747, 49.3198312352
6given(0.977055275901, 0.212985886466, 2.91281313086E-7), (-0.212985886465, 0.9770552759, -1.26602060153E-6), (-5.54242463822E-7, 1.17493329944E-6, 0.999999999999)-35.3020215278, 43.8266550781, 19.7278764932
7given(0.830807177519, 0.556560359514, 1.23309057239E-6), (-0.556560359514, 0.830807177519, -6.3332998683E-7), (-1.37694686324E-6, -1.60114233488E-7, 0.999999999999)-71.9576200259, 134.816052611, 54.2522977314
8given(0.987071892256, 0.160278131748, 8.52205595167E-7), (-0.160278131747, 0.987071892256, -1.46423934931E-6), (-1.07587373675E-6, 1.30871958458E-6, 0.999999999999)-27.3718624443, 32.1750618477, 14.7959497676
9given(0.799759697937, 0.600320269153, 8.31928631709E-7), (-0.600320269153, 0.799759697937, -7.52029974639E-8), (-7.1048887488E-7, -4.39279293568E-7, 1)-74.3189424521, 148.712196287, 59.1842294528
10given(0.994247204623, 0.107109738573, 1.27746638562E-6), (-0.107109738574, 0.994247204624, 7.11736581673E-7), (-1.1938834637E-6, -8.44471197357E-7, 0.999999999999)-18.8282294248, 20.9652497599, 9.86440052879
11given(0.766415071963, 0.642345652642, 1.38463745036E-7), (-0.642345652641, 0.766415071963, -1.50989260947E-6), (-1.07599365476E-6, 1.06826286827E-6, 0.999999999999)-75.9313690914, 162.713102436, 64.1160009096
12given(0.998560820699, 0.0536310298724, 6.91508653482E-7), (-0.0536310298718, 0.998560820698, -9.28847472418E-7), (-7.40328495081E-7, 8.9042437311E-7, 0.999999999999)-9.69521556836, 10.2300278298, 4.93197164638
13given(0.730862071147, 0.682525188515, 1.31196336948E-6), (-0.682525188515, 0.730862071148, -1.57882311211E-7), (-1.06662291971E-6, -7.80057853112E-7, 0.999999999999)-76.7909704416, 176.780947143, 69.0483637299
14given(0.930284724528, 0.366838290408, 4.64307224801E-7), (-0.366838290407, 0.930284724527, -1.76692858515E-6), (-1.08011498017E-6, 1.47342100353E-6, 0.999999999998)-55.1936209059, 81.0944975341, 34.5239184636
15given(0.948621511035, -0.316413066736, 1.32696074545E-7), (0.316413066735, 0.948621511035, 5.78057898244E-7), (-3.08783423077E-7, -5.06371385007E-7, 1)68.3210044823, -49.2329183706, -29.5918605676
16given(0.909273205942, -0.416199756073, -4.63869209108E-7), (0.416199756073, 0.909273205942, 5.06761901405E-7), (2.10869663152E-7, -6.5384727042E-7, 1)94.1668250907, -60.4599225707, -39.4559321408
17given(0.964224608454, -0.265086598022, 9.85797632676E-8), (0.265086598022, 0.964224608454, 1.26552438914E-6), (-4.30526588669E-7, -1.19411758453E-6, 0.999999999999)55.8881342509, -42.5971186945, -24.6597202046
18given(0.885640714816, -0.464371106186, -4.66206497201E-7), (0.464371106186, 0.885640714815, 7.65792411479E-7), (5.7279586206E-8, -8.94709765519E-7, 1)107.505046529, -65.0183096004, -44.3878623129
19given(0.977055369635, -0.212985456457, 2.41940013749E-6), (0.212985456437, 0.97705536962, 6.58978072264E-6), (-3.76741535075E-6, -5.92328359719E-6, 0.999999999975)43.8258846832, -35.3033423941, -19.7262940704
20given(0.859459888184, -0.511203189155, -8.56977430389E-7), (0.511203189155, 0.859459888184, 3.93732299258E-7), (5.35260519445E-7, -7.76486713344E-7, 1)121.068000277, -68.8544725985, -49.3199715876
21given(0.987071865657, -0.160278295562, -3.90457128815E-7), (0.160278295563, 0.987071865656, 1.51777204845E-6), (1.42143329621E-7, -1.5607318906E-6, 0.999999999999)32.1749642212, -27.3719857044, -14.7957641568
22given(0.830807082786, -0.556560500927, -6.20795567956E-7), (0.556560500926, 0.83080708278, 3.3263889025E-6), (-1.33557531904E-6, -3.10909775257E-6, 0.999999999994)134.81607587, -71.9580975801, -54.2512286581
23given(0.99424737403, -0.107108166049, 2.15586883187E-7), (0.107108166049, 0.99424737403, 1.0262978624E-7), (-2.2533918067E-7, -7.89482797839E-8, 1)20.9650984322, -18.8278014129, -9.86394451147
24given(0.799761162889, -0.600318317507, 3.67233466988E-8), (0.600318317507, 0.799761162889, 1.27728725125E-7), (-1.06047799826E-7, -8.01067760371E-8, 1)148.71152047, -74.3188019911, -59.1839665365
25given(0.99856085232, -0.0536304411106, -3.33851480578E-7), (0.0536304411103, 0.99856085232, -8.92054679315E-7), (3.81212304941E-7, 8.72866278725E-7, 1)10.2299032976, -9.69482305344, -4.93222037698
26given(0.766413852869, -0.642347107202, 3.74610205238E-8), (0.642347107201, 0.766413852869, -4.01489515771E-7), (2.29184983955E-7, 3.31770104835E-7, 1)162.71334634, -75.931314469, -64.1161042056
27given(0.930284131816, -0.366839793494, -3.33300238112E-7), (0.366839793494, 0.930284131815, 1.30933199971E-6), (-1.70251157744E-7, -1.34031857313E-6, 0.999999999999)81.0946558842, -55.1940634736, -34.5237436754
28given(0.730859856535, -0.682527559961, 4.8436706712E-7), (0.682527559961, 0.730859856534, -1.0049440867E-6), (3.31897590207E-7, 1.06506716348E-6, 0.999999999999)176.781675385, -76.7906309567, -69.0482488175

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Components

#1: Protein ...
TRK-fused gene protein Low Complexity Domain G269V mutant / TRK-fused gene protein / TFG


Mass: 40490.789 Da / Num. of mol.: 30 / Mutation: G269V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Purpureocillium lilacinum (fungus), (gene. exp.) Homo sapiens (human)
Gene: PCL_01928, TFG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U3DNX3, UniProt: Q92734

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: amyloid fibril of protein TFG G269V / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4 / Details: PBS
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: 8 seconds, blot force 0

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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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 15192

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Processing

EM software
IDNameCategory
1EMAN2particle selection
2crYOLOparticle selection
5CTFFINDCTF correction
8Cootmodel fitting
12RELIONclassification
13RELION3D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -3.07 ° / Axial rise/subunit: 4.93 Å / Axial symmetry: C1
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31643 / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingB value: 44.55 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.55 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00296900
ELECTRON MICROSCOPYf_angle_d0.53949360
ELECTRON MICROSCOPYf_chiral_restr0.0404855
ELECTRON MICROSCOPYf_plane_restr0.00711320
ELECTRON MICROSCOPYf_dihedral_angle_d17.77542640
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CA2ELECTRON MICROSCOPYNCS constraints1.36882078185E-13
ens_1d_3CA2ELECTRON MICROSCOPYNCS constraints1.46192684438E-13
ens_1d_4CA2ELECTRON MICROSCOPYNCS constraints9.6684096621E-14
ens_1d_5CA2ELECTRON MICROSCOPYNCS constraints1.1696643889E-13
ens_1d_6CA2ELECTRON MICROSCOPYNCS constraints1.97856468962E-13
ens_1d_7CA2ELECTRON MICROSCOPYNCS constraints8.3725773756E-14
ens_1d_8CA2ELECTRON MICROSCOPYNCS constraints1.10216646615E-13
ens_1d_9CA2ELECTRON MICROSCOPYNCS constraints1.62818933122E-13
ens_1d_10CA2ELECTRON MICROSCOPYNCS constraints8.7952545498E-14
ens_1d_11CA2ELECTRON MICROSCOPYNCS constraints1.22232393965E-13
ens_1d_12CA2ELECTRON MICROSCOPYNCS constraints1.00417768201E-13
ens_1d_13CA2ELECTRON MICROSCOPYNCS constraints1.1558286872E-13
ens_1d_14CA2ELECTRON MICROSCOPYNCS constraints1.74547484426E-13
ens_1d_15CA2ELECTRON MICROSCOPYNCS constraints1.43188323694E-13
ens_2d_2BA1ELECTRON MICROSCOPYNCS constraints9.5554943306E-14
ens_2d_3BA1ELECTRON MICROSCOPYNCS constraints8.5712952423E-14
ens_2d_4BA1ELECTRON MICROSCOPYNCS constraints1.36277640238E-13
ens_2d_5BA1ELECTRON MICROSCOPYNCS constraints1.52076947004E-13
ens_2d_6BA1ELECTRON MICROSCOPYNCS constraints2.74598389161E-13
ens_2d_7BA1ELECTRON MICROSCOPYNCS constraints9.7987963906E-14
ens_2d_8BA1ELECTRON MICROSCOPYNCS constraints2.9568918113E-12
ens_2d_9BA1ELECTRON MICROSCOPYNCS constraints1.38354716771E-13
ens_2d_10BA1ELECTRON MICROSCOPYNCS constraints1.03424199549E-13
ens_2d_11BA1ELECTRON MICROSCOPYNCS constraints1.43088478842E-13
ens_2d_12BA1ELECTRON MICROSCOPYNCS constraints1.34965008481E-13
ens_2d_13BA1ELECTRON MICROSCOPYNCS constraints1.29374607167E-13
ens_2d_14BA1ELECTRON MICROSCOPYNCS constraints8.8178748191E-14
ens_2d_15BA1ELECTRON MICROSCOPYNCS constraints8.8287222519E-14

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