[English] 日本語
Yorodumi
- EMDB-7025: Cryo-EM structure of of the large subunit of Leishmania ribosome ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 7025
TitleCryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin
SampleLeishmania donovani 91S ribosome LSU
SourceLeishmania donovani / eukaryote / ドノバンリーシュマニア
Map dataprimary map
Methodsingle particle reconstruction, at 2.5 Å resolution
AuthorsShalev-Benami M / Zhang Y
CitationNat Commun, 2017, 8, 1589-1589

Nat Commun, 2017, 8, 1589-1589 Yorodumi Papers
Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.
Moran Shalev-Benami / Yan Zhang / Haim Rozenberg / Yuko Nobe / Masato Taoka / Donna Matzov / Ella Zimmerman / Anat Bashan / Toshiaki Isobe / Charles L Jaffe / Ada Yonath / Georgios Skiniotis

Validation ReportPDB-ID: 6az3

SummaryFull reportAbout validation report
DateDeposition: Sep 9, 2017 / Header (metadata) release: Nov 1, 2017 / Map release: Dec 6, 2017 / Last update: Dec 13, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.065
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6az3
  • Surface level: 0.065
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6az3
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_7025.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.02 Å/pix.
= 391.68 Å
384 pix
1.02 Å/pix.
= 391.68 Å
384 pix
1.02 Å/pix.
= 391.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.02 Å
Density
Contour Level:0.065 (by author), 0.065 (movie #1):
Minimum - Maximum-0.40696242 - 0.62841886
Average (Standard dev.)0.0002886674 (0.02751031)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 391.68 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z391.680391.680391.680
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.4070.6280.000

-
Supplemental data

-
Sample components

+
Entire Leishmania donovani 91S ribosome LSU

EntireName: Leishmania donovani 91S ribosome LSU / Number of components: 55

+
Component #1: protein, Leishmania donovani 91S ribosome LSU

ProteinName: Leishmania donovani 91S ribosome LSU / Recombinant expression: No
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #2: protein, ribosomal protein uL2

ProteinName: ribosomal protein uL2 / Recombinant expression: No
MassTheoretical: 27.520994 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #3: protein, ribosomal protein uL3

ProteinName: ribosomal protein uL3 / Recombinant expression: No
MassTheoretical: 45.741395 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #4: protein, ribosomal protein uL4

ProteinName: ribosomal protein uL4 / Recombinant expression: No
MassTheoretical: 40.523211 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #5: protein, ribosomal protein uL5

ProteinName: ribosomal protein uL5 / Recombinant expression: No
MassTheoretical: 19.245344 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #6: protein, ribosomal protein uL6

ProteinName: ribosomal protein uL6 / Recombinant expression: No
MassTheoretical: 21.118717 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #7: protein, ribosomal protein eL6

ProteinName: ribosomal protein eL6 / Recombinant expression: No
MassTheoretical: 21.208869 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #8: protein, ribosomal protein eL8

ProteinName: ribosomal protein eL8 / Recombinant expression: No
MassTheoretical: 39.175203 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #9: protein, ribosomal protein uL13

ProteinName: ribosomal protein uL13 / Recombinant expression: No
MassTheoretical: 25.346008 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #10: protein, ribosomal protein eL13

ProteinName: ribosomal protein eL13 / Recombinant expression: No
MassTheoretical: 23.897861 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #11: protein, ribosomal protein uL14

ProteinName: ribosomal protein uL14 / Recombinant expression: No
MassTheoretical: 14.421971 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #12: protein, ribosomal protein eL14

ProteinName: ribosomal protein eL14 / Recombinant expression: No
MassTheoretical: 17.038955 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #13: protein, ribosomal protein uL15

ProteinName: ribosomal protein uL15 / Recombinant expression: No
MassTheoretical: 16.034684 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #14: protein, ribosomal protein eL15

ProteinName: ribosomal protein eL15 / Recombinant expression: No
MassTheoretical: 24.366773 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #15: protein, ribosomal protein uL16

ProteinName: ribosomal protein uL16 / Recombinant expression: No
MassTheoretical: 24.607186 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #16: protein, ribosomal protein uL18

ProteinName: ribosomal protein uL18 / Recombinant expression: No
MassTheoretical: 34.100633 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #17: protein, ribosomal protein eL18

ProteinName: ribosomal protein eL18 / Recombinant expression: No
MassTheoretical: 21.939883 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #18: protein, ribosomal protein eL19

ProteinName: ribosomal protein eL19 / Recombinant expression: No
MassTheoretical: 22.901018 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #19: protein, ribosomal protein eL20

ProteinName: ribosomal protein eL20 / Recombinant expression: No
MassTheoretical: 20.703172 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #20: protein, ribosomal protein eL21

ProteinName: ribosomal protein eL21 / Recombinant expression: No
MassTheoretical: 17.437443 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #21: protein, ribosomal protein uL22

ProteinName: ribosomal protein uL22 / Recombinant expression: No
MassTheoretical: 17.828902 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #22: protein, ribosomal protein eL22

ProteinName: ribosomal protein eL22 / Recombinant expression: No
MassTheoretical: 14.042504 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #23: protein, ribosomal protein uL23

ProteinName: ribosomal protein uL23 / Recombinant expression: No
MassTheoretical: 13.461783 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #24: protein, ribosomal protein uL24

ProteinName: ribosomal protein uL24 / Recombinant expression: No
MassTheoretical: 13.874408 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #25: protein, ribosomal protein eL24

ProteinName: ribosomal protein eL24 / Recombinant expression: No
MassTheoretical: 7.988512 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #26: protein, ribosomal protein eL27

ProteinName: ribosomal protein eL27 / Recombinant expression: No
MassTheoretical: 15.223005 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #27: protein, ribosomal protein eL28

ProteinName: ribosomal protein eL28 / Recombinant expression: No
MassTheoretical: 15.525923 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #28: protein, ribosomal protein uL29

ProteinName: ribosomal protein uL29 / Recombinant expression: No
MassTheoretical: 14.987824 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #29: protein, ribosomal protein eL29

ProteinName: ribosomal protein eL29 / Recombinant expression: No
MassTheoretical: 7.788074 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #30: protein, ribosomal protein uL30

ProteinName: ribosomal protein uL30 / Recombinant expression: No
MassTheoretical: 26.313074 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #31: protein, ribosomal protein eL30

ProteinName: ribosomal protein eL30 / Recombinant expression: No
MassTheoretical: 10.122675 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #32: protein, ribosomal protein eL31

ProteinName: ribosomal protein eL31 / Recombinant expression: No
MassTheoretical: 13.503024 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #33: protein, ribosomal protein eL32

ProteinName: ribosomal protein eL32 / Recombinant expression: No
MassTheoretical: 15.02965 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #34: protein, ribosomal protein eL33

ProteinName: ribosomal protein eL33 / Recombinant expression: No
MassTheoretical: 14.336777 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #35: protein, ribosomal protein eL34

ProteinName: ribosomal protein eL34 / Recombinant expression: No
MassTheoretical: 14.640328 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #36: protein, ribosomal protein eL36

ProteinName: ribosomal protein eL36 / Recombinant expression: No
MassTheoretical: 11.050092 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #37: protein, ribosomal protein eL37

ProteinName: ribosomal protein eL37 / Recombinant expression: No
MassTheoretical: 9.531135 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #38: protein, ribosomal protein eL38

ProteinName: ribosomal protein eL38 / Recombinant expression: No
MassTheoretical: 8.761474 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #39: protein, ribosomal protein eL39

ProteinName: ribosomal protein eL39 / Recombinant expression: No
MassTheoretical: 6.373649 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #40: protein, ribosomal protein eL40

ProteinName: ribosomal protein eL40 / Recombinant expression: No
MassTheoretical: 5.912278 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #41: protein, ribosomal protein eL41

ProteinName: ribosomal protein eL41 / Recombinant expression: No
MassTheoretical: 4.2593 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #42: protein, ribosomal protein eL43

ProteinName: ribosomal protein eL43 / Recombinant expression: No
MassTheoretical: 10.092869 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #43: protein, ribosomal protein eL44

ProteinName: ribosomal protein eL44 / Recombinant expression: No
MassTheoretical: 11.141353 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #44: nucleic-acid, rRNA alpha

Nucleic-acidName: rRNA alpha / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGACCUGAGU GUGGCAGGAC UACCCGCCGA ACUUAAGCAU AUUAC(OMU)CAGC GGAGGAAAAG AAAACA(A2M)CCG UGAUUCUCUC AGUGAGCGGC GAGCGAAGAG GGAACGAACU CGUUGCCGAA UCGGGUCUUA CAAGGCCUUG AGUUGUGGCA CAAAUAUCAU UUCGUGGUUG GUGCAGGAGU GGCGAAAUUC AAGCGCAAAG CAAACCCGUU GCUGAAUACA ACCCUUCAUG UG(A2M)GUAUUGA GCCAAAGAAG GUGUUAGCCC AUUGAGCCAU AAACCUGAGC GCCUCAUGAA CUGUAUUAAG CGAGUAGCAC UGUUUGGGAA UGCAGUGUCA AGUUGGCAGG UAUUUGUCUG CCAAAGUUAA AUACAGAGUA GGAAGACCGA UAGCGAACAA GUAGCGUGAG CGAAAGUUUG AAAAGCACUU UGGAAAGAGA GUGA(A2M)AUAGA ACCUGAAGUC GUGACAAAGA CAAUGGAAGU ACCUCCAUUU CAACGGCCAG AACCAGCCCU ACUGCAUUAU CCUGUCGGGG GUCAAAAUCC GGCGGGCAAC GAAGUGCAAG AAUUUUGGGU CUUGGUGAAA UGAGCGGAGU AUUUGAGCUG UGCACGGCGC AAGCCGCACG CACUGGUUUC UUCUCCGUGA UGCUCCAUGU UGGCGAUGGA AAUGGGGUGC CCCCACCCGU CUUGA(A2M)AC(A2M)C GGACCAAGGA GU(OMC)A(A2M)ACAGA CGCGCAAGGG AGGAGAUAUG GUUGCCAGUA CUUCUCUCGU ACUGAAAGGG AGAUGCAAAA UGCAUCUGUG GUGUGCACAC GUCAAAUCCG UUUGAUUUGC CCAACACCGA CCGGCCCUCC GUGGGUUGCG UUGGAGUGUG CC(OMU)G(OMU)UUGGA CCC(OMG)A(A2M)AGGU GGUGAACUAU GCCUGAACAA GGUGAAGCCC GGGGAAACCC AGGUGGAGGC CUGUAGCGAU GCUG(A2M)CGUGC AAAUCGCUCG UAUGAUUUGG GU(A2M)UCG(OMG)AGC GAAAGACUCA UCGAACCACC UAGUAGCUGG UUCACAUCGA AGUUUCCCUC AGGAUAGCUG GUGCUAGUAG AAGUAUUGUG CGGUAAAGCA AAUGAUUAGA GGCAUUGGUG UUCUUAGAAU AUCGACCUAU UCUCAAACUU UAAA(OMU)GUGCA AACAAACCGU GCCUUAGCCA ACUGCAAGGC CGGAAAGAAA AGAAUUAGAG GCACCAAGUG GGCCUUCUUC GGUAAGC(OMG)GA GCAGGCGAUG CGGAAUGAAC CGCUUAGGGA UAUGUGGCGU CAAAACUUAU GGGCUCAUUC (OMU)CGAUACGUG AAAAGGGUGU UGGUGGAUUG GACAGUUGGA CGGUGGCCAU GGAAGUCGGC AUCCGCUAAG GAGUGUGUAA CAACUCACCA ACCGAAUCCA CCGGCCCCGA AAAUGGA(OMU)GA CGCUUAAGCC CAAUUAGUGA UUGCCCAUUA UUCCUUUGGU AAGGGCGGAA ACAAACUCUU GGAGAAAGUG UAGCCCUUCC GAUGUAGAUG UGGCCUGGAG GUUAGGACGA AGCUUAUGGC GUGAGCCUAA GAUGGACCGG CCUCUAGUGC A(OMG)AU(OMC)UUGGU UGGCGU(A2M)(OMG)CA AAGAUCUAAC GGAGAUAUAC UCAACAUGCA ACGUUGGAUA CUGGAGCGGG GAAGGAUUUC GUGCCAACGG CACUCGUACA CGA(OMG)UUGUUC GGAAACUGAG CACAACGUUA UAUCGU(OMU)UUG UUAGGAAAGU GAAGGUGUGU CGGCGGCAGC UGCUUUCGGG UAGCUGUUCG ACUGGCCAUA ACUGAAAAGG GGCAACAGAG AACCUGGGAU UAUAUUCCAA AAAGAAAUUG CAUGUGGG
MassTheoretical: 575.707562 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #45: nucleic-acid, rRNA beta

Nucleic-acidName: rRNA beta / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CCCAACUGCA GACCGUACUC AUCACCGCAU CAGGUCCCCA AGCAUAGAAU GCUCUGGUAC AUAGAGAAA(OMG) G(OMU)ACACUCAG GGAAGUCGGC AAAAUAGAUG CGUAAGUUCG CAAGAAGCAU UGGCUCUGAG GGCAAAGUCA GAGAAAACCG GAAGGCCAGU GUCCUCUCGC AUGCAGCCGU UCUUCAGAUG UUGUUUUGGC GCUCGCCGCC UUAGCACGCU GAUAGCGACU GUACUGUCGU CUGUGAAGGC UACCUUCCCG AGGCGUCGUA ACCCGGCGUC UCACUCUGGC ACGGGCCGGU CUUGGCGGGU UCACGCUCGC CUUGUGCCGC GUCCCACAAA UUGCCAACUC AGAACUG(OMC)UU ACGGCGGGGA AUCCAACUGU (A2M)UAAUUAAAA CAUAGGUUUG UGAUGCAUCC AAGUGGUGUA UAUCGCAAAC UGAUUUCUGC C(OMC)AGUGCUCU GAAUGUCAAC GUGACGAGAU UCACCGACGC GCGGGUAAAC GGCGGGAGUA (A2M)CUAUGACUC UCUUAAGGUA GCCAA(A2M)UGCC UC(OMG)UCUUCCA AUUAGAGACG CGCAUGAA(OMU)G GAUUAAUG(A2M)G (A2M)UUCCCUCUG U(OMC)CCGAGUU(A2M) CUAUCUAGCG AA(A2M)CGACAGU CAAGGGAACG GACUUG(A2M)AGG GCUAAGCGG(OMG) GAAAGAAGAC CCU(OMG)UUGAGU UUG(A2M)C(OMU)CCAG UCUGGCUCUG UGCGGCGACA UCUGAGGUGU AGUAUAGGUG GAAGCGCAAG CGCAAAUGAA AUACCACCAC UCGGAACGUU GCUUCACUUA UCGAAUGAAG AGACCAAUGG GUUUAGCGUA GUCUUCGGGC UAUGCACCGU CUAGGUUUGG GAGUAAUUUU AUGGCGGUAA CCCCGUCCCC ACGGGAAAGG GUGGUGUGCU UUUUUCUGCG UGCGUCUUCA CGGGCGUCGC GCGGGCCCCG CUCUUUUUUA UUACGUUUCC UUCGGGGGGC GUGACUCGUG GGUACCCAAC CGUGCUGUAA ACUGAACCAA CGGGAUUGCC UCGUGCAGUU CCGGAGUCUU GUUUCGAGAC AUCUGCCAGA UGGGGAGUUU GGCUG(OMG)GGCG GCAUAUCUGU UACACG(A2M)CAA CGCAGG(OMU)(OMG)UC CUAAGGCGAG CUCAGUGGGA ACAGAAAUCU CACGUAGAAC ACAAGCGUAA AAGCUUGCUU GAUUAACGAU U(OMU)CCAGUA(OMC)G AAUCGAGACU GCGAAAGCAA GGCC(A2M)GCGAU CCUUUGCGAA GAAUAGGAAA UAUGAACAAA UCAUACCA(OMG)A (OMG)GUGUCAGAA UAAUUAC(OMC)AC AG(OMG)GAUAACU GGCUUGUGGC GGCCAAGCGU UCAUAGCGAC GUCGCUUUUU GAUCCUUCGA UGUCGG(OMC)UCU UCCUAACCUA GCGCCGCAGA AGACGCUAAG GGUUGGAU(OMU)(OMG) UUCACCCACU G(A2M)CAGGGAAC GUG(A2M)GCUGGG UUUAGA(OMC)CGU CGUGAGACAG GUUGGUUU(OMU)A CCCUACUUAG CUGGAAAUUG CGAGAAAAAG AUUAUCCGUG CAAAGCGGAC GUCGGGUCGU UCUUGGGCCU GGCGAGCGGU GGGUAGUACU UGGUACGCUC AUCACC
MassTheoretical: 492.460781 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #46: nucleic-acid, rRNA gamma

Nucleic-acidName: rRNA gamma / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGUGGUAA(OMU)G CGAAACACUG CCAGGUAACA AAUCAAUCCU CCCACGGUGA GCUUUCUUUU CACCAUAAUC CACAUCUCCG GCUUUGCUGG GGCUUGGGCC UUUUUACUUC UCGCGUUGUU CGGAGCGGGG GCUCAAGAUU GAAAAAUGCA GCUCUCCCUA CGUACUGUCA UUGUUGUGAG UUCUGCGCAU UAACGCAAAA ACCUGGGGUG U
MassTheoretical: 67.56875 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #47: nucleic-acid, rRNA delta

Nucleic-acidName: rRNA delta / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUGAGAUUGU GAAGGGAUCU CGCAGGUAUC GUGAGGGAAG UAUGGGGUAG UACGAGAGGA ACUCCCAUGC CGU(OMG)CCUCUA GUUUCUGGGG UUUGUCGAAC GGCAAGUGCC CCGAAGCCAU CGCACGGUGG UUCUCGGCUG AACGCCUCUA AGCCAGAAGC CAAUCCCAAG ACCAGAUGCC CAC
MassTheoretical: 59.144129 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #48: nucleic-acid, rRNA epsilon

Nucleic-acidName: rRNA epsilon / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UACGUCCCUC UCCAAACGAG AGAACAUGCA UGGGCUGGCA UGAGCGGCAU GCUUCACUUC GGUGGGGCUC GAGGGGCAUU UACGUCCCGA GGCGCUGAAC CUUGAGGCCU GAAAUUUCAU GCUCAGGGAC ACA
MassTheoretical: 42.869438 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #49: nucleic-acid, rRNA zeta

Nucleic-acidName: rRNA zeta / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCGAAUCGC CACCUACAAG ACUGGAGCUU GCUCCCUCGA AGGCGCCAAG UAUAUUCAUG AUCACAAGAC A
MassTheoretical: 22.72559 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #50: nucleic-acid, rRNA 5.8S

Nucleic-acidName: rRNA 5.8S / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AACGUG(OMU)CGC GAUGGAUGAC UUGGCUUCCU AUUUCGUUGA AG(A2M)ACGCAGU AAAGUGCGAU AAGUGGUAUC AAUU(OMG)CAGAA UCAUUCAAUU ACCGAAUCUU UGAACGCAAA CGGCGCAUGG GAGAAGCUCU AUUGUGUCAU CCCCGUGCAU GCCAUAUUCU C(A2M)GUGUCGAA C
MassTheoretical: 54.98957 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #51: nucleic-acid, rRNA 5S

Nucleic-acidName: rRNA 5S / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GAGUACGACC AUACUUGAGU GAAAACACCA UAUCCCGUCC GAUUUGUGAA GUUAAGCACU CACAGGCUCA GUUAGUACUG AGGUCAGUGA UGACUCGGGA ACCCUGAGUG CCGUACUC
MassTheoretical: 37.923516 kDa
SourceSpecies: Leishmania donovani / eukaryote / ドノバンリーシュマニア

+
Component #52: ligand, PAROMOMYCIN

LigandName: PAROMOMYCIN / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 0.615628 kDa

+
Component #53: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 34 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #54: ligand, CYTIDINE-5'-MONOPHOSPHATE

LigandName: CYTIDINE-5'-MONOPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.323197 kDa

+
Component #55: ligand, water

LigandName: water / Number of Copies: 1019 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 141028
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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. See below links for details.
  • 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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more