[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
Map dataprimary map
SampleLeishmania donovani 91S ribosome LSU:
(ribosomal protein ...) x 42 / (nucleic-acidNucleic acid) x 8 / (ligand) x 4
Function / homologyRibosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L14p/L23e ...Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L38e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L21 superfamily / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L30p/L7e / Ribosomal protein L6 / KOW motif / Ribosomal protein L36e domain superfamily / Ribosomal protein L10e/L16 superfamily / ribosomal L5P family C-terminus / Ribosomal protein L5, N-terminal / 60S ribosomal protein L4, C-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L28e/Mak16 / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L14 superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L4/L1 family / Ribosomal L15 / Ribosomal protein L21e signature. / Ribosomal protein L39e signature. / Ribosomal L30 N-terminal domain / Ribosomal L18 C-terminal region / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ubiquitin domain signature. / Ribosomal protein L37e / Ribosomal protein L5 signature. / Ribosomal protein L22 signature. / Ribosomal protein L30 signature. / Ribosomal protein L6 signature 2. / Ribosomal protein L30e signature 1. / Ribosomal protein L1e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L14 / Ribosomal L38e protein family / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L34e / Ribosomal L29 protein / Ribosomal L39 protein / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein L21e / Ribosomal protein L36e / Ribosomal protein L31e / Ribosomal protein L35Ae / Ribosomal L37ae protein family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L19e / Ribosomal protein L32 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L22e protein family / Ribosomal L27e protein family / Ribosomal L28e protein family / Ribosomal L29e protein family / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L4/L1e / Ribosomal protein L37e / Ribosomal protein L35A / Ribosomal protein L29/L35 / Ribosomal protein L7A/L8 / Ribosomal protein L40e / Ribosomal protein L5 / Ribosomal protein L6, conserved site-2 / Ribosomal protein L10e / Ribosomal protein L22e / Ribosomal protein L28e / Ribosomal protein L29e / Ribosomal protein L37ae / Ribosomal protein L38e / Ribosomal protein L14e domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L32e / Ribosomal protein L21e
Function and homology information
SourceLeishmania donovani (eukaryote)
Methodsingle particle reconstruction / cryo EM / 2.5 Å resolution
AuthorsShalev-Benami M / Zhang Y
CitationJournal: Nat Commun / Year: 2017
Title: Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.
Authors: 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
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
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.

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)

+
Component #2: protein, ribosomal protein uL2

ProteinName: ribosomal protein uL2 / Recombinant expression: No
MassTheoretical: 27.520994 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #3: protein, ribosomal protein uL3

ProteinName: ribosomal protein uL3 / Recombinant expression: No
MassTheoretical: 45.741395 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #4: protein, ribosomal protein uL4

ProteinName: ribosomal protein uL4 / Recombinant expression: No
MassTheoretical: 40.523211 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #5: protein, ribosomal protein uL5

ProteinName: ribosomal protein uL5 / Recombinant expression: No
MassTheoretical: 19.245344 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #6: protein, ribosomal protein uL6

ProteinName: ribosomal protein uL6 / Recombinant expression: No
MassTheoretical: 21.118717 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #7: protein, ribosomal protein eL6

ProteinName: ribosomal protein eL6 / Recombinant expression: No
MassTheoretical: 21.208869 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #8: protein, ribosomal protein eL8

ProteinName: ribosomal protein eL8 / Recombinant expression: No
MassTheoretical: 39.175203 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #9: protein, ribosomal protein uL13

ProteinName: ribosomal protein uL13 / Recombinant expression: No
MassTheoretical: 25.346008 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #10: protein, ribosomal protein eL13

ProteinName: ribosomal protein eL13 / Recombinant expression: No
MassTheoretical: 23.897861 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #11: protein, ribosomal protein uL14

ProteinName: ribosomal protein uL14 / Recombinant expression: No
MassTheoretical: 14.421971 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #12: protein, ribosomal protein eL14

ProteinName: ribosomal protein eL14 / Recombinant expression: No
MassTheoretical: 17.038955 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #13: protein, ribosomal protein uL15

ProteinName: ribosomal protein uL15 / Recombinant expression: No
MassTheoretical: 16.034684 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #14: protein, ribosomal protein eL15

ProteinName: ribosomal protein eL15 / Recombinant expression: No
MassTheoretical: 24.366773 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #15: protein, ribosomal protein uL16

ProteinName: ribosomal protein uL16 / Recombinant expression: No
MassTheoretical: 24.607186 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #16: protein, ribosomal protein uL18

ProteinName: ribosomal protein uL18 / Recombinant expression: No
MassTheoretical: 34.100633 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #17: protein, ribosomal protein eL18

ProteinName: ribosomal protein eL18 / Recombinant expression: No
MassTheoretical: 21.939883 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #18: protein, ribosomal protein eL19

ProteinName: ribosomal protein eL19 / Recombinant expression: No
MassTheoretical: 22.901018 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #19: protein, ribosomal protein eL20

ProteinName: ribosomal protein eL20 / Recombinant expression: No
MassTheoretical: 20.703172 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #20: protein, ribosomal protein eL21

ProteinName: ribosomal protein eL21 / Recombinant expression: No
MassTheoretical: 17.437443 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #21: protein, ribosomal protein uL22

ProteinName: ribosomal protein uL22 / Recombinant expression: No
MassTheoretical: 17.828902 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #22: protein, ribosomal protein eL22

ProteinName: ribosomal protein eL22 / Recombinant expression: No
MassTheoretical: 14.042504 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #23: protein, ribosomal protein uL23

ProteinName: ribosomal protein uL23 / Recombinant expression: No
MassTheoretical: 13.461783 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #24: protein, ribosomal protein uL24

ProteinName: ribosomal protein uL24 / Recombinant expression: No
MassTheoretical: 13.874408 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #25: protein, ribosomal protein eL24

ProteinName: ribosomal protein eL24 / Recombinant expression: No
MassTheoretical: 7.988512 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #26: protein, ribosomal protein eL27

ProteinName: ribosomal protein eL27 / Recombinant expression: No
MassTheoretical: 15.223005 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #27: protein, ribosomal protein eL28

ProteinName: ribosomal protein eL28 / Recombinant expression: No
MassTheoretical: 15.525923 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #28: protein, ribosomal protein uL29

ProteinName: ribosomal protein uL29 / Recombinant expression: No
MassTheoretical: 14.987824 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #29: protein, ribosomal protein eL29

ProteinName: ribosomal protein eL29 / Recombinant expression: No
MassTheoretical: 7.788074 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #30: protein, ribosomal protein uL30

ProteinName: ribosomal protein uL30 / Recombinant expression: No
MassTheoretical: 26.313074 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #31: protein, ribosomal protein eL30

ProteinName: ribosomal protein eL30 / Recombinant expression: No
MassTheoretical: 10.122675 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #32: protein, ribosomal protein eL31

ProteinName: ribosomal protein eL31 / Recombinant expression: No
MassTheoretical: 13.503024 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #33: protein, ribosomal protein eL32

ProteinName: ribosomal protein eL32 / Recombinant expression: No
MassTheoretical: 15.02965 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #34: protein, ribosomal protein eL33

ProteinName: ribosomal protein eL33 / Recombinant expression: No
MassTheoretical: 14.336777 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #35: protein, ribosomal protein eL34

ProteinName: ribosomal protein eL34 / Recombinant expression: No
MassTheoretical: 14.640328 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #36: protein, ribosomal protein eL36

ProteinName: ribosomal protein eL36 / Recombinant expression: No
MassTheoretical: 11.050092 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #37: protein, ribosomal protein eL37

ProteinName: ribosomal protein eL37 / Recombinant expression: No
MassTheoretical: 9.531135 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #38: protein, ribosomal protein eL38

ProteinName: ribosomal protein eL38 / Recombinant expression: No
MassTheoretical: 8.761474 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #39: protein, ribosomal protein eL39

ProteinName: ribosomal protein eL39 / Recombinant expression: No
MassTheoretical: 6.373649 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #40: protein, ribosomal protein eL40

ProteinName: ribosomal protein eL40 / Recombinant expression: No
MassTheoretical: 5.912278 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #41: protein, ribosomal protein eL41

ProteinName: ribosomal protein eL41 / Recombinant expression: No
MassTheoretical: 4.2593 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #42: protein, ribosomal protein eL43

ProteinName: ribosomal protein eL43 / Recombinant expression: No
MassTheoretical: 10.092869 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
Component #43: protein, ribosomal protein eL44

ProteinName: ribosomal protein eL44 / Recombinant expression: No
MassTheoretical: 11.141353 kDa
SourceSpecies: Leishmania donovani (eukaryote)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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

SpecimenSpecimen state: particle / Method: cryo EM
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

-
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

+
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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