[English] 日本語
Yorodumi
- EMDB-4427: The structure of a di-ribosome (disome) as a unit for RQC and NGD... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4427
TitleThe structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition.
Map data
SampleCryo-EM structure of a native stalled di-ribosome (disome) complex from S. cerevisiae
  • (nucleic-acidNucleic acid) x 9
  • (60S ribosomal protein ...) x 40
  • (40S ribosomal protein ...) x 31
  • Ubiquitin-40S ribosomal protein S31
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Ubiquitin-60S ribosomal protein L40
  • 60S acidic ribosomal protein P0
  • ligand
Function / homologyRibosomal protein L10e/L16 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L6 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 ...Ribosomal protein L10e/L16 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L6 / Ribosomal protein S10p/S20e / Ribosomal protein S5, N-terminal domain / Ribosomal protein L30p/L7e / Ribosomal protein S2 / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ubiquitin family / Ribosomal protein L22p/L17e / Ribosomal protein S9/S16 / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S7p/S5e / Ribosomal protein S12/S23 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein S17 / WD domain, G-beta repeat / S27a-like superfamily / Ribosomal S3Ae family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L35Ae / Ribosomal protein L24e / Ribosomal protein S8e / Ribosomal protein S28e / Ribosomal protein L34e / Ribosomal protein L31e / Ribosomal protein L6e / Ribosomal protein L36e / Ribosomal protein L21e / Ribosomal protein S6e / Ribosomal protein S19e / Ribosomal L40e family / Ribosomal protein L44 / Ribosomal protein S8 / Ribosomal family S4e / Ribosomal S17 / Ribosomal L39 protein / Ribosomal L29 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L15 / ribosomal L5P family C-terminus / Ribosomal protein L4/L1 family / Ribosomal protein L13 / KOW motif / Ribosomal protein L10 / Ribosomal protein S13/S18 / Ribosomal protein S11 / Ribosomal protein L40e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S7e / 30s ribosomal protein S13, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / 60S acidic ribosomal protein P0 / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 60S ribosomal protein L4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S19, superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L13, conserved site / Ribosomal protein L24e, conserved site / Ribosomal protein L30, central domain, archaeal type / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L19, eukaryotic / Ribosomal protein L34Ae superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S26e superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L38e superfamily
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 5.3 Å resolution
AuthorsTesina P / Cheng J / Becker T / Beckmann R
CitationJournal: EMBO J. / Year: 2019
Title: Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways.
Authors: Ken Ikeuchi / Petr Tesina / Yoshitaka Matsuo / Takato Sugiyama / Jingdong Cheng / Yasushi Saeki / Keiji Tanaka / Thomas Becker / Roland Beckmann / Toshifumi Inada
Abstract: Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ...Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an translation reaction. Cryo-EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2-mediated cleavages upstream of the disome, governed by initial Not4-mediated monoubiquitination of eS7 and followed by Hel2-mediated K63-linked polyubiquitination. We propose that Hel2-mediated ribosome ubiquitination is required both for canonical NGD (NGD) and RQC coupled to the disome and that RQC-uncoupled NGD outside the disome (NGD) can occur in a Not4-dependent manner.
Validation ReportPDB-ID: 6i7o

SummaryFull reportAbout validation report
DateDeposition: Nov 16, 2018 / Header (metadata) release: Jan 9, 2019 / Map release: Jan 16, 2019 / Last update: Jan 16, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6i7o
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_4427.map.gz (map file in CCP4 format, 518217 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
506 pix
1.5 Å/pix.
= 758.798 Å
506 pix
1.5 Å/pix.
= 758.798 Å
506 pix
1.5 Å/pix.
= 758.798 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4996 Å
Density
Contour Level:0.013 (by author), 0.013 (movie #1):
Minimum - Maximum-0.066871494 - 0.1602559
Average (Standard dev.)0.0003179695 (0.0062321145)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions506506506
Origin0.00.00.0
Limit505.0505.0505.0
Spacing506506506
CellA=B=C: 758.7976 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.49960079051381.49960079051381.4996007905138
M x/y/z506506506
origin x/y/z0.0000.0000.000
length x/y/z758.798758.798758.798
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS506506506
D min/max/mean-0.0670.1600.000

-
Supplemental data

-
Sample components

+
Entire Cryo-EM structure of a native stalled di-ribosome (disome) comple...

EntireName: Cryo-EM structure of a native stalled di-ribosome (disome) complex from S. cerevisiae
Number of components: 86

+
Component #1: protein, Cryo-EM structure of a native stalled di-ribosome (disom...

ProteinName: Cryo-EM structure of a native stalled di-ribosome (disome) complex from S. cerevisiae
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #2: nucleic-acid, 25S ribosomal RNA

Nucleic-acidName: 25S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAAC GGCGAGUGAA GCGGCAAAAG CUCAAAUUUG AAAUCUGGUA CCUUCGGUGC CCGAGUUGUA AUUUGGAGAG GGCAACUUUG GGGCCGUUCC UUGUCUAUGU UCCUUGGAAC AGGACGUCAU AGAGGGUGAG AAUCCCGUGU GGCGAGGAGU GCGGUUCUUU GUAAAGUGCC UUCGAAGAGU CGAGUUGUUU GGGAAUGCAG CUCUAAGUGG GUGGUAAAUU CCAUCUAAAG CUAAAUAUUG GCGAGAGACC GAUAGCGAAC AAGUACAGUG AUGGAAAGAU GAAAAGAACU UUGAAAAGAG AGUGAAAAAG UACGUGAAAU UGUUGAAAGG GAAGGGCAUU UGAUCAGACA UGGUGUUUUG UGCCCUCUGC UCCUUGUGGG UAGGGGAAUC UCGCAUUUCA CUGGGCCAGC AUCAGUUUUG GUGGCAGGAU AAAUCCAUAG GAAUGUAGCU UGCCUCGGUA AGUAUUAUAG CCUGUGGGAA UACUGCCAGC UGGGACUGAG GACUGCGACG UAAGUCAAGG AUGCUGGCAU AAUGGUUAUA UGCCGCCCGU CUUGAAACAC GGACCAAGGA GUCUAACGUC UAUGCGAGUG UUUGGGUGUA AAACCCAUAC GCGUAAUGAA AGUGAACGUA GGUUGGGGCC UCGCAAGAGG UGCACAAUCG ACCGAUCCUG AUGUCUUCGG AUGGAUUUGA GUAAGAGCAU AGCUGUUGGG ACCCGAAAGA UGGUGAACUA UGCCUGAAUA GGGUGAAGCC AGAGGAAACU CUGGUGGAGG CUCGUAGCGG UUCUGACGUG CAAAUCGAUC GUCGAAUUUG GGUAUAGGGG CGAAAGACUA AUCGAACCAU CUAGUAGCUG GUUCCUGCCG AAGUUUCCCU CAGGAUAGCA GAAGCUCGUA UCAGUUUUAU GAGGUAAAGC GAAUGAUUAG AGGUUCCGGG GUCGAAAUGA CCUUGACCUA UUCUCAAACU UUAAAUAUGU AAGAAGUCCU UGUUACUUAA UUGAACGUGG ACAUUUGAAU GAAGAGCUUU UAGUGGGCCA UUUUUGGUAA GCAGAACUGG CGAUGCGGGA UGAACCGAAC GUAGAGUUAA GGUGCCGGAA UACACGCUCA UCAGACACCA CAAAAGGUGU UAGUUCAUCU AGACAGCCGG ACGGUGGCCA UGGAAGUCGG AAUCCGCUAA GGAGUGUGUA ACAACUCACC GGCCGAAUGA ACUAGCCCUG AAAAUGGAUG GCGCUCAAGC GUGUUACCUA UACUCUACCG UCAGGGUUGA UAUGAUGCCC UGACGAGUAG GCAGGCGUGG AGGUCAGUGA CGAAGCCUAG ACCGUAAGGU CGGGUCGAAC GGCCUCUAGU GCAGAUCUUG GUGGUAGUAG CAAAUAUUCA AAUGAGAACU UUGAAGACUG AAGUGGGGAA AGGUUCCACG UCAACAGCAG UUGGACGUGG GUUAGUCGAU CCUAAGAGAU GGGGAAGCUC CGUUUCAAAG GCCUGAUUUU AUGCAGGCCA CCAUCGAAAG GGAAUCCGGU UAAGAUUCCG GAACCUGGAU AUGGAUUCUU CACGGUAACG UAACUGAAUG UGGAGACGUC GGCGCGAGCC CUGGGAGGAG UUAUCUUUUC UUCUUAACAG CUUAUCACCC CGGAAUUGGU UUAUCCGGAG AUGGGGUCUU AUGGCUGGAA GAGGCCAGCA CCUUUGCUGG CUCCGGUGCG CUUGUGACGG CCCGUGAAAA UCCACAGGAA GGAAUAGUUU UCAUGCCAGG UCGUACUGAU AACCGCAGCA GGUCUCCAAG GUGAACAGCC UCUAGUUGAU AGAAUAAUGU AGAUAAGGGA AGUCGGCAAA AUAGAUCCGU AACUUCGGGA UAAGGAUUGG CUCUAAGGGU CGGGUAGUGA GGGCCUUGGU CAGACGCAGC GGGCGUGCUU GUGGACUGCU UGGUGGGGCU UGCUCUGCUA GGCGGACUAC UUGCGUGCCU UGUUGUAGAC GGCCUUGGUA GGUCUCUUGU AGACCGUCGC UUGCUACAAU UAACGAUCAA CUUAGAACUG GUACGGACAA GGGGAAUCUG ACUGUCUAAU UAAAACAUAG CAUUGCGAUG GUCAGAAAGU GAUGUUGACG CAAUGUGAUU UCUGCCCAGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAC CAAGCGCGGG UAAACGGCGG GAGUAACUAU GACUCUCUUA AGGUAGCCAA AUGCCUCGUC AUCUAAUUAG UGACGCGCAU GAAUGGAUUA ACGAGAUUCC CACUGUCCCU AUCUACUAUC UAGCGAAACC ACAGCCAAGG GAACGGGCUU GGCAGAAUCA GCGGGGAAAG AAGACCCUGU UGAGCUUGAC UCUAGUUUGA CAUUGUGAAG AGACAUAGAG GGUGUAGAAU AAGUGGGAGC UUCGGCGCCA GUGAAAUACC ACUACCUUUA UAGUUUCUUU ACUUAUUCAA UGAAGCGGAG CUGGAAUUCA UUUUCCACGU UCUAGCAUUC AAGGUCCCAU UCGGGGCUGA UCCGGGUUGA AGACAUUGUC AGGUGGGGAG UUUGGCUGGG GCGGCACAUC UGUUAAACGA UAACGCAGAU GUCCUAAGGG GGGCUCAUGG AGAACAGAAA UCUCCAGUAG AACAAAAGGG UAAAAGCCCC CUUGAUUUUG AUUUUCAGUG UGAAUACAAA CCAUGAAAGU GUGGCCUAUC GAUCCUUUAG UCCCUCGGAA UUUGAGGCUA GAGGUGCCAG AAAAGUUACC ACAGGGAUAA CUGGCUUGUG GCAGUCAAGC GUUCAUAGCG ACAUUGCUUU UUGAUUCUUC GAUGUCGGCU CUUCCUAUCA UACCGAAGCA GAAUUCGGUA AGCGUUGGAU UGUUCACCCA CUAAUAGGGA ACGUGAGCUG GGUUUAGACC GUCGUGAGAC AGGUUAGUUU UACCCUACUG AUGAAUGUUA CCGCAAUAGU AAUUGAACUU AGUACGAGAG GAACAGUUCA UUCGGAUAAU UGGUUUUUGC GGCUGUCUGA UCAGGCAUUG CCGCGAAGCU ACCAUCCGCU GGAUUAUGGC UGAACGCCUC UAAGUCAGAA UCCAUGCUAG AACGCGGUGA UUUCUUUGCU CCACACAAUA UAGAUGGAUA CGAAUAAGGC GUCCUUGUGG CGUCGCUGAA CCAUAGCAGG CUAGCAACGG UGCACUUGGC GGAAAGGCCU UGGGUGCUUG CUGGCGAAUU GCAAUGUCAU UUUGCGUGGG GAUAAAUCAU UUGUAUACGA CUUAGAUGUA CAACGGGGUA UUGUAAGCAG UAGAGUAGCC UUGUUGUUAC GAUCUGCUGA GAUUAAGCCU UUGUUGUCUG AUUUGU
MassTheoretical: 1.097493875 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #3: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUGCGGCC AUAUCUACCA GAAAGCACCG UUUCCCGUCC GAUCAACUGU AGUUAAGCUG GUAAGAGCCU GACCGAGUAG UGUAGUGGGU GACCAUACGC GAAACUCAGG UGCUGCAAUC U
MassTheoretical: 38.951105 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #4: nucleic-acid, 5.8S ribosomal RNA

Nucleic-acidName: 5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAACUUUCAA CAACGGAUCU CUUGGUUCUC GCAUCGAUGA AGAACGCAGC GAAAUGCGAU ACGUAAUGUG AAUUGCAGAA UUCCGUGAAU CAUCGAAUCU UUGAACGCAC AUUGCGCCCC UUGGUAUUCC AGGGGGCAUG CCUGUUUGAG CGUCAUU
MassTheoretical: 50.376758 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #5: protein, 60S ribosomal protein L2-A

ProteinName: 60S ribosomal protein L2-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.217289 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #6: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 43.719602 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #7: protein, 60S ribosomal protein L4-A

ProteinName: 60S ribosomal protein L4-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 39.027926 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #8: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 33.415387 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #9: protein, 60S ribosomal protein L6-A

ProteinName: 60S ribosomal protein L6-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 20.000564 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #10: protein, 60S ribosomal protein L7-A

ProteinName: 60S ribosomal protein L7-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.34148 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #11: protein, 60S ribosomal protein L8-A

ProteinName: 60S ribosomal protein L8-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.65684 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #12: protein, 60S ribosomal protein L9-A

ProteinName: 60S ribosomal protein L9-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.491902 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #13: protein, 60S ribosomal protein L10

ProteinName: 60S ribosomal protein L10 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.410465 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #14: protein, 60S ribosomal protein L11-B

ProteinName: 60S ribosomal protein L11-BRibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 19.266082 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #15: protein, 60S ribosomal protein L13-A

ProteinName: 60S ribosomal protein L13-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.956312 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #16: protein, 60S ribosomal protein L14-A

ProteinName: 60S ribosomal protein L14-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.06387 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #17: protein, 60S ribosomal protein L15-A

ProteinName: 60S ribosomal protein L15-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.351162 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #18: protein, 60S ribosomal protein L16-A

ProteinName: 60S ribosomal protein L16-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.028951 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #19: nucleic-acid, 18S ribosomal RNA

Nucleic-acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ACAUGCUUAA AAUCUCGACC CUUUGGAAGA GAUGUAUUUA UUAGAUAAAA AAUCAAUGUC UUCGGACUCU UUGAUGAUUC AUAAUAACUU UUCGAAUCGC AUGGCCUUGU GCUGGCGAUG GUUCAUUCAA AUUUCUGCCC UAUCAACUUU CGAUGGUAGG AUAGUGGCCU ACCAUGGUUU CAACGGGUAA CGGGGAAUAA GGGUUCGAUU CCGGAGAGGG AGCCUGAGAA ACGGCUACCA CAUCCAAGGA AGGCAGCAGG CGCGCAAAUU ACCCAAUCCU AAUUCAGGGA GGUAGUGACA AUAAAUAACG AUACAGGGCC CAUUCGGGUC UUGUAAUUGG AAUGAGUACA AUGUAAAUAC CUUAACGAGG AACAAUUGGA GGGCAAGUCU GGUGCCAGCA GCCGCGGUAA UUCCAGCUCC AAUAGCGUAU AUUAAAGUUG UUGCAGUUAA AAAGCUCGUA GUUGAACUUU GGGCCCGGUU GGCCGGUCCG AUUUUUUCGU GUACUGGAUU UCCAACGGGG CCUUUCCUUC UGGCUAACCU UGAGUCCUUG UGGCUCUUGG CGAACCAGGA CUUUUACUUU GAAAAAAUUA GAGUGUUCAA AGCAGGCGUA UUGCUCGAAU AUAUUAGCAU GGAAUAAUAG AAUAGGACGU UUGGUUCUAU UUUGUUGGUU UCUAGGACCA UCGUAAUGAU UAAUAGGGAC GGUCGGGGGC AUCAGUAUUC AAUUGUCAGA GGUGAAAUUC UUGGAUUUAU UGAAGACUAA CUACUGCGAA AGCAUUUGCC AAGGACGUUU UCAUUAAUCA AGAACGAAAG UUAGGGGAUC GAAGAUGAUC AGAUACCGUC GUAGUCUUAA CCAUAAACUA UGCCGACUAG GGAUCGGGUG GUGUUUUUUU AAUGACCCAC UCGGCACCUU ACGAGAAAUC AAAGUCUUUG GGUUCUGGGG GGAGUAUGGU CGCAAGGCUG AAACUUAAAG GAAUUGACGG AAGGGCACCA CCAGGAGUGG AGCCUGCGGC UUAAUUUGAC UCAACACGGG GAAACUCACC AGGUCCAGAC ACAAUAAGGA UUGACAGAUU GAGAGCUCUU UCUUGAUUUU GUGGGUGGUG GUGCAUGGCC GUUCUUAGUU GGUGGAGUGA UUUGUCUGCU UAAUUGCGAU AACGAACGAG ACCUUAACCU ACUAAAUAGU GGUGCUAGCA UUUGCUGGUU AUCCACUUCU UAGAGGGACU AUCGGUUUCA AGCCGAUGGA AGUUUGAGGC AAUAACAGGU CUGUGAUGCC CUUAGACGUU CUGGGCCGCA CGCGCGCUAC ACUGACGGAG CCAGCGAGUC UAACCUUGGC CGAGAGGUCU UGGUAAUCUU GUGAAACUCC GUCGUGCUGG GGAUAGAGCA UUGUAAUUAU UGCUCUUCAA CGAGGAAUUC CUAGUAAGCG CAAGUCAUCA GCUUGCGUUG AUUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUCUGCUUAG AGAAGGGGGC AACUCCAUCU CAGAGCGGAG AAUUUGGACA AACUUGGUCA UUUAGAGGAA CUAAAAGUCG UAACAAGGUU UCCGUAGGUG AACCUGCGGA AGGAUCAUUA
MassTheoretical: 579.761938 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #20: protein, 40S ribosomal protein S0-A

ProteinName: 40S ribosomal protein S0-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.811074 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #21: protein, 40S ribosomal protein S1-A

ProteinName: 40S ribosomal protein S1-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.498365 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #22: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.212979 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #23: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.702791 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #24: protein, 40S ribosomal protein S4-A

ProteinName: 40S ribosomal protein S4-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.338133 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #25: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.908338 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #26: protein, 40S ribosomal protein S6-A

ProteinName: 40S ribosomal protein S6-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.965975 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #27: protein, 40S ribosomal protein S7-A

ProteinName: 40S ribosomal protein S7-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.07157 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #28: protein, 40S ribosomal protein S8-A

ProteinName: 40S ribosomal protein S8-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.537803 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #29: protein, 40S ribosomal protein S9-A

ProteinName: 40S ribosomal protein S9-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.210662 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #30: protein, 40S ribosomal protein S10-A

ProteinName: 40S ribosomal protein S10-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.042562 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #31: protein, 40S ribosomal protein S11-A

ProteinName: 40S ribosomal protein S11-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.588461 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #32: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.327331 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #33: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.928748 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #34: protein, 40S ribosomal protein S14-B

ProteinName: 40S ribosomal protein S14-BRibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.560528 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #35: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.421732 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #36: protein, 40S ribosomal protein S16-A

ProteinName: 40S ribosomal protein S16-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.659216 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #37: protein, 40S ribosomal protein S17-A

ProteinName: 40S ribosomal protein S17-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.268545 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #38: protein, 40S ribosomal protein S18-A

ProteinName: 40S ribosomal protein S18-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.940443 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #39: protein, 40S ribosomal protein S19-A

ProteinName: 40S ribosomal protein S19-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.81093 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #40: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.476479 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #41: protein, 40S ribosomal protein S21-A

ProteinName: 40S ribosomal protein S21-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.758829 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #42: protein, 40S ribosomal protein S22-A

ProteinName: 40S ribosomal protein S22-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.518867 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #43: protein, 40S ribosomal protein S23-A

ProteinName: 40S ribosomal protein S23-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.942699 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #44: protein, 40S ribosomal protein S24-A

ProteinName: 40S ribosomal protein S24-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.23165 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #45: protein, 40S ribosomal protein S25-A

ProteinName: 40S ribosomal protein S25-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 7.930299 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #46: protein, 40S ribosomal protein S26-B

ProteinName: 40S ribosomal protein S26-BRibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.022989 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #47: protein, 40S ribosomal protein S27-A

ProteinName: 40S ribosomal protein S27-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.762195 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #48: protein, 40S ribosomal protein S28-A

ProteinName: 40S ribosomal protein S28-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 7.116281 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #49: protein, 40S ribosomal protein S29-A

ProteinName: 40S ribosomal protein S29-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.335303 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #50: protein, 40S ribosomal protein S30-A

ProteinName: 40S ribosomal protein S30-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.779086 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #51: protein, Ubiquitin-40S ribosomal protein S31

ProteinName: Ubiquitin-40S ribosomal protein S31 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.329946 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #52: protein, Guanine nucleotide-binding protein subunit beta-like protein

ProteinName: Guanine nucleotide-binding protein subunit beta-like protein
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 34.151426 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #53: protein, 60S ribosomal protein L17-A

ProteinName: 60S ribosomal protein L17-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 20.589518 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #54: protein, 60S ribosomal protein L18-A

ProteinName: 60S ribosomal protein L18-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 20.478059 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #55: protein, 60S ribosomal protein L19-A

ProteinName: 60S ribosomal protein L19-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.631121 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #56: protein, 60S ribosomal protein L20-A

ProteinName: 60S ribosomal protein L20-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 20.478852 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #57: protein, 60S ribosomal protein L21-A

ProteinName: 60S ribosomal protein L21-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 18.148066 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #58: protein, 60S ribosomal protein L22-A

ProteinName: 60S ribosomal protein L22-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.006555 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #59: protein, 60S ribosomal protein L23-A

ProteinName: 60S ribosomal protein L23-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.218625 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #60: protein, 60S ribosomal protein L24-A

ProteinName: 60S ribosomal protein L24-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.506229 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #61: protein, 60S ribosomal protein L25

ProteinName: 60S ribosomal protein L25 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.641997 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #62: protein, 60S ribosomal protein L26-A

ProteinName: 60S ribosomal protein L26-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.892317 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #63: protein, 60S ribosomal protein L27-A

ProteinName: 60S ribosomal protein L27-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.437166 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #64: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.630471 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #65: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.560688 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #66: protein, 60S ribosomal protein L30

ProteinName: 60S ribosomal protein L30 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.902664 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #67: protein, 60S ribosomal protein L31-A

ProteinName: 60S ribosomal protein L31-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 12.649754 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #68: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.478054 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #69: protein, 60S ribosomal protein L33-A

ProteinName: 60S ribosomal protein L33-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 12.045935 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #70: protein, 60S ribosomal protein L34-A

ProteinName: 60S ribosomal protein L34-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 12.608831 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #71: protein, 60S ribosomal protein L35-A

ProteinName: 60S ribosomal protein L35-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.811444 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #72: protein, 60S ribosomal protein L36-A

ProteinName: 60S ribosomal protein L36-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.020063 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #73: protein, 60S ribosomal protein L37-A

ProteinName: 60S ribosomal protein L37-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.300709 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #74: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.714363 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #75: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.227444 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #76: protein, Ubiquitin-60S ribosomal protein L40

ProteinName: Ubiquitin-60S ribosomal protein L40 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.032321 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #77: protein, 60S ribosomal protein L41-B

ProteinName: 60S ribosomal protein L41-BRibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 3.354243 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #78: protein, 60S ribosomal protein L42-A

ProteinName: 60S ribosomal protein L42-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 12.115462 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #79: protein, 60S ribosomal protein L43-A

ProteinName: 60S ribosomal protein L43-ARibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.981756 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #80: protein, 60S acidic ribosomal protein P0

ProteinName: 60S acidic ribosomal protein P0 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 33.749121 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #81: nucleic-acid, P-site tRNA

Nucleic-acidName: P-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUCCUCGUGG CCCAAUGGUC ACGGCGUCUG GCUACGAACC AGAAGAUUCC AGGUUCAAGU CCUGGCGGGG AAGCCA
MassTheoretical: 24.468551 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #82: nucleic-acid, E-site tRNA

Nucleic-acidName: E-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCCGAUAUAG CGUAACGGCU AUCACAUCAC GCUUUCACCG UGGAGACCGG GGUUCGACUC CCCGUAUCGG AGCCA
MassTheoretical: 24.004262 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #83: nucleic-acid, A/P hybrid tRNA

Nucleic-acidName: A/P hybrid tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCCCGGAUAG CUCAGUCGGU AGAGCAGGGG AUUAGGAAUC CCCGUGUCCU UGGUUCGAUU CCGAGUCCGG GCACCA
MassTheoretical: 24.501539 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #84: nucleic-acid, P/E hybrid tRNA

Nucleic-acidName: P/E hybrid tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGGUGG AGCAGCCUGG UAGCUCGUCG GGCUCAUAAC CCGAAGGUCG UCGGUUCAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.802785 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #85: nucleic-acid, mRNA

Nucleic-acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUUUUUUUUU UUGACAAAUU UUUUUUUUAA UCCUGGAUGG AACGACCGUU UUUUUUU
MassTheoretical: 17.90427 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #86: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.2
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: 2.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 15739
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. 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

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