[English] 日本語
Yorodumi
- EMDB-16470: Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16470
TitleCryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S complex - body 1
Map dataCryo-EM map of in vitro reconstituted Otu2-Ub-40S complex - body 1
Sample
  • Complex: in vitro reconstituted yeast 40S ribosome complex with deubiquitinating enzyme Otu2 bound to ubiquitinated eS7 - body 1
    • Complex: OTU domain-containing protein 2; Ubiquitin
      • Protein or peptide: x 2 types
    • Complex: yeast 40S ribosome complex
      • RNA: x 1 types
      • Protein or peptide: x 15 types
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / protein metabolic process / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / Protein hydroxylation / : / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / protein metabolic process / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / Protein hydroxylation / : / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / protein tag activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / ribosome biogenesis / cytoplasmic translation / cysteine-type deubiquitinase activity / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / translation / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / OTU-like cysteine protease / OTU domain / OTU domain profile. / Ribosomal protein S21e, conserved site / S27a-like superfamily / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / Ribosomal protein S27a ...: / OTU-like cysteine protease / OTU domain / OTU domain profile. / Ribosomal protein S21e, conserved site / S27a-like superfamily / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8e, conserved site / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S4e, N-terminal, conserved site / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S6/S6e/A/B/2, conserved site / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S7e / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal family S4e / Ribosomal protein S7e signature. / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S2 signature 2. / Ubiquitin domain signature. / : / Ribosomal protein S17, conserved site / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ubiquitin family / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ubiquitin homologues / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S17 signature. / Ribosomal protein S5, C-terminal domain / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S8 signature. / Ribosomal protein S17/S11 / Ubiquitin-like domain / S4 domain
Similarity search - Domain/homology
Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A ...Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8B / Small ribosomal subunit protein uS17A / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS27A / OTU domain-containing protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsIkeuchi K / Buschauer R / Cheng J / Berninghausen O / Becker T / Beckmann R
Funding support Germany, Japan, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB/TRR-174 Germany
German Research Foundation (DFG)BE1814/15-1 Germany
German Research Foundation (DFG)BE1814/1-1 Germany
Japan Society for the Promotion of Science (JSPS) Japan
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Nat Commun / Year: 2023
Title: Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.
Authors: Ken Ikeuchi / Nives Ivic / Robert Buschauer / Jingdong Cheng / Thomas Fröhlich / Yoshitaka Matsuo / Otto Berninghausen / Toshifumi Inada / Thomas Becker / Roland Beckmann /
Abstract: In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its ...In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome recycling and initiation stages. Otu2 binds to several sites on the intersubunit surface of the 40S that are not occupied by any other 40S-binding factors. This binding mode explains the discrimination against 80S ribosomes via the largely helical N-terminal domain of Otu2 as well as the specificity for mono-ubiquitinated eS7 on 40S. Collectively, this study reveals mechanistic insights into the Otu2-driven deubiquitination steps for translational reset during ribosome recycling/(re)initiation.
History
DepositionJan 18, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16470.png

Downloads & links

-
Map

FileDownload / File: emd_16470.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of in vitro reconstituted Otu2-Ub-40S complex - body 1
Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.05582439 - 0.1777105
Average (Standard dev.)0.00018073732 (±0.0053414125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A

Fileemd_16470_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_16470_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : in vitro reconstituted yeast 40S ribosome complex with deubiquiti...

EntireName: in vitro reconstituted yeast 40S ribosome complex with deubiquitinating enzyme Otu2 bound to ubiquitinated eS7 - body 1
Components
  • Complex: in vitro reconstituted yeast 40S ribosome complex with deubiquitinating enzyme Otu2 bound to ubiquitinated eS7 - body 1
    • Complex: OTU domain-containing protein 2; Ubiquitin
      • Protein or peptide: OTU domain-containing protein 2
      • Protein or peptide: Ubiquitin
    • Complex: yeast 40S ribosome complex
      • RNA: 18S ribosomal RNA
      • Protein or peptide: 40S ribosomal protein S0-ARibosome
      • Protein or peptide: 40S ribosomal protein S2
      • Protein or peptide: 40S ribosomal protein S4-ARibosome
      • Protein or peptide: 40S ribosomal protein S6-ARibosome
      • Protein or peptide: 40S ribosomal protein S7-ARibosome
      • Protein or peptide: 40S ribosomal protein S8-BRibosome
      • Protein or peptide: 40S ribosomal protein S9-ARibosome
      • Protein or peptide: 40S ribosomal protein S11-ARibosome
      • Protein or peptide: 40S ribosomal protein S13
      • Protein or peptide: 40S ribosomal protein S21-ARibosome
      • Protein or peptide: 40S ribosomal protein S22-ARibosome
      • Protein or peptide: 40S ribosomal protein S23-ARibosome
      • Protein or peptide: 40S ribosomal protein S24-ARibosome
      • Protein or peptide: 40S ribosomal protein S27-ARibosome
      • Protein or peptide: 40S ribosomal protein S30-ARibosome

+
Supramolecule #1: in vitro reconstituted yeast 40S ribosome complex with deubiquiti...

SupramoleculeName: in vitro reconstituted yeast 40S ribosome complex with deubiquitinating enzyme Otu2 bound to ubiquitinated eS7 - body 1
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#18

+
Supramolecule #2: OTU domain-containing protein 2; Ubiquitin

SupramoleculeName: OTU domain-containing protein 2; Ubiquitin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

+
Supramolecule #3: yeast 40S ribosome complex

SupramoleculeName: yeast 40S ribosome complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#18
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: OTU domain-containing protein 2

MacromoleculeName: OTU domain-containing protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 36.157016 KDa
Recombinant expressionOrganism: Escharichia coli (E. coli)
SequenceString: MTGMESGENL ENMEDILARH RKENKDLQNK ITGMKKQATK SKRKEVNSKC LDLQDKLKTK QENEIRDWKI ANNEVFDAEQ EDEVTPEKL LEQLSISRDE KEQQNVPVQQ QQQGQTKKRR NRQKERLAKR DAAIAKMKEE AALEASKQPD LKKMEQESID Q LCELKKLK ...String:
MTGMESGENL ENMEDILARH RKENKDLQNK ITGMKKQATK SKRKEVNSKC LDLQDKLKTK QENEIRDWKI ANNEVFDAEQ EDEVTPEKL LEQLSISRDE KEQQNVPVQQ QQQGQTKKRR NRQKERLAKR DAAIAKMKEE AALEASKQPD LKKMEQESID Q LCELKKLK QFDIQPDGHS LFASILDQLK LRHDPKKLDQ DMDVMKLRWL SCNYVQEHRD DFIPYLFDEE TMKMKDIDEY TK EMEHTAQ WGGEIEILAL SHVFDCPISI LMSGRPIQVY NECGKNPELK LVYYKHSYAL GEHYNSLHDS

+
Macromolecule #2: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 2
Details: This protein was purchased from biotechne, Cat# U-100sc
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

+
Macromolecule #4: 40S ribosomal protein S0-A

MacromoleculeName: 40S ribosomal protein S0-A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 28.05133 KDa
SequenceString: MSLPATFDLT PEDAQLLLAA NTHLGARNVQ VHQEPYVFNA RPDGVHVINV GKTWEKLVLA ARIIAAIPNP EDVVAISSRT FGQRAVLKF AAHTGATPIA GRFTPGSFTN YITRSFKEPR LVIVTDPRSD AQAIKEASYV NIPVIALTDL DSPSEFVDVA I PCNNRGKH ...String:
MSLPATFDLT PEDAQLLLAA NTHLGARNVQ VHQEPYVFNA RPDGVHVINV GKTWEKLVLA ARIIAAIPNP EDVVAISSRT FGQRAVLKF AAHTGATPIA GRFTPGSFTN YITRSFKEPR LVIVTDPRSD AQAIKEASYV NIPVIALTDL DSPSEFVDVA I PCNNRGKH SIGLIWYLLA REVLRLRGAL VDRTQPWSIM PDLYFYRDPE EVEQQVAEEA TTEEAGEEEA KEEVTEEQAE AT EWAEENA DNVEW

+
Macromolecule #5: 40S ribosomal protein S2

MacromoleculeName: 40S ribosomal protein S2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 27.490826 KDa
SequenceString: MSAPEAQQQK RGGFGGRNRG RPNRRGPRNT EEKGWVPVTK LGRLVKAGKI TTIEEIFLHS LPVKEFQIID TLLPGLQDEV MNIKPVQKQ TRAGQRTRFK AVVVVGDSNG HVGLGIKTAK EVAGAIRAGI IIAKLSVIPI RRGYWGTNLG QPHSLATKTT G KCGSVTVR ...String:
MSAPEAQQQK RGGFGGRNRG RPNRRGPRNT EEKGWVPVTK LGRLVKAGKI TTIEEIFLHS LPVKEFQIID TLLPGLQDEV MNIKPVQKQ TRAGQRTRFK AVVVVGDSNG HVGLGIKTAK EVAGAIRAGI IIAKLSVIPI RRGYWGTNLG QPHSLATKTT G KCGSVTVR LIPAPRGSGI VASPAVKKLL QLAGVEDVYT QSNGKTRTLE NTLKAAFVAI GNTYGFLTPN LWAEQPLPVS PL DIYSDEA SAQKKRF

+
Macromolecule #6: 40S ribosomal protein S4-A

MacromoleculeName: 40S ribosomal protein S4-A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 29.46933 KDa
SequenceString: MARGPKKHLK RLAAPHHWLL DKLSGCYAPR PSAGPHKLRE SLPLIVFLRN RLKYALNGRE VKAILMQRHV KVDGKVRTDT TYPAGFMDV ITLDATNENF RLVYDVKGRF AVHRITDEEA SYKLGKVKKV QLGKKGVPYV VTHDGRTIRY PDPNIKVNDT V KIDLASGK ...String:
MARGPKKHLK RLAAPHHWLL DKLSGCYAPR PSAGPHKLRE SLPLIVFLRN RLKYALNGRE VKAILMQRHV KVDGKVRTDT TYPAGFMDV ITLDATNENF RLVYDVKGRF AVHRITDEEA SYKLGKVKKV QLGKKGVPYV VTHDGRTIRY PDPNIKVNDT V KIDLASGK ITDFIKFDAG KLVYVTGGRN LGRIGTIVHK ERHDGGFDLV HIKDSLDNTF VTRLNNVFVI GEQGKPYISL PK GKGIKLS IAEERDRRRA QQGL

+
Macromolecule #7: 40S ribosomal protein S6-A

MacromoleculeName: 40S ribosomal protein S6-A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 27.054486 KDa
SequenceString: MKLNISYPVN GSQKTFEIDD EHRIRVFFDK RIGQEVDGEA VGDEFKGYVF KISGGNDKQG FPMKQGVLLP TRIKLLLTKN VSCYRPRRD GERKRKSVRG AIVGPDLAVL ALVIVKKGEQ ELEGLTDTTV PKRLGPKRAN NIRKFFGLSK EDDVRDFVIR R EVTKGEKT ...String:
MKLNISYPVN GSQKTFEIDD EHRIRVFFDK RIGQEVDGEA VGDEFKGYVF KISGGNDKQG FPMKQGVLLP TRIKLLLTKN VSCYRPRRD GERKRKSVRG AIVGPDLAVL ALVIVKKGEQ ELEGLTDTTV PKRLGPKRAN NIRKFFGLSK EDDVRDFVIR R EVTKGEKT YTKAPKIQRL VTPQRLQRKR HQRALKVRNA QAQREAAAEY AQLLAKRLSE RKAEKAEIRK RRASSLKA

+
Macromolecule #8: 40S ribosomal protein S7-A

MacromoleculeName: 40S ribosomal protein S7-A / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 21.658209 KDa
SequenceString:
MSAPQAKILS QAPTELELQV AQAFVELENS SPELKAELRP LQFKSIREID VAGGKKALAI FVPVPSLAGF HKVQTKLTRE LEKKFQDRH VIFLAERRIL PKPSRTSRQV QKRPRSRTLT AVHDKILEDL VFPTEIVGKR VRYLVGGNKI QKVLLDSKDV Q QIDYKLES FQAVYNKLTG KQIVFEIPSE TH

+
Macromolecule #9: 40S ribosomal protein S8-B

MacromoleculeName: 40S ribosomal protein S8-B / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 22.537803 KDa
SequenceString: MGISRDSRHK RSATGAKRAQ FRKKRKFELG RQPANTKIGA KRIHSVRTRG GNKKYRALRI ETGNFSWASE GISKKTRIAG VVYHPSNNE LVRTNTLTKA AIVQIDATPF RQWFEAHYGQ TLGKKKNVKE EETVAKSKNA ERKWAARAAS AKIESSVESQ F SAGRLYAC ...String:
MGISRDSRHK RSATGAKRAQ FRKKRKFELG RQPANTKIGA KRIHSVRTRG GNKKYRALRI ETGNFSWASE GISKKTRIAG VVYHPSNNE LVRTNTLTKA AIVQIDATPF RQWFEAHYGQ TLGKKKNVKE EETVAKSKNA ERKWAARAAS AKIESSVESQ F SAGRLYAC ISSRPGQSGR CDGYILEGEE LAFYLRRLTA KK

+
Macromolecule #10: 40S ribosomal protein S9-A

MacromoleculeName: 40S ribosomal protein S9-A / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 22.487893 KDa
SequenceString: MPRAPRTYSK TYSTPKRPYE SSRLDAELKL AGEFGLKNKK EIYRISFQLS KIRRAARDLL TRDEKDPKRL FEGNALIRRL VRVGVLSED KKKLDYVLAL KVEDFLERRL QTQVYKLGLA KSVHHARVLI TQRHIAVGKQ IVNIPSFMVR LDSEKHIDFA P TSPFGGAR ...String:
MPRAPRTYSK TYSTPKRPYE SSRLDAELKL AGEFGLKNKK EIYRISFQLS KIRRAARDLL TRDEKDPKRL FEGNALIRRL VRVGVLSED KKKLDYVLAL KVEDFLERRL QTQVYKLGLA KSVHHARVLI TQRHIAVGKQ IVNIPSFMVR LDSEKHIDFA P TSPFGGAR PGRVARRNAA RKAEASGEAA DEADEADEE

+
Macromolecule #11: 40S ribosomal protein S11-A

MacromoleculeName: 40S ribosomal protein S11-A / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 17.785934 KDa
SequenceString:
MSTELTVQSE RAFQKQPHIF NNPKVKTSKR TKRWYKNAGL GFKTPKTAIE GSYIDKKCPF TGLVSIRGKI LTGTVVSTKM HRTIVIRRA YLHYIPKYNR YEKRHKNVPV HVSPAFRVQV GDIVTVGQCR PISKTVRFNV VKVSAAAGKA NKQFAKF

+
Macromolecule #12: 40S ribosomal protein S13

MacromoleculeName: 40S ribosomal protein S13 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 17.059945 KDa
SequenceString:
MGRMHSAGKG ISSSAIPYSR NAPAWFKLSS ESVIEQIVKY ARKGLTPSQI GVLLRDAHGV TQARVITGNK IMRILKSNGL APEIPEDLY YLIKKAVSVR KHLERNRKDK DAKFRLILIE SRIHRLARYY RTVAVLPPNW KYESATASAL VN

+
Macromolecule #13: 40S ribosomal protein S21-A

MacromoleculeName: 40S ribosomal protein S21-A / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 9.758829 KDa
SequenceString:
MENDKGQLVE LYVPRKCSAT NRIIKADDHA SVQINVAKVD EEGRAIPGEY VTYALSGYVR SRGESDDSLN RLAQNDGLLK NVWSYSR

+
Macromolecule #14: 40S ribosomal protein S22-A

MacromoleculeName: 40S ribosomal protein S22-A / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 14.650062 KDa
SequenceString:
MTRSSVLADA LNAINNAEKT GKRQVLIRPS SKVIIKFLQV MQKHGYIGEF EYIDDHRSGK IVVQLNGRLN KCGVISPRFN VKIGDIEKW TANLLPARQF GYVILTTSAG IMDHEEARRK HVSGKILGFV Y

+
Macromolecule #15: 40S ribosomal protein S23-A

MacromoleculeName: 40S ribosomal protein S23-A / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 16.073896 KDa
SequenceString:
MGKGKPRGLN SARKLRVHRR NNRWAENNYK KRLLGTAFKS SPFGGSSHAK GIVLEKLGIE SKQPNSAIRK CVRVQLIKNG KKVTAFVPN DGCLNFVDEN DEVLLAGFGR KGKAKGDIPG VRFKVVKVSG VSLLALWKEK KEKPRS

+
Macromolecule #16: 40S ribosomal protein S24-A

MacromoleculeName: 40S ribosomal protein S24-A / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 15.362848 KDa
SequenceString:
MSDAVTIRTR KVISNPLLAR KQFVVDVLHP NRANVSKDEL REKLAEVYKA EKDAVSVFGF RTQFGGGKSV GFGLVYNSVA EAKKFEPTY RLVRYGLAEK VEKASRQQRK QKKNRDKKIF GTGKRLAKKV ARRNAD

+
Macromolecule #17: 40S ribosomal protein S27-A

MacromoleculeName: 40S ribosomal protein S27-A / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 8.893391 KDa
SequenceString:
MVLVQDLLHP TAASEARKHK LKTLVQGPRS YFLDVKCPGC LNITTVFSHA QTAVTCESCS TILCTPTGGK AKLSEGTSFR RK

+
Macromolecule #18: 40S ribosomal protein S30-A

MacromoleculeName: 40S ribosomal protein S30-A / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 7.137541 KDa
SequenceString:
MAKVHGSLAR AGKVKSQTPK VEKTEKPKKP KGRAYKRLLY TRRFVNVTLV NGKRRMNPGP SVQ

+
Macromolecule #3: 18S ribosomal RNA

MacromoleculeName: 18S ribosomal RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 579.871062 KDa
SequenceString: UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUG CGAAUGGCUC AUUAAAUCAG UUAUCGUUUA UUUGAUAGUU CCUUUACUAC AUGGUAUAAC UGUGGUAAUU C UAGAGCUA ...String:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUG CGAAUGGCUC AUUAAAUCAG UUAUCGUUUA UUUGAUAGUU CCUUUACUAC AUGGUAUAAC UGUGGUAAUU C UAGAGCUA AUACAUGCUU AAAAUCUCGA CCCUUUGGAA GAGAUGUAUU UAUUAGAUAA AAAAUCAAUG UCUUCGGACU CU UUGAUGA UUCAUAAUAA CUUUUCGAAU CGCAUGGCCU UGUGCUGGCG AUGGUUCAUU CAAAUUUCUG CCCUAUCAAC UUU CGAUGG UAGGAUAGUG GCCUACCAUG GUUUCAACGG GUAACGGGGA AUAAGGGUUC GAUUCCGGAG AGGGAGCCUG AGAA ACGGC UACCACAUCC AAGGAAGGCA GCAGGCGCGC AAAUUACCCA AUCCUAAUUC AGGGAGGUAG UGACAAUAAA UAACG AUAC AGGGCCCAUU CGGGUCUUGU AAUUGGAAUG AGUACAAUGU AAAUACCUUA ACGAGGAACA AUUGGAGGGC AAGUCU GGU GCCAGCAGCC GCGGUAAUUC CAGCUCCAAU AGCGUAUAUU AAAGUUGUUG CAGUUAAAAA GCUCGUAGUU GAACUUU GG GCCCGGUUGG CCGGUCCGAU UUUUUCGUGU ACUGGAUUUC CAACGGGGCC UUUCCUUCUG GCUAACCUUG AGUCCUUG U GGCUCUUGGC GAACCAGGAC UUUUACUUUG AAAAAAUUAG AGUGUUCAAA GCAGGCGUAU UGCUCGAAUA UAUUAGCAU GGAAUAAUAG AAUAGGACGU UUGGUUCUAU UUUGUUGGUU UCUAGGACCA UCGUAAUGAU UAAUAGGGAC GGUCGGGGGC AUCAGUAUU CAAUUGUCAG AGGUGAAAUU CUUGGAUUUA UUGAAGACUA ACUACUGCGA AAGCAUUUGC CAAGGACGUU U UCAUUAAU CAAGAACGAA AGUUAGGGGA UCGAAGAUGA UCAGAUACCG UCGUAGUCUU AACCAUAAAC UAUGCCGACU AG GGAUCGG GUGGUGUUUU UUUAAUGACC CACUCGGCAC CUUACGAGAA AUCAAAGUCU UUGGGUUCUG GGGGGAGUAU GGU CGCAAG GCUGAAACUU AAAGGAAUUG ACGGAAGGGC ACCACCAGGA GUGGAGCCUG CGGCUUAAUU UGACUCAACA CGGG GAAAC UCGCCACGUC CAGACACAAU AAGGAUUGAC CGAUUGAGAG CUCUUUCUUG AUUUUGUGGC UGGUAGUGCA UGGCC GUUC UUAGUUGGUG GAGUGAUUUG UCUGCUUAAU UGCGAGAAGG AAGGGCAACU UAACCAUCUA CAGAGCGGUG CUAGAA UUU GCUGGUUAUC CACUUCUUAG AGGGACUAUC GGUUUCAAGC CGAUGGAAGU UAGAGGAACU AACAAGUCUG UAAUGCC CU UAGAGGUUCU GGGCCGUACG CGUGCAACAC UGACGGAGCC AGCGAGUCUA ACCUUGGCCG AGAGGUCUUG GUAAUCUU G UGAAACUCCG UCGUGCUGGG GAUAGAGCAU UGUAAUUAUU GCUCUUCAAC GAGGAAUUCC UAGUAAGCGC AAGUCAUCA GCUUGCGUUG AUUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUCUGCUUA GAGAAGGGGG CAACUCCAUC UCAGAGCGGA GAAUUUGGAC AAACUUGGUC AUUUAGAGGA ACUAAAAGUC G UAACAAGG UUUCCGUAGG UGAACCUGCG GAAGGAUCAU UA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 46.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: OTHER / Details: Relion
Final angle assignmentType: OTHER / Details: Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31646
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more