[English] 日本語
Yorodumi
- EMDB-54789: Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54789
TitleCryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit
Map data
Sample
  • Complex: 60S LSU Arabidopsis (root) ribosome complex
    • RNA: x 1 types
    • Protein or peptide: x 19 types
  • Ligand: x 3 types
KeywordsArabidopsis / Ribosome / CryoEM
Function / homology
Function and homology information


trichome morphogenesis / cytokinesis by cell plate formation / leaf morphogenesis / chloroplast organization / plant-type cell wall / plasmodesma / plant-type vacuole / plastid / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) ...trichome morphogenesis / cytokinesis by cell plate formation / leaf morphogenesis / chloroplast organization / plant-type cell wall / plasmodesma / plant-type vacuole / plastid / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / cytosolic ribosome / chloroplast / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / defense response to bacterium / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal ...: / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S7e signature. / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S27e signature. / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S8e / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S2 signature 2. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / : / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / Ribosomal S11, conserved site / Ribosomal protein S11 signature.
Similarity search - Domain/homology
Small ribosomal subunit protein uS17z / Small ribosomal subunit protein uS11x / Small ribosomal subunit protein uS8z/uS8w / Small ribosomal subunit protein uS12y / Small ribosomal subunit protein eS30z/eS30y/eS30x / Small ribosomal subunit protein eS6y / Small ribosomal subunit protein uS15y / Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v / Small ribosomal subunit protein uS2y / Small ribosomal subunit protein eS8z ...Small ribosomal subunit protein uS17z / Small ribosomal subunit protein uS11x / Small ribosomal subunit protein uS8z/uS8w / Small ribosomal subunit protein uS12y / Small ribosomal subunit protein eS30z/eS30y/eS30x / Small ribosomal subunit protein eS6y / Small ribosomal subunit protein uS15y / Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v / Small ribosomal subunit protein uS2y / Small ribosomal subunit protein eS8z / Small ribosomal subunit protein eS4z / Small ribosomal subunit protein eS7z / Small ribosomal subunit protein eS1z / Small ribosomal subunit protein uS4y / Small ribosomal subunit protein eS26x / Small ribosomal subunit protein eS27y / Small ribosomal subunit protein eS21z / Small ribosomal subunit protein uS5w / Small ribosomal subunit protein eS24z
Similarity search - Component
Biological speciesArabidopsis (plant) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKarki S / Lu X / Paatero AO / Ruonala R / Tranter D / Guryanov S / Rehan S / Hellmann E / Haakonsson A / Butcher SJ ...Karki S / Lu X / Paatero AO / Ruonala R / Tranter D / Guryanov S / Rehan S / Hellmann E / Haakonsson A / Butcher SJ / Huiskonen JT / Kajander T / Helariutta Y / Paavilainen VO
Funding support United States, Finland, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132649[PVO1] United States
Academy of Finland338836 and 314672 Finland
CitationJournal: To Be Published
Title: Cryo-EM structure of the Arabidopsis thaliana ribosome in translating and non-translating states
Authors: Karki S / Paavilainen V
History
DepositionAug 14, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54789.png

Downloads & links

-
Map

FileDownload / File: emd_54789.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 450 pix.
= 378. Å		0.84 Å/pix.
x 450 pix.
= 378. Å		0.84 Å/pix.
x 450 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.11574677 - 0.31933743
Average (Standard dev.)0.0029591837 (±0.016527385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_54789_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54789_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : 60S LSU Arabidopsis (root) ribosome complex

EntireName: 60S LSU Arabidopsis (root) ribosome complex
Components
  • Complex: 60S LSU Arabidopsis (root) ribosome complex
    • RNA: 18S RNA
    • Protein or peptide: Small ribosomal subunit protein uS2y
    • Protein or peptide: Small ribosomal subunit protein eS1z
    • Protein or peptide: Small ribosomal subunit protein uS5w
    • Protein or peptide: Small ribosomal subunit protein eS4z
    • Protein or peptide: Small ribosomal subunit protein eS6y
    • Protein or peptide: Small ribosomal subunit protein eS7z
    • Protein or peptide: Small ribosomal subunit protein eS8z
    • Protein or peptide: Small ribosomal subunit protein uS4y
    • Protein or peptide: Small ribosomal subunit protein uS17z
    • Protein or peptide: Small ribosomal subunit protein uS15y
    • Protein or peptide: Small ribosomal subunit protein uS11x
    • Protein or peptide: Small ribosomal subunit protein eS21z
    • Protein or peptide: Small ribosomal subunit protein uS8z/uS8w
    • Protein or peptide: Small ribosomal subunit protein uS12y
    • Protein or peptide: Small ribosomal subunit protein eS24z
    • Protein or peptide: Small ribosomal subunit protein eS26x
    • Protein or peptide: Small ribosomal subunit protein eS27y
    • Protein or peptide: Small ribosomal subunit protein eS30z/eS30y/eS30x
    • Protein or peptide: Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

+
Supramolecule #1: 60S LSU Arabidopsis (root) ribosome complex

SupramoleculeName: 60S LSU Arabidopsis (root) ribosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Arabidopsis (plant)
Molecular weightTheoretical: 4.3 MDa

+
Macromolecule #1: 18S RNA

MacromoleculeName: 18S RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 581.965688 KDa
SequenceString: UACCUGGUUG AUCCUGCCAG UAGUCAU(A2M)UG CUUGUCU(OMC)AA AGAUUAAGCC AUGCAUGUGU AAGUAUGAAC GA AUUCAGA CUGUGAAACU GCGAAUGGCU CAUUAAAUCA GUUAUAGUUU GUU(OMU)GAUGGU AACUACUACU (OMC)GGAU AACC GUAGUAAUUC ...String:
UACCUGGUUG AUCCUGCCAG UAGUCAU(A2M)UG CUUGUCU(OMC)AA AGAUUAAGCC AUGCAUGUGU AAGUAUGAAC GA AUUCAGA CUGUGAAACU GCGAAUGGCU CAUUAAAUCA GUUAUAGUUU GUU(OMU)GAUGGU AACUACUACU (OMC)GGAU AACC GUAGUAAUUC UAGAGCUAAU ACGUGCAACA AACCCCGACU UAUGGAAGGG ACGCAUUUAU UAGAUAAAAG GUCGAC GCG GGCUCUGGCU UGCUCU(OMG)AUG AUUCAUGAUA ACUCGACGGA UCGCAUGGCC UCUGUGCUGG CGACGCAUCA UUC AAAUUU CUGCCCUAUC AACUUUCGAU GGUAGGAUAG UGGCCUACCA UGGUGGUAAC GGGUGACGGA GAAUUAGGGU UCGA UUCCG GAGA(OMG)GGAGC CUGAGAAACG GCUACCACAU CCAAGGAAGG CAGCAGGCGC GCAAAUUACC CAAUCCUGAC A CGGGGAGG U(A2M)GUGA(OMC)AAU AAAUAACAAU ACCGGGCUCU UUCGAGUCUG GUAAUUGGAA UGAGUACAAU CUAA AUCCC UUAACGAGGA UCCAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUA(UY1)A U UUAAGUUG (OMU)UGCAGUU(A2M)A AAAGCUCGUA GUUGAACCUU GGGAUGGGUC GGCCGGUCCG CCUUUGGUGU GCAU UGGUC GGCUUGUCCC UUCGGUCGGC GAUACGCUCC UGGUCUUAAU UGGCCGGGUC GUGCCUCCGG CGCUGUUACU UUGAA GAAA UUAGAGUGCU CAAAGCAAGC CUACGCUCUG GAUACAUUAG CAUGGGAUAA CAUCAUAGGA UUUCGAUCCU AUUGUG UUG GCUUCGGGAU CGGAGUAAUG AUUAACAGGG ACAGUCGGGG GCAUUCGUAU UUCAUAGUCA GAGGUGAAAU UCUUGGA UU UAUGAAAGAC GAACAACUGC GAAAGCAUUU GCCAAGGAUG UUUUCAUUAA UCAAGA(A2M)CGA AAGUUGGGGG CUCG AAGAC GAUCAGAUAC CG(OMU)CCUAGUC UCAACCAUAA ACGAUGCCGA CCAGGGAUCA GCGGAUGUUG CUUAUAGGAC U CCGCUGGC ACCUUAUGAG AAAUCAAAGU UUUUGGGUUC CGGGGGGAGU AUGGUCGCAA GGCUGAAACU UAAAGGAAUU GA CGGAAGG GCACCACCAG GAGUGGAGCC UGCGGCUUAA UUUGACUCAA CACGGGGAAA CUUACCAGGU CCAGACAUAG UAA GGAUUG ACAGACUGAG AGCUCUUUCU UGAUUCUAUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGCGAUUU GUCU GGUUA AUUCCGUUAA CGAACGAGAC CUCAGCCUGC UAACUAGCUA CGUGGAGGCA UCCCUUCACG GCCGGCUUCU UAGAG GGAC UAUGGCCGUU UAGGCCAAGG AAGUUUGAGG CAAUAACAGG UCUGUGAUGC CCUUAGAUGU UCUGGGCCGC ACGCGC GCU ACACUGAUGU AUUCAACGAG UUCACACCUU GCCGACAGGC CCGGGUAAUC UUUGAAAUUU CAUCGUGAUG GGGAUAG AU CAUUGCAAUU GUUGGUCUUC AACGAGGAAU UCCUAGUAAG CGCGAGUCAU CAGCUCGCGU UGACUACGUC CCUGCCCU U UGUACACACC G(OMC)CCGUCGCU CCUACCGAUU GAAUGAUCCG GUGAAGUGUU CGGAUCGCGG CGACGUGGGU GGUUC GCCG CCCGCGACGU CGCGAGAAGU CCACUAAACC UUAUCAUUUA GAGGA(A2M)GGAG AAGUCGUAAC AAGGUUUC (4AC) GUAGGUG(MA6)(MA6)C CUGCGGAAGG AUCAUUG

GENBANK: GENBANK: X16077.1

+
Macromolecule #2: Small ribosomal subunit protein uS2y

MacromoleculeName: Small ribosomal subunit protein uS2y / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 30.682752 KDa
SequenceString: MAANGVATAG RQVSEKEADI QMMLSADVHL GTKNCNYQME RYVFKRRDDG IYIINLGKTW DKLQMAARVI VAIENPKDII VQSARPYGQ RAVLKFAQYT GVNAIAGRHT PGTFTNQMQT SFSEPRLLIL TDPRTDHQPI KEGALGNIPT IAFCDTDSPM G FVDIGIPA ...String:
MAANGVATAG RQVSEKEADI QMMLSADVHL GTKNCNYQME RYVFKRRDDG IYIINLGKTW DKLQMAARVI VAIENPKDII VQSARPYGQ RAVLKFAQYT GVNAIAGRHT PGTFTNQMQT SFSEPRLLIL TDPRTDHQPI KEGALGNIPT IAFCDTDSPM G FVDIGIPA NNKGKHSIGC LFWLLARMVL QMRGTILAAQ KWDVMVDLFF YREPEEAKQE GDEEAEVQAD YGMVGGDQWT TA QISDAAW SGEVEQPISA APAVGVTVAA GWEAASVPAA GWE

UniProtKB: Small ribosomal subunit protein uS2y

+
Macromolecule #3: Small ribosomal subunit protein eS1z

MacromoleculeName: Small ribosomal subunit protein eS1z / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 29.906732 KDa
SequenceString: MAVGKNKRIS KGRKGGKKKA VDPFSKKDWY DVKAPSIFTH RNVGKTLVSR TQGTKIASEG LKHRVFEVSL ADLQGDEDNA YRKIRLRAE DVQGRNVLCQ FWGMDFTTDK LRSLVKKWQT LIEAHVDVKT TDSYTLRLFC IAFTKRRANQ VKRTCYAQSS Q IRQIRRKM ...String:
MAVGKNKRIS KGRKGGKKKA VDPFSKKDWY DVKAPSIFTH RNVGKTLVSR TQGTKIASEG LKHRVFEVSL ADLQGDEDNA YRKIRLRAE DVQGRNVLCQ FWGMDFTTDK LRSLVKKWQT LIEAHVDVKT TDSYTLRLFC IAFTKRRANQ VKRTCYAQSS Q IRQIRRKM RDIMVREASS CDLKDLVAKF IPEAIGREIE KATQGIYPLQ NVFIRKVKIL KAPKFDLGKL MDVHGDYSAE DV GVKVDRP ADEMAVEEPT EIIGA

UniProtKB: Small ribosomal subunit protein eS1z

+
Macromolecule #4: Small ribosomal subunit protein uS5w

MacromoleculeName: Small ribosomal subunit protein uS5w / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 30.169191 KDa
SequenceString: MAERGVERGG DRGDFGRGFG GRGGGRGGPR GRGRRAGRAP EEEKWVPVTK LGRLVKEGKI TKIEQIYLHS LPVKEYQIID LLVGPSLKD EVMKIMPVQK QTRAGQRTRF KAFIVVGDSN GHVGLGVKCS KEVATAIRGA IILAKLSVVP IRRGYWGNKI G KPHTVPCK ...String:
MAERGVERGG DRGDFGRGFG GRGGGRGGPR GRGRRAGRAP EEEKWVPVTK LGRLVKEGKI TKIEQIYLHS LPVKEYQIID LLVGPSLKD EVMKIMPVQK QTRAGQRTRF KAFIVVGDSN GHVGLGVKCS KEVATAIRGA IILAKLSVVP IRRGYWGNKI G KPHTVPCK VTGKCGSVTV RMVPAPRGSG IVAARVPKKV LQFAGIDDVF TSSRGSTKTL GNFVKATFDC LQKTYGFLTP EF WKETRFS KSPYQEHTDF LLIPPGVKIS EVVVDKSVE

UniProtKB: Small ribosomal subunit protein uS5w

+
Macromolecule #5: Small ribosomal subunit protein eS4z

MacromoleculeName: Small ribosomal subunit protein eS4z / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 29.862006 KDa
SequenceString: MARGLKKHLK RLNAPKHWML DKLGGAFAPK PSSGPHKSRE CLPLVLIIRN RLKYALTYRE VISILMQRHI QVDGKVRTDK TYPAGFMDV VSIPKTNENF RLLYDTKGRF RLHSIKDEEA KFKLCKVRSI QFGQKGIPYL NTYDGRTIRY PDPLIKPNDT I KLDLEENK ...String:
MARGLKKHLK RLNAPKHWML DKLGGAFAPK PSSGPHKSRE CLPLVLIIRN RLKYALTYRE VISILMQRHI QVDGKVRTDK TYPAGFMDV VSIPKTNENF RLLYDTKGRF RLHSIKDEEA KFKLCKVRSI QFGQKGIPYL NTYDGRTIRY PDPLIKPNDT I KLDLEENK IVEFIKFDVG NVVMVTGGRN RGRVGVIKNR EKHKGSFETI HIQDSTGHEF ATRLGNVYTI GKGTKPWVSL PK GKGIKLT IIEEARKRLS AQQA

UniProtKB: Small ribosomal subunit protein eS4z

+
Macromolecule #6: Small ribosomal subunit protein eS6y

MacromoleculeName: Small ribosomal subunit protein eS6y / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 28.228201 KDa
SequenceString: MKFNVANPTT GCQKKLEIDD DQKLRAFFDK RLSQEVSGDA LGEEFKGYVF KIMGGCDKQG FPMKQGVLTP GRVRLLLHRG TPCFRGHGR RTGERRRKSV RGCIVSPDLS VLNLVIVKKG VSDLPGLTDT EKPRMRGPKR ASKIRKLFNL GKEDDVRKYV N TYRRTFTN ...String:
MKFNVANPTT GCQKKLEIDD DQKLRAFFDK RLSQEVSGDA LGEEFKGYVF KIMGGCDKQG FPMKQGVLTP GRVRLLLHRG TPCFRGHGR RTGERRRKSV RGCIVSPDLS VLNLVIVKKG VSDLPGLTDT EKPRMRGPKR ASKIRKLFNL GKEDDVRKYV N TYRRTFTN KKGKKVSKAP KIQRLVTPLT LQRKRARIAD KKKRIAKANS DAADYQKLLA SRLKEQRDRR SESLAKKRSR LS SAPAKPV AA

UniProtKB: Small ribosomal subunit protein eS6y

+
Macromolecule #7: Small ribosomal subunit protein eS7z

MacromoleculeName: Small ribosomal subunit protein eS7z / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 21.964521 KDa
SequenceString:
MFSAQHKIHK EKGVELSELD EQVAQAFFDL ENTNQELKSE LKDLYVNSAV QVDISGGRKA IVVNVPYRLR KAYRKIHVRL VRELEKKFS GKDVILIATR RIVRPPKKGS AAKRPRNRTL TSVHEAILDD VVLPAEIVGK RTRYRLDGTK IMKVFLDPKE R NNTEYKVE AFSAVYKKLT GKDVVFEFPI TEA

UniProtKB: Small ribosomal subunit protein eS7z

+
Macromolecule #8: Small ribosomal subunit protein eS8z

MacromoleculeName: Small ribosomal subunit protein eS8z / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 25.047752 KDa
SequenceString: MGISRDSIHK RRATGGKQKQ WRKKRKYEMG RQPANTKLSS NKTVRRIRVR GGNVKWRALR LDTGNYSWGS EATTRKTRVL DVVYNASNN ELVRTKTLVK SAIVQVDAAP FKQWYLSHYG VELGRKKKSA SSTKKDGEEG EEAAVAAPEE VKKSNHLLRK I ASRQEGRS ...String:
MGISRDSIHK RRATGGKQKQ WRKKRKYEMG RQPANTKLSS NKTVRRIRVR GGNVKWRALR LDTGNYSWGS EATTRKTRVL DVVYNASNN ELVRTKTLVK SAIVQVDAAP FKQWYLSHYG VELGRKKKSA SSTKKDGEEG EEAAVAAPEE VKKSNHLLRK I ASRQEGRS LDSHIEDQFA SGRLLACISS RPGQCGRADG YILEGKELEF YMKKIQKKKG KGAA

UniProtKB: Small ribosomal subunit protein eS8z

+
Macromolecule #9: Small ribosomal subunit protein uS4y

MacromoleculeName: Small ribosomal subunit protein uS4y / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.207768 KDa
SequenceString: MVNVRFYRNY GKTFKKPRRP YEKERLDAEL KLVGEYGLRC KRELWRVQYT LSRIRNAARE LLTLDEKNPR RIFEGEALLR RMNRYGLLD ETQNKLDYVL ALTVENFLER RLQTIVFKSG MAKSIHHARV LIRQRHIRVG RQLVNIPSFM VRVESQKHVD F SLTSPFGG ...String:
MVNVRFYRNY GKTFKKPRRP YEKERLDAEL KLVGEYGLRC KRELWRVQYT LSRIRNAARE LLTLDEKNPR RIFEGEALLR RMNRYGLLD ETQNKLDYVL ALTVENFLER RLQTIVFKSG MAKSIHHARV LIRQRHIRVG RQLVNIPSFM VRVESQKHVD F SLTSPFGG GRPGRVKRRN ERAGAKKASG GDGDEDDEE

UniProtKB: Small ribosomal subunit protein uS4y

+
Macromolecule #10: Small ribosomal subunit protein uS17z

MacromoleculeName: Small ribosomal subunit protein uS17z / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.996197 KDa
SequenceString:
MAEQTEKAFL KQPKVFLSSK KSGKGKRPGK GGNRFWKNIG LGFKTPREAI DGAYVDKKCP FTGTVSIRGR ILAGTCHSAK MQRTIIVRR DYLHFVKKYQ RYEKRHSNIP AHVSPCFRVK EGDHIIIGQC RPLSKTVRFN VLKVIPAGSS SSFGKKAFTG M

UniProtKB: Small ribosomal subunit protein uS17z

+
Macromolecule #11: Small ribosomal subunit protein uS15y

MacromoleculeName: Small ribosomal subunit protein uS15y / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 17.123189 KDa
SequenceString:
MGRMHSRGKG ISASALPYKR SSPSWLKTTS QDVDESICKF AKKGLTPSQI GVILRDSHGI PQVKSVTGSK ILRILKAHGL APEIPEDLY HLIKKAVAIR KHLERNRKDK DSKFRLILVE SRIHRLARYY KKTKKLPPVW KYESTTASTL VA

UniProtKB: Small ribosomal subunit protein uS15y

+
Macromolecule #12: Small ribosomal subunit protein uS11x

MacromoleculeName: Small ribosomal subunit protein uS11x / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.268776 KDa
SequenceString:
MSKRKTKEPK VENVTLGPAV REGEQVFGVV HVFASFNDTF IHVTDLSGRE TLVRITGGMK VKADRDESSP YAAMLAAQDV AQRCKELGI TAIHVKLRAT GGNKTKTPGP GAQSALRALA RSGMKIGRIE DVTPIPTDST RRKGGRRGRR L

UniProtKB: Small ribosomal subunit protein uS11x

+
Macromolecule #13: Small ribosomal subunit protein eS21z

MacromoleculeName: Small ribosomal subunit protein eS21z / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.086206 KDa
SequenceString:
MENDAGQVTE LYIPRKCSAT NRMITSKDHA SVQLNIGHLD ANGLYTGQFT TFALCGFVRA QGDADSGVDR LWQKKKVEAK QQ

UniProtKB: Small ribosomal subunit protein eS21z

+
Macromolecule #14: Small ribosomal subunit protein uS8z/uS8w

MacromoleculeName: Small ribosomal subunit protein uS8z/uS8w / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 14.829391 KDa
SequenceString:
MVRISVLNDA LKSMYNAEKR GKRQVMIRPS SKVIIKFLIV MQKHGYIGEF EYVDDHRSGK IVVELNGRLN KCGVISPRFD VGVKEIEGW TARLLPSRQF GYIVLTTSAG IMDHEEARRK NVGGKVLGFF Y

UniProtKB: Small ribosomal subunit protein uS8z/uS8w

+
Macromolecule #15: Small ribosomal subunit protein uS12y

MacromoleculeName: Small ribosomal subunit protein uS12y / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.770618 KDa
SequenceString:
MGKTRGMGAG RKLKRLRINQ RWADKQYKKS HLGNEWKKPF AGSSHAKGIV LEKIGIEAKQ PNSAIRKCAR VQLIKNGKKI AAFVPNDGC LNYIEENDEV LIAGFGRKGH AVGDIPGVRF KVVKVSGVSL LALFKEKKEK PRS

UniProtKB: Small ribosomal subunit protein uS12y

+
Macromolecule #16: Small ribosomal subunit protein eS24z

MacromoleculeName: Small ribosomal subunit protein eS24z / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.412304 KDa
SequenceString:
MAEKAVTIRT RKFMTNRLLS RKQFVIDVLH PGRANVSKAE LKEKLARMYE VKDPNAIFVF KFRTHFGGGK SSGFGLIYDT VESAKKFEP KYRLIRNGLD TKIEKSRKQI KERKNRAKKI RGVKKTKAGD AKKK

UniProtKB: Small ribosomal subunit protein eS24z

+
Macromolecule #17: Small ribosomal subunit protein eS26x

MacromoleculeName: Small ribosomal subunit protein eS26x / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 14.662092 KDa
SequenceString:
MTFKRRNGGR NKHNRGHVKP IRCSNCGKCC PKDKAIKRFI VRNIVEQAAI RDVQEASVYE GYTLPKLYAK TQYCVSCAIH SHVVRVRSR TNRRVRTPPP RFARRKEDTP KPAQPGQAPR PAGGAPAAPR A

UniProtKB: Small ribosomal subunit protein eS26x

+
Macromolecule #18: Small ribosomal subunit protein eS27y

MacromoleculeName: Small ribosomal subunit protein eS27y / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.61421 KDa
SequenceString:
MVLQNDIDLL NPPAELEKRK HKLKRLVQSP NSFFMDVKCQ GCFNITTVFS HSQTVVVCGN CQTILCQPTG GKAKLTEGCS FRRKGD

UniProtKB: Small ribosomal subunit protein eS27y

+
Macromolecule #19: Small ribosomal subunit protein eS30z/eS30y/eS30x

MacromoleculeName: Small ribosomal subunit protein eS30z/eS30y/eS30x / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 6.910188 KDa
SequenceString:
MGKVHGSLAR AGKVRGQTPK VAKQDKKKKP RGRAHKRLQH NRRFVTAVVG FGKKRGPNSS EK

UniProtKB: Small ribosomal subunit protein eS30z/eS30y/eS30x

+
Macromolecule #20: Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v

MacromoleculeName: Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v
type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.445437 KDa
SequenceString:
MRAKWKKKRM RRLKRKRRKM RQRSK

UniProtKB: Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v

+
Macromolecule #21: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 21 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

+
Macromolecule #22: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 22 / Number of copies: 14 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #23: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

-
Sample preparation

BufferpH: 7.4
Details: 50 mM Hepes, pH 7.4, 5 mM MgAc, 100 mM KAc, pH 7.5, 1 mM DTT, Complete protease inhibitor
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 24.512 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 115070
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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