[English] 日本語
Yorodumi
- EMDB-37733: Structural basis of translation inhibition by a valine tRNA-deriv... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37733
TitleStructural basis of translation inhibition by a valine tRNA-derived fragment
Map data
Sample
  • Complex: Sulfolobus acidocaldarius ribosome
    • RNA: x 2 types
    • Protein or peptide: x 26 types
  • Ligand: x 1 types
KeywordsSulfolobus acidocaldarius ribosome / RIBOSOME
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / : ...Ribosomal protein S27ae / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / : / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S27e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / 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 L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / K Homology domain / K homology RNA-binding domain / Ribosomal protein S2 signature 2. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature.
Similarity search - Domain/homology
Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 ...Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic) / Haloferax volcanii (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang YH / Zhou J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971226 China
CitationJournal: Life Sci Alliance / Year: 2024
Title: Structural basis of translation inhibition by a valine tRNA-derived fragment.
Authors: Yun Wu / Meng-Ting Ni / Ying-Hui Wang / Chen Wang / Hai Hou / Xing Zhang / Jie Zhou /
Abstract: Translational regulation by non-coding RNAs is a mechanism commonly used by cells to fine-tune gene expression. A fragment derived from an archaeal valine tRNA (Val-tRF) has been previously ...Translational regulation by non-coding RNAs is a mechanism commonly used by cells to fine-tune gene expression. A fragment derived from an archaeal valine tRNA (Val-tRF) has been previously identified to bind the small subunit of the ribosome and inhibit translation in Here, we present three cryo-electron microscopy structures of Val-tRF bound to the small subunit of ribosomes at resolutions between 4.02 and 4.53 Å. Within these complexes, Val-tRF was observed to bind to conserved RNA-interacting sites, including the ribosomal decoding center. The binding of Val-tRF destabilizes helices h24, h44, and h45 and the anti-Shine-Dalgarno sequence of 16S rRNA. The binding position of this molecule partially overlaps with the translation initiation factor aIF1A and occludes the mRNA P-site codon. Moreover, we found that the binding of Val-tRF is associated with steric hindrance of the H69 base of 23S rRNA in the large ribosome subunit, thereby preventing 70S assembly. Our data exemplify how tRNA-derived fragments bind to ribosomes and provide new insights into the mechanisms underlying translation inhibition by Val-tRFs.
History
DepositionOct 10, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37733.png

Downloads & links

-
Map

FileDownload / File: emd_37733.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 300 pix.
= 326.1 Å		1.09 Å/pix.
x 300 pix.
= 326.1 Å		1.09 Å/pix.
x 300 pix.
= 326.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-0.5674737 - 1.3375285
Average (Standard dev.)0.014805354 (±0.08856701)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 326.1 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_37733_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37733_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Sulfolobus acidocaldarius ribosome

EntireName: Sulfolobus acidocaldarius ribosome
Components
  • Complex: Sulfolobus acidocaldarius ribosome
    • RNA: RNA (26-MER)
    • RNA: RNA (1328-MER)
    • Protein or peptide: 30S ribosomal protein S2
    • Protein or peptide: 30S ribosomal protein S4e
    • Protein or peptide: 30S ribosomal protein S4
    • Protein or peptide: 30S ribosomal protein S5
    • Protein or peptide: 30S ribosomal protein S6e
    • Protein or peptide: 30S ribosomal protein S8e
    • Protein or peptide: Small ribosomal subunit protein uS8
    • Protein or peptide: 30S ribosomal protein S11
    • Protein or peptide: 30S ribosomal protein S12
    • Protein or peptide: 30S ribosomal protein S15
    • Protein or peptide: 30S ribosomal protein S17
    • Protein or peptide: 30S ribosomal protein S24e
    • Protein or peptide: 30S ribosomal protein S27e
    • Protein or peptide: 30S ribosomal protein S3Ae
    • Protein or peptide: 30S ribosomal protein S3
    • Protein or peptide: 30S ribosomal protein S7
    • Protein or peptide: 30S ribosomal protein S9
    • Protein or peptide: 30S ribosomal protein S10
    • Protein or peptide: 30S ribosomal protein S13
    • Protein or peptide: 30S ribosomal protein S14 type Z
    • Protein or peptide: 30S ribosomal protein S17e
    • Protein or peptide: 30S ribosomal protein S19e
    • Protein or peptide: 30S ribosomal protein S19
    • Protein or peptide: 30S ribosomal protein S27ae
    • Protein or peptide: 30S ribosomal protein S28e
    • Protein or peptide: 50S ribosomal protein L7Ae
  • Ligand: UNKNOWN LIGAND

+
Supramolecule #1: Sulfolobus acidocaldarius ribosome

SupramoleculeName: Sulfolobus acidocaldarius ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1, #3-#8, #28, #9-#27
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)

+
Macromolecule #1: RNA (1328-MER)

MacromoleculeName: RNA (1328-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 486.920531 KDa
SequenceString: CGCCCCGAUU CCGGUUGAUC CUGCCGGACC CGACCGCUAU CGGGGUAGGG AUAAGCCAUG GGAGUCUUAC ACUCCCGGGU AAGGGAGUG UGGCGGACGG CUGAGUAACA CGUGGCUAAC CUACCCUCGG GACGGGGAUA ACCCCGGGAA ACUGGGGAUA A UCCCCGAU ...String:
CGCCCCGAUU CCGGUUGAUC CUGCCGGACC CGACCGCUAU CGGGGUAGGG AUAAGCCAUG GGAGUCUUAC ACUCCCGGGU AAGGGAGUG UGGCGGACGG CUGAGUAACA CGUGGCUAAC CUACCCUCGG GACGGGGAUA ACCCCGGGAA ACUGGGGAUA A UCCCCGAU AGGGAAGGAG UCCUGGAAUG GUUCCUUCCC UAAAGGGCUA UAGGCUAUUU CCCGUUUGUA GCCGCCCGAG GA UGGGGCU ACGGCCCAUC AGGCUGUCGG UGGGGUAAAG GCCCACCGAA CCUAUAACGG GUAGGGGCCG UGGAAGCGGG AGC CUCCAG UUGGGCACUG AGACAAGGGC CCAGGCCCUA CGGGGCGCAC CAGGCGCGAA ACGUCCCCAA UGCGCGAAAG CGUG AGGGC GCUACCCCGA GUGCCUCCGC AAGGAGGCUU UUCCCCGCUC UAAAAAGGCG GGGGAAUAAG CGGGGGGCAA GUCUG GUGU CAGCCGCCGC GGUAAUACCA GCUCCGCGAG UGGUCGGGGU GAUUACUGGG CCUAAAGCGC CUGUAGCCGG CCCACC AAG UCGCCCCUUA AAGUCCCCGG CUCAACCGGG GAACUGGGGG CGAUACUGGU GGGCUAGGGG GCGGGAGAGG CGGGGGG UA CUCCCGGAGU AGGGGCGAAA UCCUUAGAUA CCGGGAGGAC CACCAGUGGC GGAAGCGCCC CGCUAGAACG CGCCCGAC G GUGAGAGGCG AAAGCCGGGG CAGCAAACGG GAUUAGAUAC CCCGGUAGUC CCGGCUGUAA ACGAUGCGGG CUAGGUGUC GAGUAGGCUU AGAGCCUACU CGGUGCCGCA GGGAAGCCGU UAAGCCCGCC GCCUGGGGAG UACGGUCGCA AGACUGAAAC UUAAAGGAA UUGGCGGGGG AGCACCACAA GGGGUGGAAC CUGCGGCUCA AUUGGAGUCA ACGCCUGGAA UCUUACCGGG G GAGACCGC AGUAUGACGG CCAGGCUAAC GACCUUGCCU GACUCGCGGA GAGGAGGUGC AUGGCCGUCG CCAGCUCGUG UU GUGAAAU GUCCGGUUAA GUCCGGCAAC GAGCGAGACC CCCACCCCUA GUUGGUAUUC UGGACUCCGG UCCAGAACCA CAC UAGGGG GACUGCCGGC GUAAGCCGGA GGAAGGAGGG GGCCACGGCA GGUCAGCAUG CCCCGAAACC CGGGCCGCAC GCGG GUUAC AAUGGCAGGG ACAACGGGAU GCUACCUCGA AAGGGGGAGC CAAUCCUUAA ACCCUGCCGC AGUUGGGAUC GAGGG CUGA AACCCGCCCU CGUGAACGAG GAAUCCCUAG UAACCGCGGG UCAACAACCC GCGGUGAAUA CGUCCCUGCU CCUUGC ACA CACCGCCCGU CGCUCCACCC GAGCGAGAAA GGGGUGAGGU CCCUUGCGAU AAGUGGGGGA UCGAACUCCU UUCCCGC GA GGGGGGAGAA GUCGUAACAA GGUAGCCGUA GGGGAACCUG CGGCUGGAUC ACCUCAUAU

GENBANK: GENBANK: CP046615.1

+
Macromolecule #2: RNA (26-MER)

MacromoleculeName: RNA (26-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Haloferax volcanii (archaea)
Molecular weightTheoretical: 8.411946 KDa
SequenceString:
GGGUUGGUGG UCUAGUCUGG UUAUGA

+
Macromolecule #3: 30S ribosomal protein S2

MacromoleculeName: 30S ribosomal protein S2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 22.474012 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString: ELLVPLDTYL SAGVHIGTHT CTRYMERFIY RVRPEGLYVL DVRKIDERLR VAAKFISRFR PEAVLTVASR PYAFTPVQKF SEVVRGKEI SGRFPPGTLT NPYLDNYIEP EVLIVTDPRT DLQAIKEASK VGIPIVAFTD TDARVDFIDV IIPANNKGRK S LALLYWVL ...String:
ELLVPLDTYL SAGVHIGTHT CTRYMERFIY RVRPEGLYVL DVRKIDERLR VAAKFISRFR PEAVLTVASR PYAFTPVQKF SEVVRGKEI SGRFPPGTLT NPYLDNYIEP EVLIVTDPRT DLQAIKEASK VGIPIVAFTD TDARVDFIDV IIPANNKGRK S LALLYWVL ARQILRERKE IPLDGDIPLR VEDFETRL

UniProtKB: Small ribosomal subunit protein uS2

+
Macromolecule #4: 30S ribosomal protein S4e

MacromoleculeName: 30S ribosomal protein S4e / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 27.339988 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString: VHITRFEAPW FLKVGKKEYK WIIRSRAGPH KIQESVPLAI LLKYYLKAVD TTREAKRIIF DGKVLVDGKV RRDYKYPVGL MDVVEIPSA DLRVRIIPDN VRYLTTINIS REDAKYKFVR IMNKTTLKSG VLQLNLEDGR NILLKGEELS QYNLPTLTTL K IELPEQKI ...String:
VHITRFEAPW FLKVGKKEYK WIIRSRAGPH KIQESVPLAI LLKYYLKAVD TTREAKRIIF DGKVLVDGKV RRDYKYPVGL MDVVEIPSA DLRVRIIPDN VRYLTTINIS REDAKYKFVR IMNKTTLKSG VLQLNLEDGR NILLKGEELS QYNLPTLTTL K IELPEQKI TTAYTIKEGV YAMIIGGRNA GLHGKISKIQ LAKYKRIKYS LVTLEGKDGS TFQTNLINVM AIGENEADSN LG

UniProtKB: Small ribosomal subunit protein eS4

+
Macromolecule #5: 30S ribosomal protein S4

MacromoleculeName: 30S ribosomal protein S4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 19.440623 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
DPRKSKKKWM GPSHPWIKIN LGKEQILIGK YGLRNKKEIW IAQTMIRNFR HQARSLLALP PAERNIREKQ LIQKLYRMGI LEKDNSTLD DILSLTEENY LERRLQTIVY KKGLARTIYQ ARQLITHGHI AISGRKVTSP GYVVLRGEED LIDYYPTSPF K QNPPSQ

UniProtKB: Small ribosomal subunit protein uS4

+
Macromolecule #6: 30S ribosomal protein S5

MacromoleculeName: 30S ribosomal protein S5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 22.782686 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString: EDWKPRTKVG QLIKEGKINS MKELFERNLP IVEPEIVDVL LPKLRYDIVD IGIVQKQTDA GELSRYKVLI VMGNMDGYIS YGTGKAKQL RVAIQKAIRD AKMRIIPVRR GCGSWECTCG ESHSLPFIVS GKAGSVEVTL LPAPKGTGLV VGSVLKTFLS L AGLKDVWS ...String:
EDWKPRTKVG QLIKEGKINS MKELFERNLP IVEPEIVDVL LPKLRYDIVD IGIVQKQTDA GELSRYKVLI VMGNMDGYIS YGTGKAKQL RVAIQKAIRD AKMRIIPVRR GCGSWECTCG ESHSLPFIVS GKAGSVEVTL LPAPKGTGLV VGSVLKTFLS L AGLKDVWS RTKGSTYTHE NFIKAAYIAL YNTYRFVTPV DWGRMK

UniProtKB: Small ribosomal subunit protein uS5

+
Macromolecule #7: 30S ribosomal protein S6e

MacromoleculeName: 30S ribosomal protein S6e / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 11.479355 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
ALAYRTRAFQ LSLDQSKLPN LVGTKIGDVI DINVSGVNLK LKITGGSDNS GFSMRFDVGG GAKRKILVSG PPGYYPKEDG LRRKRTVRG NMITPEIVQI NTIMIR

UniProtKB: Small ribosomal subunit protein eS6

+
Macromolecule #8: 30S ribosomal protein S8e

MacromoleculeName: 30S ribosomal protein S8e / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 14.113179 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
SYYQGNDSRK ITGGQKGKNR DKRKYELGSP PTETKISDKD IKEKDRVAGG NFKLRLRYAS YANVYDPQSK TAKKVKIISV LESPANREY ARRGIIVKGT LIQTELGKAK VTSRPGQDGI INALLLR

UniProtKB: Small ribosomal subunit protein eS8

+
Macromolecule #9: 30S ribosomal protein S11

MacromoleculeName: 30S ribosomal protein S11 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 13.652649 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
REIRWGNARI YASQNNTIIT ITDITGAEII SKASGGMVVK ADREKPSPYA AMLAANKAAN DAFDKGISAI HIKVRAQGGY GSKTPGPGA QPAIRALARA GFIIGRIEDV TPLPHDTIRR PGGRRGRRV

UniProtKB: Small ribosomal subunit protein uS11

+
Macromolecule #10: 30S ribosomal protein S12

MacromoleculeName: 30S ribosomal protein S12 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 15.703551 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
GSKSPKGLFA ARKLRLKRLK FSWSQRSFKR RMLALKEKFD PLEGAPMARG IVLEKVGIES RQPNSAVRKA VRVQLVKNGR IVTAFVPGD GGVNFIDEHD EVVIAGIGGT LGRSMGDLPG VRYKVVMVNG VSLDALYKGK KQKP

UniProtKB: Small ribosomal subunit protein uS12

+
Macromolecule #11: 30S ribosomal protein S15

MacromoleculeName: 30S ribosomal protein S15 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 17.438426 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
MNKKRAKGNS HSIRPVRSGP PKWVRFTREE VELLVEELAK RGYPPSMIGM VLRDQYGVPL VKQITGRKLT AILQDRNMKP KIPEDLFNL MRRAVNIRRH LFEYPKDKSA KRGLEEVESK IRRLASYYKE TGKLPQEWSY DPAKAELLVT

UniProtKB: Small ribosomal subunit protein uS15

+
Macromolecule #12: 30S ribosomal protein S17

MacromoleculeName: 30S ribosomal protein S17 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 12.602619 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
KKGQLVKNVG IEGVSAPSKT CDDEYCPYHG SLKVRGIVLE GKLIRARANR TGTVEREYIF YDSKYKRYER RRSRIHVHIP SCLEVKEGD NVIIGESRPI AKSISFVILG VK

UniProtKB: Small ribosomal subunit protein uS17

+
Macromolecule #13: 30S ribosomal protein S24e

MacromoleculeName: 30S ribosomal protein S24e / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 10.765213 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
VSDKVEGIVE RDIQNNVANR RELYIKLFHI GSGTPSRKEL VKAIASTFST AEDLVVVKKV FTNYGSGISY ARVNVYKDKD SLQKLEPQY LIGRDTG

UniProtKB: Small ribosomal subunit protein eS24

+
Macromolecule #14: 30S ribosomal protein S27e

MacromoleculeName: 30S ribosomal protein S27e / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 6.576969 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
MKAKFKILIP EPKSKFIRVK CRQCNNEQVI FSNATFPVRC LSCGAQIVIP KGGKAKIEG

UniProtKB: Small ribosomal subunit protein eS27

+
Macromolecule #15: 30S ribosomal protein S3Ae

MacromoleculeName: 30S ribosomal protein S3Ae / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 21.876621 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
IRDKWKLKKW YVITAPKVFG EALLGSTPAY DINKALSRKI EVTLYDLTGD YNLVYIHLYF KILGNISGDK LSTIFYGHEL SRDYIRSLV RRKSSKINAV VDVTTKDGYM LRVKGLVLTT YRAHISQKTA IRKVISDITR KKAEESDFDQ FVQDVIFGKL S NDIFQEAK KIYPLRKVEI EKTKLLKAPK V

UniProtKB: Small ribosomal subunit protein eS1

+
Macromolecule #16: 30S ribosomal protein S3

MacromoleculeName: 30S ribosomal protein S3 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 22.396506 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString: VLIKRHFLQK AAIKVMVDEY LAKQFYNAEY AGVEIVKTPI GTRVIIYAGR PPLIIGKGGK TIKQLAQVLE KFFGLENPQI TVTAAENPE LNARVMAFRL AIALEKGYHF RRAAFITIRR IMSSGAVGAE VIVSGKLTSE RAKYEKLKEG TVYKSGQQLE K IIDRAIGI ...String:
VLIKRHFLQK AAIKVMVDEY LAKQFYNAEY AGVEIVKTPI GTRVIIYAGR PPLIIGKGGK TIKQLAQVLE KFFGLENPQI TVTAAENPE LNARVMAFRL AIALEKGYHF RRAAFITIRR IMSSGAVGAE VIVSGKLTSE RAKYEKLKEG TVYKSGQQLE K IIDRAIGI AMLKPGVYGV EVVITKPTRS IDKIELKEKV EKT

UniProtKB: Small ribosomal subunit protein uS3

+
Macromolecule #17: 30S ribosomal protein S7

MacromoleculeName: 30S ribosomal protein S7 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 21.86232 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString: ENIEVSNLNV KVFGKWDTKV EVRDPSLKKY IDLMSIYLPH TGGRHEHRRF GKSRIPIVER LINNLMRPGR NKGKKMLAYN IVKTTFDII AVKTGQNPIQ VLVRAIENAA PREEVTRIMY GGIVYYVAVD VAPQRRVDLA LRHLVTGASE ASFNNPKPIE E ALAEEIIA ...String:
ENIEVSNLNV KVFGKWDTKV EVRDPSLKKY IDLMSIYLPH TGGRHEHRRF GKSRIPIVER LINNLMRPGR NKGKKMLAYN IVKTTFDII AVKTGQNPIQ VLVRAIENAA PREEVTRIMY GGIVYYVAVD VAPQRRVDLA LRHLVTGASE ASFNNPKPIE E ALAEEIIA AANNDNKSVA IRKKEEIERI ALSSR

UniProtKB: Small ribosomal subunit protein uS7

+
Macromolecule #18: 30S ribosomal protein S9

MacromoleculeName: 30S ribosomal protein S9 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 15.638136 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
QAEQNFMITY ARRKSARASC YIKPGNGKVF VNDIPIEIIP IEVVRYKIME PLVLAGDKIT SSIEARIYTQ GGGIMGQADA ARMALARAL VKFTNSKELV EIYKSYDRTM LAGDPRQTES EKWMRYSARR WRQKAYR

UniProtKB: Small ribosomal subunit protein uS9

+
Macromolecule #19: 30S ribosomal protein S10

MacromoleculeName: 30S ribosomal protein S10 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 11.775886 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
TKARIRLWSS NIDSLNFVVN QIRNMAQKTG IQVSGPIPLP TTRMEVPVMR LPHGEGKKKW EHWEMKVHKR IIDIAADERV MRQLMRVRV PDDVYIEIEL I

UniProtKB: Small ribosomal subunit protein uS10

+
Macromolecule #20: 30S ribosomal protein S13

MacromoleculeName: 30S ribosomal protein S13 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 17.140783 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
QQQFKYIVRL FGQDVDGTMK LPYALAMIKG IGYNTAMIII RKLNLDKDKR LGEISDEDIK KIENLLNNKI IPESPNWIYN RQKDYESGA DMHLVTSDLI FYVRNDIERE RRSRSWRGVR HSLGLKVRGQ RTRTTGRTGA TIGVRRAK

UniProtKB: Small ribosomal subunit protein uS13

+
Macromolecule #21: 30S ribosomal protein S14 type Z

MacromoleculeName: 30S ribosomal protein S14 type Z / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 6.190371 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
KYKPPAERRF GKGVQLCKRC GSRDSVIQKY GLYLCRQCFR EVAYPMGFRK TR

UniProtKB: Small ribosomal subunit protein uS14

+
Macromolecule #22: 30S ribosomal protein S17e

MacromoleculeName: 30S ribosomal protein S17e / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 7.336366 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
GNVYTKDIKR VARELYDKFK DQASDKYDDN KKLVDEYVNV SSKKVKNRIA GYLTRYVKIS KN

UniProtKB: Small ribosomal subunit protein eS17

+
Macromolecule #23: 30S ribosomal protein S19e

MacromoleculeName: 30S ribosomal protein S19e / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 17.55966 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
TVQMVPADIL IPKLAEYLKN NVKELNPPNW VYFAKTASFK ERVPDDIENW WYIRAASLLR HLYIYKEPIG LQKTRKLYSG SKRRGTKPP RSVKAPTHSI RTILQQLEKA GLVTKTRRGR ILSPKGRSLL DKLAYEMFKE LAEKKQDLKK Y

UniProtKB: Small ribosomal subunit protein eS19

+
Macromolecule #24: 30S ribosomal protein S19

MacromoleculeName: 30S ribosomal protein S19 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 13.800354 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
WKKFRYRGKS LEDLLNMPMD EFIKLLPSRQ RRSLKRGFSD KQRRLLEKIR KISREGKQNK VIKTHVRNMV ILPEMVGLRF AVYNGKEFV EFQVVPEMIG RYLGEYSITT KKVEHG

UniProtKB: Small ribosomal subunit protein uS19

+
Macromolecule #25: 30S ribosomal protein S27ae

MacromoleculeName: 30S ribosomal protein S27ae / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 6.261392 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
QSKAVVRTYY EVEQDSIKLK NKKCPRCGSI MAHHMKPLER WACGKCGYTE FIGK

UniProtKB: Small ribosomal subunit protein eS31

+
Macromolecule #26: 30S ribosomal protein S28e

MacromoleculeName: 30S ribosomal protein S28e / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 7.094255 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
GFPAEVIQIL DRTGVTGEVT QVRVRVLEGR DKGRILTRNV KGPVRLGDIL ILRETEREAR KLS

UniProtKB: Small ribosomal subunit protein eS28

+
Macromolecule #27: 50S ribosomal protein L7Ae

MacromoleculeName: 50S ribosomal protein L7Ae / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 13.351481 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
PSYVKFEVPQ ELADKVLEAV KKAKDSGKIK KGTNETTKAV ERSQAKLVVI AEDVQPEEIV AHLPLLCEEK KIPYVYVPSK KSLGEACGL QVAAASVALM DPGEAKDLVD EIVKRVNEIK GKSS

UniProtKB: Large ribosomal subunit protein eL8

+
Macromolecule #28: Small ribosomal subunit protein uS8

MacromoleculeName: Small ribosomal subunit protein uS8 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Molecular weightTheoretical: 14.624191 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
SequenceString:
INPLANALAT LYNNEMRRNK QALITPASKL IISVLRVMQK EGYIGEFEYI DDGRAGKIIV QLLGRINKCG PISPRYPLDY NGLLRLPDY IRKYLPSKEI GIIIISTPKG VMSHRDGIRE KIGGVTLGYV Y

UniProtKB: Small ribosomal subunit protein uS8

+
Macromolecule #29: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 29 / Number of copies: 57 / Formula: UNL
Molecular weightTheoretical: 103.12 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 26.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4v67

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9742
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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