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- EMDB-8124: Structure of the yeast Kluyveromyces lactis small ribosomal subun... -

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Basic information

Entry
Database: EMDB / ID: EMD-8124
TitleStructure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.
Map dataNone
Sample
  • Complex: Kluyveromyces lactis small ribosomal subunit in complex with the Cricket paralysis virus IRES
    • Protein or peptide: x 33 types
    • RNA: x 2 types
  • Ligand: x 2 types
Function / homology
Function and homology information


translation regulator activity / cytosolic ribosome / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / ribosome binding / small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome ...translation regulator activity / cytosolic ribosome / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / ribosome binding / small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Ribosomal protein S26e signature. / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e ...: / Ribosomal protein S26e signature. / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / 40S Ribosomal protein S10 / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S7e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S11, N-terminal / Ribosomal protein S4, KOW domain / Ribosomal_S17 N-terminal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / Ribosomal S3Ae family / Ribosomal protein S28e signature. / 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 S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S14/S29
Similarity search - Domain/homology
Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS10 / KLLA0F18040p / Small ribosomal subunit protein uS5 / KLLA0F07843p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / KLLA0E23673p ...Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS10 / KLLA0F18040p / Small ribosomal subunit protein uS5 / KLLA0F07843p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / KLLA0E23673p / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / KLLA0E12277p / 40S ribosomal protein S27 / Small ribosomal subunit protein uS14 / KLLA0D10659p / 40S ribosomal protein S3 / 40S ribosomal protein S26 / 40S ribosomal protein S7 / 40S ribosomal protein S24 / 40S ribosomal protein S30 / KLLA0B08173p / Small ribosomal subunit protein uS8 / 40S ribosomal protein S25 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S4 / KLLA0B01562p / KLLA0B01474p / KLLA0A10483p / KLLA0A07194p / Small ribosomal subunit protein eS21 / RPS23 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesKluyveromyces lacti (yeast) / Kluyveromyces lactis (yeast) / Cricket paralysis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMurray J / Savva CG / Shin BS / Dever TE / Ramakrishnan V / Fernandez IS
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
National Institutes of HealthIntramural Research Program United States
Wellcome TrustWT096570 United Kingdom
CitationJournal: Elife / Year: 2016
Title: Structural characterization of ribosome recruitment and translocation by type IV IRES.
Authors: Jason Murray / Christos G Savva / Byung-Sik Shin / Thomas E Dever / V Ramakrishnan / Israel S Fernández /
Abstract: Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps ...Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation.
History
DepositionApr 12, 2016-
Header (metadata) releaseMay 18, 2016-
Map releaseMay 18, 2016-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5it9
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8124.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.14
Minimum - Maximum-0.64123625 - 0.9734524
Average (Standard dev.)-0.00009443460 (±0.041961007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 375.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z375.200375.200375.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.6410.973-0.000

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Supplemental data

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Mask #1

Fileemd_8124_msk_1.map
Projections & Slices
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Mask #2

Fileemd_8124_msk_2.map
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Additional map: None

Fileemd_8124_additional_1.map
AnnotationNone
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Additional map: None

Fileemd_8124_additional_2.map
AnnotationNone
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Half map: None

Fileemd_8124_half_map_1.map
AnnotationNone
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Half map: None

Fileemd_8124_half_map_2.map
AnnotationNone
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Sample components

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Entire : Kluyveromyces lactis small ribosomal subunit in complex with the ...

EntireName: Kluyveromyces lactis small ribosomal subunit in complex with the Cricket paralysis virus IRES
Components
  • Complex: Kluyveromyces lactis small ribosomal subunit in complex with the Cricket paralysis virus IRES
    • Protein or peptide: Ribosomal protein uS2
    • Protein or peptide: Ribosomal protein eS1
    • Protein or peptide: Ribosomal protein uS5
    • Protein or peptide: Ribosomal protein uS3
    • Protein or peptide: Ribosomal protein eS4
    • Protein or peptide: Ribosomal protein uS7
    • Protein or peptide: Ribosomal protein eS6
    • Protein or peptide: Ribosomal protein eS7
    • Protein or peptide: Ribosomal protein eS8
    • Protein or peptide: Ribosomal protein uS4
    • Protein or peptide: Ribosomal protein eS10
    • Protein or peptide: Ribosomal protein uS17
    • Protein or peptide: Ribosomal protein eS12
    • Protein or peptide: Ribosomal protein uS15
    • Protein or peptide: Ribosomal protein uS14
    • Protein or peptide: Ribosomal protein uS19
    • Protein or peptide: Ribosomal protein uS9
    • Protein or peptide: Ribosomal protein eS17
    • Protein or peptide: Ribosomal protein uS13
    • Protein or peptide: Ribosomal protein eS19
    • Protein or peptide: Ribosomal protein uS10
    • Protein or peptide: Ribosomal protein eS21
    • Protein or peptide: Ribosomal protein uS8
    • Protein or peptide: Ribosomal protein uS21
    • Protein or peptide: Ribosomal protein eS24
    • Protein or peptide: Ribosomal protein eS25
    • Protein or peptide: Ribosomal protein eS26
    • Protein or peptide: Ribosomal protein eS27
    • Protein or peptide: Ribosomal protein eS28
    • Protein or peptide: Ribosomal protein eS29
    • Protein or peptide: Ribosomal protein eS30
    • Protein or peptide: Ribosomal protein eS31
    • Protein or peptide: Ribosomal protein RACK1
    • RNA: 18S ribosomal RNA
    • RNA: Cricket paralysis virus IRES RNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Kluyveromyces lactis small ribosomal subunit in complex with the ...

SupramoleculeName: Kluyveromyces lactis small ribosomal subunit in complex with the Cricket paralysis virus IRES
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
Source (natural)Organism: Kluyveromyces lacti (yeast)
Molecular weightTheoretical: 2 MDa

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Macromolecule #1: Ribosomal protein uS2

MacromoleculeName: Ribosomal protein uS2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 22.882172 KDa
SequenceString: SLPSTFDLTS EDAQLLLAAR VHLGAKNVQV HQEPYVYKAR PDGVNVINVG KTWEKIVLAA RIIAAIPNPE DVVAISSRTY GQRAVLKYA AHTGATPIAG RFTPGSFTNY ITRSFKEPRL VIVTDPRSDA QAIKESSYVN IPVIALTDLD SPSEYVDVAI P CNNRGKHS ...String:
SLPSTFDLTS EDAQLLLAAR VHLGAKNVQV HQEPYVYKAR PDGVNVINVG KTWEKIVLAA RIIAAIPNPE DVVAISSRTY GQRAVLKYA AHTGATPIAG RFTPGSFTNY ITRSFKEPRL VIVTDPRSDA QAIKESSYVN IPVIALTDLD SPSEYVDVAI P CNNRGKHS IGLIWYLLAR EVLRLRGALP DRTQPWAIMP DLYFYRNP

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Macromolecule #2: Ribosomal protein eS1

MacromoleculeName: Ribosomal protein eS1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 24.488287 KDa
SequenceString: VVDPFTRKEW YDIKAPSTFE NRNVGKTLVN KSVGLKNASD SLKGRVVEVC LADLQGSEDH SFRKVKLRVD EVQGKNLLTN FHGMDFTTD KLRSMVRKWQ TLIEANVTVK TSDDYVLRIF AIAFTRKQAN QVKRTSYAQS SHIRQIRKVI SEILTREVQN S TLAQLTSK ...String:
VVDPFTRKEW YDIKAPSTFE NRNVGKTLVN KSVGLKNASD SLKGRVVEVC LADLQGSEDH SFRKVKLRVD EVQGKNLLTN FHGMDFTTD KLRSMVRKWQ TLIEANVTVK TSDDYVLRIF AIAFTRKQAN QVKRTSYAQS SHIRQIRKVI SEILTREVQN S TLAQLTSK LIPEVINKEI ENATKDIFPL QNVHIRKVKL LKQPKFDLGS LLSLHG

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Macromolecule #3: Ribosomal protein uS5

MacromoleculeName: Ribosomal protein uS5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 23.162922 KDa
SequenceString: GWVPVTKLGR LVKAGKISSI EEIFLHSLPV KEFQIIDQLL PNLKDEVMNI KPVQKQTRAG QRTRFKAVVV VGDSNGHVGL GIKTAKEVA GAIRAGIIIA KLSVIPIRRG YWGTNLGQPH SLATKTSGKC GSVSVRLIPA PRGSGIVASP AVKKLMQLAG V EDVYTSST ...String:
GWVPVTKLGR LVKAGKISSI EEIFLHSLPV KEFQIIDQLL PNLKDEVMNI KPVQKQTRAG QRTRFKAVVV VGDSNGHVGL GIKTAKEVA GAIRAGIIIA KLSVIPIRRG YWGTNLGQPH SLATKTSGKC GSVSVRLIPA PRGSGIVASP AVKKLMQLAG V EDVYTSST GSTRTLENTL KAAFVAIGNT YGFLTPNLWE VQALTPSPMD VYADYATAS

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Macromolecule #4: Ribosomal protein uS3

MacromoleculeName: Ribosomal protein uS3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 24.830895 KDa
SequenceString: AIISKKRKLV ADGVFYAELN EFFTRELAEE GYSGVEVRVT PTKTEIIIRA TKVQDVVGEN GRRINELTLL IEKRFKYKRG TIALYAERV HDRGLSAVAQ AESMKFKLLN GLAIRRAAYG VVRYVMESGA KGCEVVISGK LRAARAKSMK FADGFLIHSG Q PVNDFIET ...String:
AIISKKRKLV ADGVFYAELN EFFTRELAEE GYSGVEVRVT PTKTEIIIRA TKVQDVVGEN GRRINELTLL IEKRFKYKRG TIALYAERV HDRGLSAVAQ AESMKFKLLN GLAIRRAAYG VVRYVMESGA KGCEVVISGK LRAARAKSMK FADGFLIHSG Q PVNDFIET ATRHVLLRQG VLGIKVKIMK DPSRNTSGPK ALPDAVTIIE PKEEEPVLEP SVKDY

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Macromolecule #5: Ribosomal protein eS4

MacromoleculeName: Ribosomal protein eS4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 29.486312 KDa
SequenceString: ARGPKKHLKR LAAPHHWMLD KLSGCYAPRP SAGPHKLRES LPLIVFLRNR LKYALNGREV KAILMQRHVK VDGKVRTDTT FPAGFMDVI TLEATNENFR LVYDVKGRFA VHRITDEEAS YKLAKVKKVQ LGKKGIPYVV THDGRTIRYP DPNIKVNDTV K VDLATGTI ...String:
ARGPKKHLKR LAAPHHWMLD KLSGCYAPRP SAGPHKLRES LPLIVFLRNR LKYALNGREV KAILMQRHVK VDGKVRTDTT FPAGFMDVI TLEATNENFR LVYDVKGRFA VHRITDEEAS YKLAKVKKVQ LGKKGIPYVV THDGRTIRYP DPNIKVNDTV K VDLATGTI TDFIKFDTGK LVYVTGGRNL GRVGTIVHRE RHEGGFDLVH IKDSLENTFV TRLNNVFVIG EPGRPWISLP KG KGIKLTI SEERDRRRAQ HGL

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Macromolecule #6: Ribosomal protein uS7

MacromoleculeName: Ribosomal protein uS7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 22.912369 KDa
SequenceString: FVPVELATTI PVEIQQAQQE IKLFNKWSFE DVEVKDASLV DYIQISKPIY VAHTAGRYAN KRFRKAQCPI VERLTNSLMM NGRNNGKKL KAVRIVKHTL EIINVLTDQN PLQVVVDAII NSGPREDTTR VGGGGAARRQ AVDVSPLRRV NQSIALLTIG A REAAFRNI ...String:
FVPVELATTI PVEIQQAQQE IKLFNKWSFE DVEVKDASLV DYIQISKPIY VAHTAGRYAN KRFRKAQCPI VERLTNSLMM NGRNNGKKL KAVRIVKHTL EIINVLTDQN PLQVVVDAII NSGPREDTTR VGGGGAARRQ AVDVSPLRRV NQSIALLTIG A REAAFRNI KTIAETLAEE LINAAKGSST SYAIKKKDEL ERVAKSNR

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Macromolecule #7: Ribosomal protein eS6

MacromoleculeName: Ribosomal protein eS6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 25.810977 KDa
SequenceString: MKLNISYPIN GTQKCIEIDD EHRVRVFYDK RIGQEVDGES VGDEFKGYVF KIAGGNDKQG FPMKQGVLLP TRVKLLLAKG HSCYRPRRN GERKRKSVRG AIVGPDLAVL ALIITKKGEQ EIEGITNDTV PKRLGPKRAN NIRKFFGLTK EDDVRDYVIR R EVTKGDKS ...String:
MKLNISYPIN GTQKCIEIDD EHRVRVFYDK RIGQEVDGES VGDEFKGYVF KIAGGNDKQG FPMKQGVLLP TRVKLLLAKG HSCYRPRRN GERKRKSVRG AIVGPDLAVL ALIITKKGEQ EIEGITNDTV PKRLGPKRAN NIRKFFGLTK EDDVRDYVIR R EVTKGDKS YTKAPKIQRL VTPQRLQRKR QQKSLKIKNA QAQREAAAEY AQLLAKRLSE RKAEKAEV

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Macromolecule #8: Ribosomal protein eS7

MacromoleculeName: Ribosomal protein eS7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 21.03357 KDa
SequenceString:
PQAKILSQAP TELELQVAQA FIDLENNSPE LKADLRALQF KSIREIEVAG GKKALAVFVP VPSLAAYHKV QIKLTRELEK KFQDRHVIF LAERRILPKP SRKSRQTQKR PRSRTLTAVH DKILEDLVFP TEIVGKRVRY LVGGNKIQKI LLNSKDVQHI D NKLESFQA VYNKLTGKQI VFEIPS

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Macromolecule #9: Ribosomal protein eS8

MacromoleculeName: Ribosomal protein eS8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 22.511531 KDa
SequenceString: GISRDSRHKR AATGAKRAQF RKKRKFELGR QAANTKIGTK RIHPVRTRGG NQKFRALRIE TGNFSWASEG VARKTRITGV VYHPSNNEL VRTNTLTKAA IVQIDATPFR QWYESHYGQS LGKKKNTKAE EETATTSKNT ERKWAARAAE AKIEHAVDSQ F GAGRLYAA ...String:
GISRDSRHKR AATGAKRAQF RKKRKFELGR QAANTKIGTK RIHPVRTRGG NQKFRALRIE TGNFSWASEG VARKTRITGV VYHPSNNEL VRTNTLTKAA IVQIDATPFR QWYESHYGQS LGKKKNTKAE EETATTSKNT ERKWAARAAE AKIEHAVDSQ F GAGRLYAA ISSRPGQSGR CDGYILEGEE LAFYLRRLTA KK

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Macromolecule #10: Ribosomal protein uS4

MacromoleculeName: Ribosomal protein uS4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 20.882344 KDa
SequenceString:
PRAPRTYSKT YSTPKRPYES ARLDAELKLA GEYGLKNKRE IYRISFQLSK IRRAARDLLT RDEKDPKRLF EGNALIRRLV RIGVLSEDK KKLDYVLALK VEDFLERRLQ TQVYKLGLAK SVHHARVLIS QRHIAVGKQI VNIPSFMVRL ESEKHIDFAR T SPFGGARP GRVARKRAAA AGGE

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Macromolecule #11: Ribosomal protein eS10

MacromoleculeName: Ribosomal protein eS10 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 11.423085 KDa
SequenceString:
MLIPKEDRKK IYQHLFQEGV LVAKKDFNQP KHEEIDTKNL FVIKALQSLT SKGFVKTQFS WQYYYYTLTE EGVVYLREYL NLPEHIFPA TYLAGQS

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Macromolecule #12: Ribosomal protein uS17

MacromoleculeName: Ribosomal protein uS17 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 17.712734 KDa
SequenceString:
STELTVQSER AFQKQPHIFT NPKAKANRKT KRWYKNVGLG FKTPKTAIEG SYIDKKCPFT GLVSIRGKIL TGTVVSTRMH RTIVIRRDY LHYVPKYNRY EKRHKNVPAH VSPAFRVQVG DIVTVGQCRP ISKTVRFNVL KVASATGKAN KQFAKF

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Macromolecule #13: Ribosomal protein eS12

MacromoleculeName: Ribosomal protein eS12 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 13.124912 KDa
SequenceString:
AELTIEDALK VVLRTSLVHD GLARGLRESA KALTRGEGQL AVLVESVTEE AISKLVQGLA TENNVPLIKV ADAKQLGEWA GLGKIDRDG NARKVVGASV VVVKNWGADT QEREILLEHF SQQ

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Macromolecule #14: Ribosomal protein uS15

MacromoleculeName: Ribosomal protein uS15 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 16.858678 KDa
SequenceString:
GRMHSKGKGM SSSAIPYSRN APAWFKGSSD GVVEQIIKYA RKGLTPSQIG VLLRDAHGVT QAKVITGNKI LRILKSNGLA PEIPEDLYF LIKKAVSVRK HLERNRKDKD AKFRLILIES RIHRLARYYR TVSVLPPNWK YESATASALV N

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Macromolecule #15: Ribosomal protein uS14

MacromoleculeName: Ribosomal protein uS14 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 13.458439 KDa
SequenceString:
SQVFGVARIF ASFNDTFVHV TDLSGRETIA RVTGGMKVKA DRDESSPYAA MLAAQDVAAK CKEVGITAVH IKIRATGGTR SKTPGPGGQ AALRALARSG LRIGRIEDVT PVPSDSTRKK GGRRGRRL

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Macromolecule #16: Ribosomal protein uS19

MacromoleculeName: Ribosomal protein uS19 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 14.055573 KDa
SequenceString:
RKRSFKTYSY KGVDLEKLLE MPTEDFVKLA PARVRRKFAR GLSEKPAGLM KKLRAAKLSA PENEKPAVVR THLRNMIIVP EMIGSVVGV YNGKVFNQVE IRPEMVGHYL GEFSITYTPV RHGR

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Macromolecule #17: Ribosomal protein uS9

MacromoleculeName: Ribosomal protein uS9 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 15.656257 KDa
SequenceString:
TVPSVQTFGK KKSATAVAHV KAGKGLIKVN GSPITLVQPE ILRFKVYEPL LLVGLDKFAN IDIRVKVTGG GHVSQVYAIR QAIAKGLVA YHQKFVDEQS KNELKKAFTS YDRTLLIADS RRPEPKKFGG RGARSRFQKS YR

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Macromolecule #18: Ribosomal protein eS17

MacromoleculeName: Ribosomal protein eS17 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 14.72898 KDa
SequenceString:
GRVRTKTVKR ASKALIEKYY PKLTMDFQTN KRLCDEIATI QSKRLRNKIA GYTTHLMKRI QKGPVRGISF KLQEEERERK DQYVPDVSA LDLSHSNDVL NVDTQTAELV NSLGLKLPLS VSSVSAVRDR

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Macromolecule #19: Ribosomal protein uS13

MacromoleculeName: Ribosomal protein uS13 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 16.953404 KDa
SequenceString:
SLVVQEQGSF QHILRLLNTN VDGNINVVYA LTTIRGVGRR YANLVCKKAD VDLHKRAGEL TQEELERIVQ IMQNPTHYKI PAWFLNRQK DVNDGKDYHS LANNLESKLR DDLERLKKIR SHRGIRHFWG LRVRGQHTKT TGRRRA

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Macromolecule #20: Ribosomal protein eS19

MacromoleculeName: Ribosomal protein eS19 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 15.747814 KDa
SequenceString:
PGVSVRDVPA QDFINNYASF LQRQGKLEVP GYVDIVKTSA GNELPPQDSE GWFYKRAASV ARHIYLRKQV GVGKLNKLYG GAKNRGVRP HKHVDASGSI NRKVLQSLEK LGVVEISPKG GRRISDNGLR DLDRIAAATL EDEE

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Macromolecule #21: Ribosomal protein uS10

MacromoleculeName: Ribosomal protein uS10 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 12.032146 KDa
SequenceString:
QEVVIHKIRI NLTSTKVKQL ENVSANIIKN AETFKLVKKG PVRLPTKVLK ISTRKTPNGE GSKTWDTYEM RIHKRYIDLE APAHIVKRI TQITIEPGVD VEVIIAA

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Macromolecule #22: Ribosomal protein eS21

MacromoleculeName: Ribosomal protein eS21 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 9.797949 KDa
SequenceString:
MENDKGQLVE LYVPRKCSAT NRIIKAKDHS SVQINIAQVD EEGRAIPGEY VTYALSGYIR ARGEADDSLN RLAQQDGLLK NVWSYSR

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Macromolecule #23: Ribosomal protein uS8

MacromoleculeName: Ribosomal protein uS8 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 14.513846 KDa
SequenceString:
TRTSVLADAL NAINNAEKTG KRQVLIRPSS KVIIKFLQVM QKHGYIGEFE YIDDHRSGKI VVQLNGRLNK CGVISPRFNV KIADVEKWT ANLLPARQFG YVILTTSAGI MDHEEAHRKH VSGKILGFVY

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Macromolecule #24: Ribosomal protein uS21

MacromoleculeName: Ribosomal protein uS21 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 16.047897 KDa
SequenceString:
MGKGKPRGLN SARKLRVHRR NNRWAETTYK KRLLGTAFKS SPFGGSSHAK GIVLEKIGIE SKQPNSAIRK CVRVQLIKNG KKVTAFVPN DGCLNFVDEN DEVLLAGFGR KGKAKGDIPG VRFKVVKVSG VSLLALWKEK KEKPRS

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Macromolecule #25: Ribosomal protein eS24

MacromoleculeName: Ribosomal protein eS24 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 15.063354 KDa
SequenceString:
SDAITIRTRK VISNPLLARK QFVVDVLHPN RANVSKDELR EKLAEAYKAE KDAVSVFGFR TQYGGGKSTG FGLVYNSVAD AKKFEPAYR LVRYGLAEKV EKASRQQRKQ RKNRGKKIFG TGKSIAKKAA RRNAD

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Macromolecule #26: Ribosomal protein eS25

MacromoleculeName: Ribosomal protein eS25 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 7.939246 KDa
SequenceString:
AKHAVVLDQD KFDRIMKEAP TYRYVSVSVL VDRFKLGGSL ARVALRHLEN EGIIKPVSKH SKQAIYTRAT

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Macromolecule #27: Ribosomal protein eS26

MacromoleculeName: Ribosomal protein eS26 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 11.454568 KDa
SequenceString:
MPKKRASNGR NKKGRGHVKP VRCVNCSRSV PKDKAIKRMA IRNIVEAAAI RDLSEASVYA EYALPKTYNK LHYCISCAIH ARIVRVRSR TDRRIRAPPQ R

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Macromolecule #28: Ribosomal protein eS27

MacromoleculeName: Ribosomal protein eS27 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 8.884362 KDa
SequenceString:
MVLVQDLLHP TAASEARKHK LKTLVQSPRS HFLDVKCPGC LNITTVFSHA QTAVTCESCS TVLCTPTGGK AKLSEGTSFR RK

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Macromolecule #29: Ribosomal protein eS28

MacromoleculeName: Ribosomal protein eS28 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 7.073256 KDa
SequenceString:
TPVTLAKVIK VLGRTGSRGG VTQVRVEFLE DTTRTIVRNV KGPVREGDIL VLMESEREAR RLR

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Macromolecule #30: Ribosomal protein eS29

MacromoleculeName: Ribosomal protein eS29 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 6.322149 KDa
SequenceString:
ENVWYSHPRK FGKGSRQCRI SGSHSGLIRK YGLNIDRQSF REKANDIGFY KYR

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Macromolecule #31: Ribosomal protein eS30

MacromoleculeName: Ribosomal protein eS30 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 6.329429 KDa
SequenceString:
ARAGKVKSQT PKVEKQEKPK QPKGRAYKRL LYTRRFVNVT LTNGKRKMNP SPSSQ

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Macromolecule #32: Ribosomal protein eS31

MacromoleculeName: Ribosomal protein eS31 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 7.958424 KDa
SequenceString:
KKVYTTPKKI RHKHKKVKLA VLNYYKVDDE GKVAKLRKEC PNCGPGIFLA NHGDRFYCGK CHSTFATQK

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Macromolecule #33: Ribosomal protein RACK1

MacromoleculeName: Ribosomal protein RACK1 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 35.612676 KDa
SequenceString: SSNIMLVLRG TLEGHNGWVT SLSTSAAQPN LLVSGSRDKT LISWRLTENE QQFGVPVRSY KGHSHIVQDV VVSADGNYAV SASWDKTLR LWNLATGNSE ARFVGHTGDV LSVAIDANSS KIISASRDKT IRVWNTVGDC AYVLLGHTDW VTKVRVAPKN L EDGEVDDG ...String:
SSNIMLVLRG TLEGHNGWVT SLSTSAAQPN LLVSGSRDKT LISWRLTENE QQFGVPVRSY KGHSHIVQDV VVSADGNYAV SASWDKTLR LWNLATGNSE ARFVGHTGDV LSVAIDANSS KIISASRDKT IRVWNTVGDC AYVLLGHTDW VTKVRVAPKN L EDGEVDDG RITFVSAGMD KIVRSWSLNE DSYRIEADFI GHNNYINVVQ PSPDGSLAAS AGKDGQIYVW NLKHKSAFMN FD AKDEVFA LAFSPSRFWL TAATASGIKI YDLENEVLID ELKPEFAGYT KAQDPHAVSL AWSADGQTLF AGYTDNVIRV WQV MTAN

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Macromolecule #34: 18S ribosomal RNA

MacromoleculeName: 18S ribosomal RNA / type: rna / ID: 34 / Number of copies: 1
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 573.508938 KDa
SequenceString: UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUG CGAAUGGCUC AUUAAAUCAG UUAUCGUUUA UUUGAUAGUU CCUUUACUAC AUGGAUAUCU GUGGUAAUUC U AGAGCUAA ...String:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUG CGAAUGGCUC AUUAAAUCAG UUAUCGUUUA UUUGAUAGUU CCUUUACUAC AUGGAUAUCU GUGGUAAUUC U AGAGCUAA UACAUGCUUA AAAUCUCGAC CCUUUGGAAG AGAUGUAUUU AUUAGAUAAA AAAUCAAUGU CUUCGGACUC CU UGAUGAU UCAUAAUAAC UUUUCGAAUC GCAUGGCCUU GUGCUGGCGA UGGUUCAUUC AAAUUUCUGC CCUAUCAACU UUC GAUGGU AGGAUAGUGG CCUACCAUGG UUUCAACGGG UAACGGGGAA UAAGGGUUCG AUUCCGGAGA GGGAGCCUGA GAAA CGGCU ACCACAUCCA AGGAAGGCAG CAGGCGCGCA AAUUACCCAA UCCUAAUUCA GGGAGGUAGU GACAAUAAAU AACGA UACA GGGCCCAUUC GGGUCUUGUA AUUGGAAUGA GUACAAUGUA AAUACCUUAA CGAGGAACAA CUGGAGGGCA AGUCUG GUG CCAGCAGCCG CGGUAAUUCC AGCUCCAGUA GCGUAUAUUA AAGUUGUUGC AGUUAAAAAG CUCGUAGUUG AACUUUG GG UCUGGUUGUC CGGUCGGUUU UUCAACCGGA UCUUUCCUUC UGGCUAACCU GUACUCCUUG UGGGUGCAGG CGAACCAG G ACUUUUACUU UGAAAAAAUU AGAGUGUUCA AAGCAGGCGA AAGCUCGAAU AUAUUAGCAU GGAAUAAUGG AAUAGGACG UUUGGUUCUA UUUUGUUGGU UUCUAGGACC AUCGUAAUGA UUAAUAGGGA CGGUCGGGGG CAUCAGUAUU CAAUUGUCAG AGGUGAAAU UCUUGGAUUU AUUGAAGACU AACUACUGCG AAAGCAUUUG CCAAGGACGU UUUCAUUAAU CAAGAACGAA A GUUAGGGG AUCGAAGAUG AUCAGAUACC GUCGUAGUCU UAACCAUAAA CUAUGCCGAC UAGGGAUCGG GUGGUGUUUU UC UUAUGAC CCACUCGGCA CCUUACGAGA AAUCAAAGUC UUUGGGUUCU GGGGGGAGUA UGGUCGCAAG GCUGAAACUU AAA GGAAUU GACGGAAGGG CACCACCAGG AGUGGAGCCU GCGGCUUAAU UUGACUCAAC ACGGGGAAAC UCACCAGGUC CAGA CACAA UAAGGAUUGA CAGAUUGAGA GCUCUUUCUU GAUUUUGUGG GUGGUGGUGC AUGGCCGUUC UUAGUUGGUG GAGUG AUUU GUCUGCUUAA UUGCGAUAAC GAACGAGACC UUAACCUACU AAAUAGGGUU GCUGGCACUU GCCGGUUGAC UCUUCU UAG AGGGACUAUC GGUUUCAAGC CGAUGGAAGU UUGAGGCAAU AACAGGUCUG UGAUGCCCUU AGACGUUCUG GGCCGCA CG CGCGCUACAC UGACGGAGCC AGCGAGUACA ACCUUGGCCG AGAGGUCUGG GUAAUCUUGU GAAACUCCGU CGUGCUGG G GAUAGAGCAU UGUAAUUAUU GCUCUUCAAC GAGGAAUUCC UAGUAAGCGC AAGUCAUCAG CUUGCGUUGA UUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUUUGCUUAG AGAAGGGGGC AACUCCAUC UCAGAGCGAA GAAUCUGGUC AAACUUGGUC AUUUAGAGGA ACUAAAAGUC GUAACAAGGU UUCCGUAGGU G AACCUGCG GAAGGAUCAU UA

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Macromolecule #35: Cricket paralysis virus IRES RNA

MacromoleculeName: Cricket paralysis virus IRES RNA / type: rna / ID: 35 / Number of copies: 1
Source (natural)Organism: Cricket paralysis virus
Molecular weightTheoretical: 61.462207 KDa
SequenceString: AAAAAUGUGA UCUUGCUUGU AAAUACAAUU UUGAGAGGUU AAUAAAUUAC AAGUAGUGCU AUUUUUGUAU UUAGGUUAGC UAUUUAGCU UUACGUUCCA GGAUGCCUAG UGGCAGCCCC ACAAUAUCCA GGAAGCCCUC UCUGCGGCUU UUCAGAUUAG G UAGUCGAA ...String:
AAAAAUGUGA UCUUGCUUGU AAAUACAAUU UUGAGAGGUU AAUAAAUUAC AAGUAGUGCU AUUUUUGUAU UUAGGUUAGC UAUUUAGCU UUACGUUCCA GGAUGCCUAG UGGCAGCCCC ACAAUAUCCA GGAAGCCCUC UCUGCGGCUU UUCAGAUUAG G UAGUCGAA AAACCUAAGA AAUUUACCUG CUAC

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Macromolecule #36: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 36 / Number of copies: 80 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #37: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 37 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
Component:
ConcentrationName
20.0 milimolarMES-KOH
100.0 milimolarKCL
8.0 milimolarMgCl(2)
2.0 milimolarDTT
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: EMDB MAP
EMDB ID:
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54481
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-5it9:
Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.

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