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- PDB-5it7: Structure of the Kluyveromyces lactis 80S ribosome in complex wit... -

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Entry
Database: PDB / ID: 5it7
TitleStructure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2
Components
  • (40S ribosomal protein ...) x 14
  • (60S ribosomal protein ...) x 10
  • (Ribosomal protein ...) x 2
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Eft2p
  • KLLA0A06336p
  • KLLA0A07194p
  • KLLA0A07227p
  • KLLA0A10483p
  • KLLA0B01474p
  • KLLA0B01562p
  • KLLA0B02937p
  • KLLA0B04686p
  • KLLA0B05742p
  • KLLA0B06182p
  • KLLA0B07139p
  • KLLA0B08173p
  • KLLA0B13409p
  • KLLA0C04809p
  • KLLA0C08371p
  • KLLA0C13519p
  • KLLA0C18216p
  • KLLA0D03410p
  • KLLA0D05115p
  • KLLA0D05181p
  • KLLA0D05643p
  • KLLA0D06941p
  • KLLA0D07405p
  • KLLA0D08305p
  • KLLA0D10659p
  • KLLA0D16027p
  • KLLA0D16071p
  • KLLA0E00573p
  • KLLA0E03455p
  • KLLA0E05941p
  • KLLA0E06843p
  • KLLA0E06997p
  • KLLA0E12277p
  • KLLA0E12453p
  • KLLA0E23651p
  • KLLA0E23673p
  • KLLA0F04499p
  • KLLA0F04675p
  • KLLA0F05247p
  • KLLA0F07843p
  • KLLA0F08261p
  • KLLA0F09812p
  • KLLA0F18040p
  • KLLA0F25542p
  • RPL2860S ribosomal protein L28
  • RPS2340S ribosomal protein S23
  • Ribosomal protein
  • Ubiquitin fusion protein
  • Ubiquitin-40S ribosomal protein S27a
  • cricket paralysis virus IRES
  • uL11
KeywordsRIBOSOME / translocation / IRES / eEF2
Function / homology
Function and homology information


response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome ...response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / ribosome binding / large ribosomal subunit / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S12e / 50S ribosomal protein L10, insertion domain superfamily / : / Small (40S) ribosomal subunit Asc1/RACK1 / 60S ribosomal protein L10P, insertion domain ...60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S12e / 50S ribosomal protein L10, insertion domain superfamily / : / Small (40S) ribosomal subunit Asc1/RACK1 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein S19A/S15e / Ribosomal protein S21e signature. / Ribosomal L29e protein family / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein L24e, conserved site / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L34e, conserved site / Ribosomal protein L1, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L38e protein family / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / 40S Ribosomal protein S10 / 60S ribosomal protein L35 / Ribosomal protein L1 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein S7e / Ribosomal protein L23, N-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal L27e protein family
Similarity search - Domain/homology
(2S)-1-amino-N,N,N-trimethyl-1-oxobutan-2-aminium / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA/RNA hybrid (> 100) / DNA/RNA hybrid (> 1000) / RNA ...(2S)-1-amino-N,N,N-trimethyl-1-oxobutan-2-aminium / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / DNA/RNA hybrid (> 100) / DNA/RNA hybrid (> 1000) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L8 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS32A / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Ubiquitin-ribosomal protein eS31 fusion protein / KLLA0F25542p / KLLA0F18040p / Ribosomal protein L15 / Large ribosomal subunit protein uL3 / KLLA0F09812p / KLLA0F08261p / KLLA0F07843p / KLLA0F05247p / KLLA0F04675p / KLLA0F04499p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / KLLA0E23673p / KLLA0E23651p / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / KLLA0E12453p / KLLA0E12277p / 40S ribosomal protein S27 / KLLA0E06997p / KLLA0E06843p / KLLA0E05941p / Small ribosomal subunit protein uS14 / KLLA0E03455p / 60S ribosomal protein L29 / KLLA0D16027p / 60S ribosomal protein L36 / KLLA0D10659p / 40S ribosomal protein S3 / KLLA0D07405p / KLLA0D06941p / KLLA0D05643p / KLLA0D05181p / 40S ribosomal protein S26 / KLLA0D03410p / KLLA0C18216p / 40S ribosomal protein S7 / KLLA0C08371p / 40S ribosomal protein S24 / 40S ribosomal protein S30 / Ribosomal protein L37 / KLLA0B13409p / KLLA0B08173p / Small ribosomal subunit protein uS8 / KLLA0B07139p / 40S ribosomal protein S25 / 60S acidic ribosomal protein P0 / KLLA0B05742p / Small ribosomal subunit protein eS1 / KLLA0B04686p / 40S ribosomal protein S4 / KLLA0B02937p / Ribosomal protein / KLLA0B01562p / KLLA0B01474p / KLLA0A10483p / KLLA0A07227p / KLLA0A07194p / KLLA0A06336p / Small ribosomal subunit protein eS21 / 60S ribosomal protein L13 / RPS23 / Small ribosomal subunit protein uS9 / RPL28 / Ubiquitin fusion protein / :
Similarity search - Component
Biological speciesCricket paralysis virus
Saccharomyces cerevisiae P283 (yeast)
Kluyveromyces lactis (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMurray, J. / Savva, C.G. / Shin, B.S. / Dever, T.E. / Ramakrishnan, V. / Fernandez, I.S.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
National Institutes of HealthIntramural Research Program United States
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
DepositionMar 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Derived calculations
Category: em_image_scans / em_software ...em_image_scans / em_software / pdbx_struct_conn_angle / struct_conn
Item: _em_software.name / _em_software.version
Revision 1.2Mar 28, 2018Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _struct_conn_type.id

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Structure visualization

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Assembly

Deposited unit
5: 25S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
AA: KLLA0D16027p
BB: 60S ribosomal protein L3
CC: KLLA0B07139p
DD: KLLA0D06941p
EE: KLLA0B04686p
FF: KLLA0D03410p
GG: KLLA0E00573p
HH: KLLA0F04499p
II: KLLA0D05643p
JJ: KLLA0F08261p
LL: 60S ribosomal protein L13
MM: KLLA0B13409p
NN: Ribosomal protein L15
OO: KLLA0F04675p
PP: KLLA0A06336p
QQ: KLLA0A07227p
RR: KLLA0E12453p
SS: 60S ribosomal protein L20
TT: KLLA0E23651p
UU: KLLA0D05181p
VV: KLLA0E06997p
WW: 60S ribosomal protein L24
XX: 60S ribosomal protein L25
YY: KLLA0B05742p
ZZ: KLLA0E03455p
aa: RPL28
bb: KLLA0D16071p
cc: 60S ribosomal protein L30
dd: KLLA0B02937p
ee: KLLA0E06843p
ff: KLLA0D07405p
gg: KLLA0C08371p
hh: KLLA0F05247p
ii: 60S ribosomal protein L36
jj: Ribosomal protein L37
kk: KLLA0C18216p
ll: 60S ribosomal protein L39
mm: Ubiquitin fusion protein
nn: 60S ribosomal protein L41-A
oo: 60S ribosomal protein L44
pp: KLLA0E05941p
qq: Ribosomal protein
rr: 60S acidic ribosomal protein P0
KK: uL11
A: 40S ribosomal protein S0
B: 40S ribosomal protein S1
C: KLLA0F09812p
D: KLLA0D08305p
E: 40S ribosomal protein S4
F: KLLA0D10659p
G: 40S ribosomal protein S6
H: KLLA0C13519p
I: 40S ribosomal protein S8
J: KLLA0E23673p
K: KLLA0B08173p
L: KLLA0A10483p
M: 40S ribosomal protein S12
N: KLLA0F18040p
O: 40S ribosomal protein S14
P: KLLA0F07843p
Q: 40S ribosomal protein S16
R: KLLA0B01474p
S: KLLA0B01562p
T: KLLA0A07194p
U: KLLA0F25542p
V: 40S ribosomal protein S21
W: 40S ribosomal protein S22
X: RPS23
Y: 40S ribosomal protein S24
Z: KLLA0B06182p
a: KLLA0D05115p
b: 40S ribosomal protein S27
c: 40S ribosomal protein S28
d: 40S ribosomal protein S29
e: KLLA0C04809p
f: Ubiquitin-40S ribosomal protein S27a
g: KLLA0E12277p
2: 18S ribosomal RNA
4: cricket paralysis virus IRES
1: Eft2p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,190,108171
Polymers3,187,10583
Non-polymers3,00388
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA/RNA hybrid , 2 types, 2 molecules 54

#1: DNA/RNA hybrid 25S ribosomal RNA /


Mass: 1056706.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast)
#82: DNA/RNA hybrid cricket paralysis virus IRES


Mass: 60732.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricket paralysis virus / Production host: Escherichia coli (E. coli)

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RNA chain , 3 types, 3 molecules 782

#2: RNA chain 5S ribosomal RNA /


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: GenBank: 768843563
#3: RNA chain 5.8S ribosomal RNA /


Mass: 50293.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: GenBank: 820806853
#81: RNA chain 18S ribosomal RNA /


Mass: 579239.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: GenBank: 49642208

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Protein , 52 types, 52 molecules AACCDDEEFFGGHHIIJJMMOOPPQQRRTTUUVVYYZZaabbddeeffgghhkkmmppqq...

#4: Protein KLLA0D16027p


Mass: 26843.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CQM3
#6: Protein KLLA0B07139p


Mass: 38993.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW41
#7: Protein KLLA0D06941p


Mass: 33734.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRR9
#8: Protein KLLA0B04686p


Mass: 19492.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWE7
#9: Protein KLLA0D03410p


Mass: 25111.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS71
#10: Protein KLLA0E00573p


Mass: 25954.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: B4UN96
#11: Protein KLLA0F04499p


Mass: 21730.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CLA6
#12: Protein KLLA0D05643p


Mass: 24997.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRX7
#13: Protein KLLA0F08261p


Mass: 19203.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKT4
#15: Protein KLLA0B13409p


Mass: 14835.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVB1
#17: Protein KLLA0F04675p


Mass: 22254.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CL98
#18: Protein KLLA0A06336p


Mass: 20322.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXQ6
#19: Protein KLLA0A07227p


Mass: 20479.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXL8
#20: Protein KLLA0E12453p


Mass: 21688.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNH9
#22: Protein KLLA0E23651p


Mass: 17969.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM20
#23: Protein KLLA0D05181p


Mass: 11419.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRZ8
#24: Protein KLLA0E06997p


Mass: 13997.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CP75
#27: Protein KLLA0B05742p


Mass: 14127.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW97
#28: Protein KLLA0E03455p


Mass: 15398.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPN9
#29: Protein RPL28 / 60S ribosomal protein L28


Mass: 16382.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q8J287
#30: Protein KLLA0D16071p


Mass: 6500.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CQM1
#32: Protein KLLA0B02937p


Mass: 12360.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWM6
#33: Protein KLLA0E06843p


Mass: 13941.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CP82
#34: Protein KLLA0D07405p


Mass: 11863.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRP7
#35: Protein KLLA0C08371p


Mass: 13579.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU17
#36: Protein KLLA0F05247p


Mass: 13677.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CL71
#39: Protein KLLA0C18216p


Mass: 8794.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CSS8
#41: Protein Ubiquitin fusion protein


Mass: 5933.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q9Y854
#44: Protein KLLA0E05941p


Mass: 9497.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPC5
#45: Protein Ribosomal protein /


Mass: 24554.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWR9
#46: Protein 60S acidic ribosomal protein P0 /


Mass: 21411.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW89
#47: Protein uL11


Mass: 12528.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast)
#50: Protein KLLA0F09812p


Mass: 23162.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKL3
#51: Protein KLLA0D08305p


Mass: 24830.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRK7
#53: Protein KLLA0D10659p


Mass: 22912.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRA3
#55: Protein KLLA0C13519p


Mass: 21033.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CTD6
#57: Protein KLLA0E23673p


Mass: 20882.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM18
#58: Protein KLLA0B08173p


Mass: 11423.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVZ5
#59: Protein KLLA0A10483p


Mass: 17712.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CX80
#61: Protein KLLA0F18040p


Mass: 16858.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJK0
#63: Protein KLLA0F07843p


Mass: 13969.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKV4
#65: Protein KLLA0B01474p


Mass: 14728.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWU3
#66: Protein KLLA0B01562p


Mass: 16953.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWT9
#67: Protein KLLA0A07194p


Mass: 15747.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXM0
#68: Protein KLLA0F25542p


Mass: 12032.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CIM1
#71: Protein RPS23 / 40S ribosomal protein S23


Mass: 16047.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875M3
#73: Protein KLLA0B06182p


Mass: 7939.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW78
#74: Protein KLLA0D05115p


Mass: 11454.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS01
#78: Protein KLLA0C04809p


Mass: 6329.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUH5
#79: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 7958.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P69061
#80: Protein KLLA0E12277p


Mass: 35612.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNI7
#83: Protein Eft2p


Mass: 91592.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae P283 (yeast) / Gene: Eft2, P283_D20866 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: W7R097

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60S ribosomal protein ... , 10 types, 10 molecules BBLLSSWWXXcciillnnoo

#5: Protein 60S ribosomal protein L3 /


Mass: 43422.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJR7
#14: Protein 60S ribosomal protein L13 /


Mass: 22441.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875M0
#21: Protein 60S ribosomal protein L20 /


Mass: 20046.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast)
#25: Protein 60S ribosomal protein L24 / / Ribosomal protein L30


Mass: 7279.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P38665
#26: Protein 60S ribosomal protein L25 /


Mass: 13700.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P48045
#31: Protein 60S ribosomal protein L30 / / L32


Mass: 10511.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P38664
#37: Protein 60S ribosomal protein L36 /


Mass: 10925.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CR18
#40: Protein/peptide 60S ribosomal protein L39 / / L46 / YL40


Mass: 6114.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04650
#42: Protein/peptide 60S ribosomal protein L41-A / Ribosome / L47 / YL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P0CX86
#43: Protein 60S ribosomal protein L44 / / 60S ribosomal protein L41


Mass: 11676.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P31027

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Ribosomal protein ... , 2 types, 2 molecules NNjj

#16: Protein Ribosomal protein L15 /


Mass: 24193.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJL7
#38: Protein Ribosomal protein L37 /


Mass: 9679.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUW0

-
40S ribosomal protein ... , 14 types, 14 molecules ABEGIMOQVWYbcd

#48: Protein 40S ribosomal protein S0 /


Mass: 22882.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CN12
#49: Protein 40S ribosomal protein S1 /


Mass: 24488.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWD0
#52: Protein 40S ribosomal protein S4 /


Mass: 29486.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWJ2
#54: Protein 40S ribosomal protein S6 /


Mass: 25810.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM04
#56: Protein 40S ribosomal protein S8 /


Mass: 22511.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CMG3
#60: Protein 40S ribosomal protein S12 /


Mass: 13124.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CLU4
#62: Protein 40S ribosomal protein S14 / / RP59


Mass: 13458.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P27069
#64: Protein 40S ribosomal protein S16 /


Mass: 15656.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875N2
#69: Protein 40S ribosomal protein S21 /


Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXT6
#70: Protein 40S ribosomal protein S22 /


Mass: 14513.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW21
#72: Protein 40S ribosomal protein S24 /


Mass: 15063.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU44
#75: Protein 40S ribosomal protein S27 /


Mass: 8884.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNL2
#76: Protein 40S ribosomal protein S28 / / S33


Mass: 7073.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P33285
#77: Protein 40S ribosomal protein S29 /


Mass: 6322.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPG3

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Non-polymers , 4 types, 88 molecules

#84: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 80 / Source method: obtained synthetically / Formula: Mg
#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#86: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#87: Chemical ChemComp-6EM / (2S)-1-amino-N,N,N-trimethyl-1-oxobutan-2-aminium


Mass: 145.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17N2O

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2RIBOSOME#1-#830MULTIPLE SOURCES
2Kluyveromyces lactis 80S ribosomeRIBOSOME#1-#810NATURAL
3Cricket paralysis virus IRESCOMPLEX#820RECOMBINANT
4eEF2COMPLEX#830RECOMBINANT
Molecular weightValue: 4 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Kluyveromyces lactis (yeast)28985
23Cricket paralysis virus12136
34Saccharomyces cerevisiae P283 (yeast)1177187
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24Saccharomyces cerevisiae (brewer's yeast)4932
Buffer solutionpH: 6.5
Buffer componentConc.: 20 mM / Name: MES-KOH
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
13REFMAC5.8model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37844 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL

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