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- PDB-6uz7: K.lactis 80S ribosome with p/PE tRNA and eIF5B -

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Basic information

Entry
Database: PDB / ID: 6uz7
TitleK.lactis 80S ribosome with p/PE tRNA and eIF5B
Components
  • (40S ribosomal protein ...) x 18
  • (60S ribosomal protein ...) x 11
  • (Ribosomal protein ...) x 2
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • GDPCP
  • KLLA0A06336p
  • KLLA0A07194p
  • KLLA0A07227p
  • KLLA0A10483p
  • KLLA0B01474p
  • KLLA0B01562p
  • KLLA0B02937p
  • KLLA0B04686p
  • KLLA0B05742p
  • KLLA0B07139p
  • KLLA0B08173p
  • KLLA0B13409p
  • KLLA0C08371p
  • KLLA0C18216p
  • KLLA0D03410p
  • KLLA0D05181p
  • KLLA0D05643p
  • KLLA0D06941p
  • KLLA0D07405p
  • KLLA0D08305p
  • KLLA0D10659p
  • KLLA0D16027p
  • KLLA0E00573p
  • KLLA0E03455p
  • KLLA0E05941p
  • KLLA0E06843p
  • KLLA0E06997p
  • KLLA0E12277p
  • KLLA0E12453p
  • KLLA0E23651p
  • KLLA0E23673p
  • KLLA0F04499p
  • KLLA0F04675p
  • KLLA0F05247p
  • KLLA0F07843p
  • KLLA0F08261p
  • KLLA0F09812p
  • KLLA0F18040p
  • KLLA0F23265p
  • KLLA0F25542p
  • RNA (121-MER)
  • RNA (76-MER)
  • RPL28
  • RPS23
  • Ribosomal protein
  • Ubiquitin fusion protein
  • Ubiquitin-40S ribosomal protein S27a
KeywordsRIBOSOME / translation / initiation / eIF5B
Function / homology
Function and homology information


response to cycloheximide / 90S preribosome / protein-RNA complex assembly / translation regulator activity / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome ...response to cycloheximide / 90S preribosome / protein-RNA complex assembly / translation regulator activity / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosome biogenesis / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P ...Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / : / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Elongation factor Tu domain 2 / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature.
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L8 / Small ribosomal subunit protein uS11 ...PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L8 / 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 / KLLA0F23265p / KLLA0F18040p / Ribosomal protein L15 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS5 / 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 speciesKluyveromyces lactis (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFernandez, I.S. / Huang, B.Y.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Long-range interdomain communications in eIF5B regulate GTP hydrolysis and translation initiation.
Authors: Bridget Y Huang / Israel S Fernández /
Abstract: Translation initiation controls protein synthesis by regulating the delivery of the first aminoacyl-tRNA to messenger RNAs (mRNAs). In eukaryotes, initiation is sophisticated, requiring dozens of ...Translation initiation controls protein synthesis by regulating the delivery of the first aminoacyl-tRNA to messenger RNAs (mRNAs). In eukaryotes, initiation is sophisticated, requiring dozens of protein factors and 2 GTP-regulated steps. The GTPase eIF5B gates progression to elongation during the second GTP-regulated step. Using electron cryomicroscopy (cryo-EM), we imaged an in vitro initiation reaction which is set up with purified yeast components and designed to stall with eIF5B and a nonhydrolyzable GTP analog. A high-resolution reconstruction of a "dead-end" intermediate at 3.6 Å allowed us to visualize eIF5B in its ribosome-bound conformation. We identified a stretch of residues in eIF5B, located close to the γ-phosphate of GTP and centered around the universally conserved tyrosine 837 ( numbering), that contacts the catalytic histidine of eIF5B (H480). Site-directed mutagenesis confirmed the essential role that these residues play in regulating ribosome binding, GTP hydrolysis, and translation initiation both in vitro and in vivo. Our results illustrate how eIF5B transmits the presence of a properly delivered initiator aminoacyl-tRNA at the P site to the distant GTPase center through interdomain communications and underscore the importance of the multidomain architecture in translation factors to sense and communicate ribosomal states.
History
DepositionNov 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_ref.db_name / _struct_ref_seq_dif.pdbx_seq_db_name

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Structure visualization

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  • EMDB-20952
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Assembly

Deposited unit
5: 25S ribosomal RNA
7: RNA (121-MER)
8: 5.8S ribosomal RNA
AA: KLLA0D16027p
AB: 60S ribosomal protein L3
AC: KLLA0B07139p
AD: KLLA0D06941p
AE: KLLA0B04686p
AF: KLLA0D03410p
AG: KLLA0E00573p
AH: KLLA0F04499p
AI: KLLA0D05643p
AJ: KLLA0F08261p
AL: 60S ribosomal protein L13
AM: KLLA0B13409p
AN: Ribosomal protein L15
AO: KLLA0F04675p
AP: KLLA0A06336p
AQ: KLLA0A07227p
AR: KLLA0E12453p
AS: 60S ribosomal protein L20
AT: KLLA0E23651p
AU: KLLA0D05181p
AV: KLLA0E06997p
AW: 60S ribosomal protein L24
AX: 60S ribosomal protein L25
AY: KLLA0B05742p
AZ: KLLA0E03455p
Ba: RPL28
Bb: 60S ribosomal protein L29
Bc: 60S ribosomal protein L30
Bd: KLLA0B02937p
Be: KLLA0E06843p
Bf: KLLA0D07405p
Bg: KLLA0C08371p
Bh: KLLA0F05247p
Bi: 60S ribosomal protein L36
Bj: Ribosomal protein L37
Bk: KLLA0C18216p
Bl: 60S ribosomal protein L39
Bm: Ubiquitin fusion protein
Bn: 60S ribosomal protein L41
Bo: 60S ribosomal protein L44
Bp: KLLA0E05941p
Bq: Ribosomal protein
Br: 60S acidic ribosomal protein P0
AK: GDPCP
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: 40S ribosomal protein S7
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: 40S ribosomal protein S25
a: 40S ribosomal protein S26
b: 40S ribosomal protein S27
c: 40S ribosomal protein S28
d: 40S ribosomal protein S29
e: 40S ribosomal protein S30
f: Ubiquitin-40S ribosomal protein S27a
g: KLLA0E12277p
2: 18S ribosomal RNA
1: KLLA0F23265p
3: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,159,14990
Polymers4,158,23583
Non-polymers9147
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules 57823

#1: RNA chain 25S ribosomal RNA


Mass: 1086985.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: GenBank: 1241923359
#2: RNA chain RNA (121-MER)


Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: GenBank: 1195002887
#3: RNA chain 5.8S ribosomal RNA


Mass: 910658.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: GenBank: 1195002887
#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
#83: RNA chain RNA (76-MER)


Mass: 24532.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Protein , 47 types, 47 molecules AAACADAEAFAGAHAIAJAMAOAPAQARATAUAVAYAZBaBdBeBfBgBhBkBmBpBqBr...

#4: Protein KLLA0D16027p


Mass: 27448.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CQM3
#6: Protein KLLA0B07139p


Mass: 39283.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW41
#7: Protein KLLA0D06941p


Mass: 33937.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRR9
#8: Protein KLLA0B04686p


Mass: 20022.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWE7
#9: Protein KLLA0D03410p


Mass: 27127.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS71
#10: Protein KLLA0E00573p


Mass: 28080.920 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: 25400.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRX7
#13: Protein KLLA0F08261p


Mass: 19821.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKT4
#15: Protein KLLA0B13409p


Mass: 15037.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVB1
#17: Protein KLLA0F04675p


Mass: 22385.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CL98
#18: Protein KLLA0A06336p


Mass: 20696.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXQ6
#19: Protein KLLA0A07227p


Mass: 20668.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXL8
#20: Protein KLLA0E12453p


Mass: 21819.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNH9
#22: Protein KLLA0E23651p


Mass: 18214.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM20
#23: Protein KLLA0D05181p


Mass: 13993.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRZ8
#24: Protein KLLA0E06997p


Mass: 14485.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CP75
#27: Protein KLLA0B05742p


Mass: 14329.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW97
#28: Protein KLLA0E03455p


Mass: 15600.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPN9
#29: Protein RPL28


Mass: 16584.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q8J287
#32: Protein KLLA0B02937p


Mass: 13177.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWM6
#33: Protein KLLA0E06843p


Mass: 14686.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CP82
#34: Protein KLLA0D07405p


Mass: 12108.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRP7
#35: Protein KLLA0C08371p


Mass: 14056.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU17
#36: Protein KLLA0F05247p


Mass: 14079.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CL71
#39: Protein KLLA0C18216p


Mass: 8996.661 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: 14597.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q9Y854
#44: Protein KLLA0E05941p


Mass: 9970.605 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: 24488.783 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: 33606.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW89
#47: Protein GDPCP


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


Mass: 27649.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKL3
#51: Protein KLLA0D08305p


Mass: 26300.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRK7
#53: Protein KLLA0D10659p


Mass: 25385.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CRA3
#57: Protein KLLA0E23673p


Mass: 21587.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM18
#58: Protein KLLA0B08173p


Mass: 12584.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CVZ5
#59: Protein KLLA0A10483p


Mass: 17843.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CX80
#61: Protein KLLA0F18040p


Mass: 16989.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CJK0
#63: Protein KLLA0F07843p


Mass: 15986.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CKV4
#65: Protein KLLA0B01474p


Mass: 15722.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWU3
#66: Protein KLLA0B01562p


Mass: 17084.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CWT9
#67: Protein KLLA0A07194p


Mass: 15879.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CXM0
#68: Protein KLLA0F25542p


Mass: 13337.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CIM1
#71: Protein RPS23


Mass: 16047.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q875M3
#79: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 17110.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P69061
#80: Protein KLLA0E12277p


Mass: 35830.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CNI7
#82: Protein KLLA0F23265p


Mass: 108918.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CIX3

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60S ribosomal protein ... , 11 types, 11 molecules ABALASAWAXBbBcBiBlBnBo

#5: Protein 60S ribosomal protein L3


Mass: 43781.500 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: 22702.346 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: 20494.939 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: 17638.668 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: 15746.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: P48045
#30: Protein 60S ribosomal protein L29


Mass: 7090.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CQM1
#31: Protein 60S ribosomal protein L30 / L32


Mass: 11382.281 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: 11128.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CR18
#40: Protein 60S ribosomal protein L39


Mass: 6358.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast)
#42: Protein/peptide 60S ribosomal protein L41


Mass: 3137.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast)
#43: Protein 60S ribosomal protein L44 / 60S ribosomal protein L41


Mass: 12267.632 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 ANBj

#16: Protein Ribosomal protein L15


Mass: 24454.307 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: 9968.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUW0

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40S ribosomal protein ... , 18 types, 18 molecules ABEGHIMOQVWYZabcde

#48: Protein 40S ribosomal protein S0


Mass: 28264.525 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: 28971.643 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: 29617.514 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: 26970.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CM04
#55: Protein 40S ribosomal protein S7


Mass: 21735.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CTD6
#56: Protein 40S ribosomal protein S8


Mass: 22642.727 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: 14466.398 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: 14530.655 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: 15874.531 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: 14645.041 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: 15194.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CU44
#73: Protein 40S ribosomal protein S25


Mass: 12002.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CW78
#74: Protein 40S ribosomal protein S26


Mass: 13539.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CS01
#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: 7549.824 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: 6662.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CPG3
#78: Protein 40S ribosomal protein S30


Mass: 7141.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kluyveromyces lactis (yeast) / References: UniProt: Q6CUH5

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Non-polymers , 2 types, 7 molecules

#84: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#85: 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

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Kluyveromyces lactis 80S ribosome in complex with eIF5B
Type: RIBOSOME / Entity ID: #1-#83 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Kluyveromyces lactis (yeast)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 16

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Processing

EM softwareName: RELION / Category: classification
CTF correctionType: NONE
Particle selectionNum. of particles selected: 64815
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29712 / Symmetry type: POINT
Atomic model buildingB value: 110.6
Atomic model buildingPDB-ID: 3U5B

3u5b
PDB Unreleased entry


Accession code: 3U5B / Source name: PDB / Type: experimental model

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