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- PDB-8bsj: Giardia Ribosome in PRE-T Classical State (C) -

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Basic information

Entry
Database: PDB / ID: 8bsj
TitleGiardia Ribosome in PRE-T Classical State (C)
Components
  • (40S ribosomal protein ...) x 10
  • (60S ribosomal protein ...) x 6
  • (Ribosomal protein ...) x 51
  • (tRNA) x 2
  • 5.8S rRNA
  • 5S rRNA
  • Large Subunit rRNA
  • Ribosomal L22e
  • Ribosomal L38e
  • SSU ribosomal protein S12P
  • Small Subunit rRNA
  • Ubiquitin/Ribosomal protein L40e
  • mRNA
KeywordsRIBOSOME / Translation / Giardia / Eukaryote / Eukaryotic / Macromolecule / tRNA
Function / homology
Function and homology information


endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / modification-dependent protein catabolic process ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L40e, archaeal / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e ...Ribosomal protein L40e, archaeal / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e / Plectin/S10, N-terminal / Ribosomal protein L24e, conserved site / Plectin/S10 domain / Ribosomal protein L24e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S25 / S25 ribosomal protein / : / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L35Ae, conserved site / : / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / 60S ribosomal protein L35 / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / : / 60S ribosomal protein L19 / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L7A/L8 / Ribosomal protein S6, eukaryotic / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L30/YlxQ / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / 60S ribosomal protein L4, C-terminal domain / 40S ribosomal protein S11, N-terminal / 60S ribosomal protein L4 C-terminal domain / Ribosomal_S17 N-terminal / Ribosomal protein L31e, conserved site
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L39 / Ribosomal protein S27 / 40S ribosomal protein S30 / Ribosomal protein S19e / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS2 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L39 / Ribosomal protein S27 / 40S ribosomal protein S30 / Ribosomal protein S19e / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS2 / Ribosomal protein L10a / Ribosomal protein L29 / Large ribosomal subunit protein eL22 / Ribosomal protein L27 / 40S ribosomal protein S8 / Ribosomal protein L21 / Ribosomal L38e / 40S ribosomal protein S21 / Ribosomal protein S28 / Ribosomal protein L14 / Ribosomal protein S20 / Ribosomal protein L18 / Ribosomal protein S24 / Ribosomal protein L30 / 40S ribosomal protein S6 / 60S ribosomal protein L13 / Ribosomal protein S29A / Large ribosomal subunit protein uL4 / Ribosomal protein L24e / 40S ribosomal protein S25 / 40S ribosomal protein S3 / Ribosomal protein L15 / Ribosomal protein S15 / Ribosomal protein S13 / Ribosomal protein L17 / 40S ribosomal protein S4 / Ribosomal protein L26 / Ribosomal protein L19 / Ribosomal protein L11 / Ribosomal protein S16 / Ribosomal protein L35a / Ribosomal protein S9 / 60S ribosomal protein L7a / Ribosomal protein L37 / Ribosomal protein L10 / Ribosomal protein L32 / Ribosomal protein L34 / Ribosomal protein L31e / Ribosomal protein L23A / Small ribosomal subunit protein uS5 / Ribosomal protein L37a / Ribosomal protein L6 / Ribosomal protein L44 / 40S ribosomal protein S26 / Ribosomal protein S17 / Ribosomal protein S10B / Ribosomal protein L7 / Ribosomal protein L3 / Ribosomal protein L23 / 60S ribosomal protein L18a / 40S ribosomal protein S7 / Ribosomal protein L13a / Ribosomal protein S11 / 50S ribosomal protein L40e / Ribosomal protein L36e / 60S ribosomal protein L29 / Ribosomal protein S18 / Ribosomal protein L27a / Ribosomal protein S5 / Ribosomal protein L8 / Ribosomal protein L5 / Ribosomal protein S15A / Ribosomal protein S14 / SSU ribosomal protein S12P / 60S ribosomal protein L41
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.49 Å
AuthorsMajumdar, S. / Emmerich, A.G. / Sanyal, S.
Funding support Sweden, United States, 7items
OrganizationGrant numberCountry
Swedish Research Council2016-06264 Sweden
Swedish Research Council2018-05946 Sweden
Swedish Research Council2018-05498 Sweden
Knut and Alice Wallenberg FoundationKAW 2017.0055 Sweden
Carl Trygger FoundationCTS 18:338 Sweden
Carl Trygger FoundationCTS 19:806 Sweden
Wenner-Gren FoundationUPD2017:0238 United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis.
Authors: Soneya Majumdar / Andrew Emmerich / Sascha Krakovka / Chandra Sekhar Mandava / Staffan G Svärd / Suparna Sanyal /
Abstract: Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated ...Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly from actively growing Giardia cells. The highly compact and uniquely GC-rich Giardia ribosomes possess eukaryotic rRNAs and ribosomal proteins, but retain some bacterial features. The translocation intermediates, with naturally bound tRNAs and eukaryotic elongation factor 2 (eEF2), display characteristic ribosomal intersubunit rotation and small subunit's head swiveling-universal for translocation. In addition, we observe the eukaryote-specific 'subunit rolling' dynamics, albeit with limited features. Finally, the eEF2·GDP state features a uniquely positioned 'leaving phosphate (Pi)' that proposes hitherto unknown molecular events of Pi and eEF2 release from the ribosome at the final stage of translocation. In summary, our study elucidates the mechanism of translocation in the protists and illustrates evolution of the translation machinery from bacteria to eukaryotes from both the structural and mechanistic perspectives.
History
DepositionNov 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 3, 2023Group: 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 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
LA: Ribosomal protein L2
LB: Ribosomal protein L3
LC: Ribosomal protein L4
LD: 5.8S rRNA
LE: 5S rRNA
LF: Ribosomal protein L5
LG: Ribosomal protein L39
LH: Ribosomal protein L7
LI: 60S ribosomal protein L7a
LJ: Ribosomal protein L6
LK: Ribosomal protein L10
LL: Ribosomal protein L11
LM: 60S ribosomal protein L13
LN: Ribosomal protein L14
LO: Ribosomal protein L15
LP: Ribosomal protein L13a
LQ: Ribosomal protein L17
LR: Ribosomal protein L18
LS: Ribosomal protein L19
LT: 60S ribosomal protein L18a
LU: Ribosomal protein L21
LV: Ribosomal L22e
LW: Ribosomal protein L23
LX: Ribosomal protein L24
LY: Ribosomal protein L23A
LZ: Ribosomal protein L26
La: 60S ribosomal protein L27
Lb: Ribosomal protein L27a
Lc: 60S ribosomal protein L29
Ld: Ribosomal protein L30
Le: Ribosomal protein L31B
Lf: Ribosomal protein L32
Lg: Ribosomal protein L35a
Lh: Ribosomal protein L34
Li: Ribosomal protein L29
Lj: Ribosomal protein L36-1
Lk: Ribosomal protein L37
Ll: Ribosomal L38e
Ln: Ribosomal protein L10a
Lo: 60S ribosomal protein L41
Lp: Ribosomal protein L44
Lq: Ribosomal protein L37a
Ls: Ubiquitin/Ribosomal protein L40e
Lt: Large Subunit rRNA
SA: 40S ribosomal protein SA
SB: Ribosomal protein S2
SC: Ribosomal protein S3
SD: 40S ribosomal protein S3a
SE: 40S ribosomal protein S4
SF: Ribosomal protein S5
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SJ: Ribosomal protein S15A
SK: Ribosomal protein S9
SL: Ribosomal protein S10B
SM: Ribosomal protein S11
SO: SSU ribosomal protein S12P
SP: Ribosomal protein S13
SQ: Ribosomal protein S14
SR: Ribosomal protein S15
ST: Ribosomal protein S16
SU: Ribosomal protein S17
SV: Ribosomal protein S18
SW: Ribosomal protein S19e
SX: Ribosomal protein S20
SY: 40S ribosomal protein S21
Sb: Ribosomal protein S24
Sc: 40S ribosomal protein S25
Sd: 40S ribosomal protein S26
Se: Ribosomal protein S27
Sg: Ribosomal protein S28
Sh: Ribosomal protein S29A
Sj: 40S ribosomal protein S30
St: Small Subunit rRNA
u: tRNA
v: tRNA
x: tRNA
y: mRNA


Theoretical massNumber of molelcules
Total (without water)2,782,93879
Polymers2,782,93879
Non-polymers00
Water00
1


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

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Components

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Ribosomal protein ... , 51 types, 51 molecules LALBLCLFLGLHLJLKLLLNLOLPLQLRLSLULWLXLYLZLbLdLeLfLgLhLiLjLkLn...

#1: Protein Ribosomal protein L2


Mass: 27090.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: E2RTN4
#2: Protein Ribosomal protein L3


Mass: 42715.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BRZ3
#3: Protein Ribosomal protein L4


Mass: 35048.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B7H8
#6: Protein Ribosomal protein L5


Mass: 33961.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: E2RU47
#7: Protein Ribosomal protein L39


Mass: 6353.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644EZB9
#8: Protein Ribosomal protein L7


Mass: 27103.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BRY6
#10: Protein Ribosomal protein L6


Mass: 20889.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BNT5
#11: Protein Ribosomal protein L10


Mass: 24283.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BM86
#12: Protein Ribosomal protein L11


Mass: 19767.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BI95
#14: Protein Ribosomal protein L14


Mass: 14785.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B4F8
#15: Protein Ribosomal protein L15


Mass: 24353.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B8Z6
#16: Protein Ribosomal protein L13a


Mass: 22921.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BU75
#17: Protein Ribosomal protein L17


Mass: 18722.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BE76
#18: Protein Ribosomal protein L18


Mass: 20207.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B4T7
#19: Protein Ribosomal protein L19


Mass: 23199.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BH61
#21: Protein Ribosomal protein L21


Mass: 18296.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B2Q4
#23: Protein Ribosomal protein L23


Mass: 15450.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BS37
#24: Protein Ribosomal protein L24


Mass: 22751.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B7P2
#25: Protein Ribosomal protein L23A


Mass: 16053.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMP6
#26: Protein Ribosomal protein L26


Mass: 15621.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BFT3
#28: Protein Ribosomal protein L27a


Mass: 17166.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BZ78
#30: Protein Ribosomal protein L30


Mass: 11698.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B5N7
#31: Protein Ribosomal protein L31B


Mass: 12184.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMP3
#32: Protein Ribosomal protein L32


Mass: 15985.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMD9
#33: Protein Ribosomal protein L35a


Mass: 13913.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BKK5
#34: Protein Ribosomal protein L34


Mass: 13528.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMF7
#35: Protein Ribosomal protein L29


Mass: 14292.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644FBK5
#36: Protein Ribosomal protein L36-1


Mass: 10586.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BYA6
#37: Protein Ribosomal protein L37


Mass: 10329.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BLV7
#39: Protein Ribosomal protein L10a


Mass: 24630.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644FB74
#41: Protein Ribosomal protein L44


Mass: 12311.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BQU8
#42: Protein Ribosomal protein L37a


Mass: 10508.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BN26
#46: Protein Ribosomal protein S2


Mass: 26765.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BMZ1
#47: Protein Ribosomal protein S3


Mass: 24779.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B8Z2
#50: Protein Ribosomal protein S5


Mass: 21058.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BZD3
#54: Protein Ribosomal protein S15A


Mass: 14770.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: E2RU77
#55: Protein Ribosomal protein S9


Mass: 21699.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BKS8
#56: Protein Ribosomal protein S10B


Mass: 15406.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BRX3
#57: Protein Ribosomal protein S11


Mass: 18104.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BVU0
#59: Protein Ribosomal protein S13


Mass: 17627.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BE02
#60: Protein Ribosomal protein S14


Mass: 15755.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: Q76KS3
#61: Protein Ribosomal protein S15


Mass: 16728.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BBP3
#62: Protein Ribosomal protein S16


Mass: 17634.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BKC6
#63: Protein Ribosomal protein S17


Mass: 15757.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BRG5
#64: Protein Ribosomal protein S18


Mass: 17510.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BZ58
#65: Protein Ribosomal protein S19e


Mass: 15463.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644F964
#66: Protein Ribosomal protein S20


Mass: 14073.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B4G0
#68: Protein Ribosomal protein S24


Mass: 14872.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B593
#71: Protein Ribosomal protein S27


Mass: 9144.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644F5K9
#72: Protein Ribosomal protein S28


Mass: 7358.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B4F3
#73: Protein Ribosomal protein S29A


Mass: 6142.263 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B7H6

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RNA chain , 7 types, 8 molecules LDLELtStuvxy

#4: RNA chain 5.8S rRNA


Mass: 45891.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)
#5: RNA chain 5S rRNA


Mass: 38993.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)
#44: RNA chain Large Subunit rRNA


Mass: 874762.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)
#75: RNA chain Small Subunit rRNA


Mass: 471227.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)
#76: RNA chain tRNA


Mass: 24231.510 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)
#77: RNA chain tRNA


Mass: 23850.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)
#78: RNA chain mRNA


Mass: 3562.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote)

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60S ribosomal protein ... , 6 types, 6 molecules LILMLTLaLcLo

#9: Protein 60S ribosomal protein L7a


Mass: 25427.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BLL7
#13: Protein 60S ribosomal protein L13


Mass: 26640.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B6M8
#20: Protein 60S ribosomal protein L18a


Mass: 20624.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BT04
#27: Protein 60S ribosomal protein L27


Mass: 15374.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B1T3
#29: Protein 60S ribosomal protein L29


Mass: 7363.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BYY2
#40: Protein/peptide 60S ribosomal protein L41


Mass: 3283.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: V6TX21

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Protein , 4 types, 4 molecules LVLlLsSO

#22: Protein Ribosomal L22e


Mass: 14427.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644FC41
#38: Protein Ribosomal L38e


Mass: 8605.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B481
#43: Protein Ubiquitin/Ribosomal protein L40e


Mass: 14343.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BXE1
#58: Protein SSU ribosomal protein S12P


Mass: 15897.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: V6T9I6

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40S ribosomal protein ... , 10 types, 10 molecules SASDSESGSHSISYScSdSj

#45: Protein 40S ribosomal protein SA


Mass: 28101.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644FB17
#48: Protein 40S ribosomal protein S3a


Mass: 28413.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644F9A2
#49: Protein 40S ribosomal protein S4


Mass: 30464.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BFE3
#51: Protein 40S ribosomal protein S6


Mass: 28084.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B6L8
#52: Protein 40S ribosomal protein S7


Mass: 21786.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BT38
#53: Protein 40S ribosomal protein S8


Mass: 19451.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B252
#67: Protein 40S ribosomal protein S21


Mass: 9686.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B484
#69: Protein 40S ribosomal protein S25


Mass: 10121.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8B8H7
#70: Protein 40S ribosomal protein S26


Mass: 12791.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A8BQZ7
#74: Protein 40S ribosomal protein S30


Mass: 7932.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia intestinalis (eukaryote) / References: UniProt: A0A644F843

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Details

Has protein modificationY

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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: Giardia Ribosome in PRE-T Classical State (C) / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Giardia lamblia ATCC 50803 (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: OTHER / Nominal defocus max: 1900 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 383193
3D reconstructionResolution: 6.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4000 / Symmetry type: POINT

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