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- PDB-8g5z: mRNA decoding in human is kinetically and structurally distinct f... -

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Basic information

Entry
Database: PDB / ID: 8g5z
TitlemRNA decoding in human is kinetically and structurally distinct from bacteria (GA state)
Components
  • (40S ribosomal protein ...) x 19
  • (60S ribosomal protein ...) x 36
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • 60S acidic ribosomal protein P0
  • A-site tRNA Phe
  • Elongation factor 1-alpha 1
  • P-site tRNA fMet
  • Receptor of activated protein C kinase 1
  • Ribosomal protein L36a
  • eIF5A1
  • eL24
  • eL29
  • eL40
  • eL6
  • eS10
  • eS12
  • eS25
  • eS27
  • eS31
  • eS4
  • mRNA
  • uL1
  • uL2
  • uL23
  • uS10
  • uS11
  • uS12
  • uS13
  • uS17
  • uS19
  • uS9
KeywordsRIBOSOME / Human 80S / tRNA / mRNA eEF1A / eIF5A / tRNA selection
Function / homology
Function and homology information


guanyl nucleotide binding / embryonic brain development / translation at presynapse / eukaryotic 80S initiation complex / regulation of translation involved in cellular response to UV / negative regulation of protein neddylation / negative regulation of formation of translation preinitiation complex / axial mesoderm development / kinase activator activity / regulation of G1 to G0 transition ...guanyl nucleotide binding / embryonic brain development / translation at presynapse / eukaryotic 80S initiation complex / regulation of translation involved in cellular response to UV / negative regulation of protein neddylation / negative regulation of formation of translation preinitiation complex / axial mesoderm development / kinase activator activity / regulation of G1 to G0 transition / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / 90S preribosome assembly / nucleolus organization / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / alpha-beta T cell differentiation / GAIT complex / negative regulation of RNA splicing / negative regulation of DNA repair / positive regulation of DNA damage response, signal transduction by p53 class mediator / G1 to G0 transition / supercoiled DNA binding / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / neural crest cell differentiation / oxidized purine DNA binding / positive regulation of ubiquitin-protein transferase activity / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / homeostatic process / laminin receptor activity / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / macrophage chemotaxis / lung morphogenesis / cellular response to actinomycin D / fibroblast growth factor binding / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / monocyte chemotaxis / negative regulation of translational frameshifting / TOR signaling / BH3 domain binding / Protein hydroxylation / positive regulation of activated T cell proliferation / SARS-CoV-1 modulates host translation machinery / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / iron-sulfur cluster binding / mTORC1-mediated signalling / regulation of cell division / Peptide chain elongation / cellular response to ethanol / positive regulation of protein binding / positive regulation of GTPase activity / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Eukaryotic Translation Termination / blastocyst development / protein serine/threonine kinase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase inhibitor activity / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein binding / positive regulation of signal transduction by p53 class mediator / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / translation elongation factor activity / L13a-mediated translational silencing of Ceruloplasmin expression
Similarity search - Function
Translation elongation factor EF1A, eukaryotic/archaeal / : / GTP-eEF1A C-terminal domain-like / : / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain ...Translation elongation factor EF1A, eukaryotic/archaeal / : / GTP-eEF1A C-terminal domain-like / : / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Translation elongation factor EFTu-like, domain 2 / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein S2, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L44e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L10e / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Elongation factor Tu domain 2 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S30 / Ribosomal protein S30 / : / : / Ribosomal protein S7e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L35Ae signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S17e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S17e signature. / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L35 / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L7A/L8 / Ribosomal protein S3, eukaryotic/archaeal
Similarity search - Domain/homology
Chem-3H3 / ANISOMYCIN / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / : / METHIONINE / PHENYLALANINE / 1,4-DIAMINOBUTANE / SPERMIDINE / plitidepsin / : ...Chem-3H3 / ANISOMYCIN / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / : / METHIONINE / PHENYLALANINE / 1,4-DIAMINOBUTANE / SPERMIDINE / plitidepsin / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L36a / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Elongation factor 1-alpha 1 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsHolm, M. / Natchiar, K.S. / Rundlet, E.J. / Myasnikov, A.G. / Altman, R.B. / Blanchard, S.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2023
Title: mRNA decoding in human is kinetically and structurally distinct from bacteria.
Authors: Mikael Holm / S Kundhavai Natchiar / Emily J Rundlet / Alexander G Myasnikov / Zoe L Watson / Roger B Altman / Hao-Yuan Wang / Jack Taunton / Scott C Blanchard /
Abstract: In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives ...In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives principally from studies on bacterial systems. Although key features are conserved across evolution, eukaryotes achieve higher-fidelity mRNA decoding than bacteria. In human, changes in decoding fidelity are linked to ageing and disease and represent a potential point of therapeutic intervention in both viral and cancer treatment. Here we combine single-molecule imaging and cryogenic electron microscopy methods to examine the molecular basis of human ribosome fidelity to reveal that the decoding mechanism is both kinetically and structurally distinct from that of bacteria. Although decoding is globally analogous in both species, the reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower. These distinctions arise from eukaryote-specific structural elements in the human ribosome and in the elongation factor eukaryotic elongation factor 1A (eEF1A) that together coordinate faithful tRNA incorporation at each mRNA codon. The distinct nature and timing of conformational changes within the ribosome and eEF1A rationalize how increased decoding fidelity is achieved and potentially regulated in eukaryotic species.
History
DepositionFeb 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S2: 18S rRNA
L8: 5.8S rRNA
L5: 28S rRNA
L7: 5S rRNA
SB: 40S ribosomal protein S3a
SA: 40S ribosomal protein SA
SD: 40S ribosomal protein S3
SJ: 40S ribosomal protein S9
SE: eS4
SC: 40S ribosomal protein S2
SG: 40S ribosomal protein S6
SF: 40S ribosomal protein S5
SH: 40S ribosomal protein S7
SW: 40S ribosomal protein S15a
SI: 40S ribosomal protein S8
SQ: uS9
SU: uS10
SK: eS10
SO: uS11
SX: uS12
SM: eS12
SS: uS13
Sd: 40S ribosomal protein S29
SN: 40S ribosomal protein S13
SL: uS17
SR: 40S ribosomal protein S17
SP: uS19
ST: 40S ribosomal protein S19
SV: 40S ribosomal protein S21
SY: 40S ribosomal protein S24
SZ: eS25
Sa: 40S ribosomal protein S26
Sb: eS27
Sc: 40S ribosomal protein S28
Se: 40S ribosomal protein S30
Sf: eS31
Sg: Receptor of activated protein C kinase 1
Lz: uL1
LA: uL2
LB: 60S ribosomal protein L3
LC: 60S ribosomal protein L4
LJ: 60S ribosomal protein L11
LH: 60S ribosomal protein L9
LE: eL6
LG: 60S ribosomal protein L7a
Lq: 60S acidic ribosomal protein P0
LK: 60S ribosomal protein L12
LO: 60S ribosomal protein L13a
LL: 60S ribosomal protein L13
LV: 60S ribosomal protein L23
LM: 60S ribosomal protein L14
La: 60S ribosomal protein L27a
LN: 60S ribosomal protein L15
LI: 60S ribosomal protein L10
LD: 60S ribosomal protein L5
LQ: 60S ribosomal protein L18
LR: 60S ribosomal protein L19
LS: 60S ribosomal protein L18a
LT: 60S ribosomal protein L21
LP: 60S ribosomal protein L17
LU: 60S ribosomal protein L22
LX: uL23
LY: 60S ribosomal protein L26
LW: eL24
LZ: 60S ribosomal protein L27
Lr: 60S ribosomal protein L28
Lh: 60S ribosomal protein L35
Lb: eL29
LF: 60S ribosomal protein L7
Lc: 60S ribosomal protein L30
Ld: 60S ribosomal protein L31
Le: 60S ribosomal protein L32
Lf: 60S ribosomal protein L35a
Lg: 60S ribosomal protein L34
Li: 60S ribosomal protein L36
Lj: 60S ribosomal protein L37
Lk: 60S ribosomal protein L38
Ll: 60S ribosomal protein L39
Lm: eL40
Ln: 60S ribosomal protein L41
Lo: Ribosomal protein L36a
Lp: 60S ribosomal protein L37a
mR: mRNA
At: A-site tRNA Phe
Pt: P-site tRNA fMet
5A: eIF5A1
EF: Elongation factor 1-alpha 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,348,416597
Polymers3,330,76587
Non-polymers17,651510
Water6,575365
1


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

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Components

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RNA chain , 7 types, 7 molecules S2L8L5L7mRAtPt

#1: RNA chain 18S rRNA


Mass: 549676.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: RNA chain 5.8S rRNA


Mass: 50171.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 555853
#3: RNA chain 28S rRNA


Mass: 1195713.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: RNA chain 5S rRNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#83: RNA chain mRNA


Mass: 3468.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#84: RNA chain A-site tRNA Phe


Mass: 24634.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1850831943
#85: RNA chain P-site tRNA fMet


Mass: 24848.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1841332652

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40S ribosomal protein ... , 19 types, 19 molecules SBSASDSJSCSGSFSHSWSISdSNSRSTSVSYSaScSe

#5: Protein 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 25859.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#6: Protein 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 24903.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#7: Protein 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 25043.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#8: Protein 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 21649.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#10: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 24587.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#11: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#12: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 21327.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#13: Protein 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 21603.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#14: Protein 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#15: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 24003.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#23: Protein 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6559.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#24: Protein 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#26: Protein 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 15446.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#28: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 15822.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#29: Protein 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 9166.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#30: Protein 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15203.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#32: Protein 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 11341.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#34: Protein 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7263.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#35: Protein 40S ribosomal protein S30 / Small ribosomal subunit protein eS30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861

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Protein , 25 types, 25 molecules SESQSUSKSOSXSMSSSLSPSZSbSfSgLzLALELqLXLWLbLmLo5AEF

#9: Protein eS4


Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#16: Protein uS9


Mass: 15975.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#17: Protein uS10


Mass: 11508.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#18: Protein eS10


Mass: 11529.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#19: Protein uS11


Mass: 14457.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#20: Protein uS12


Mass: 15729.470 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#21: Protein eS12


Mass: 13652.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#22: Protein uS13


Mass: 17241.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#25: Protein uS17


Mass: 16699.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#27: Protein uS19


Mass: 15601.372 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#31: Protein eS25


Mass: 9601.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#33: Protein eS27


Mass: 9348.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#36: Protein eS31


Mass: 8845.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#37: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#38: Protein uL1


Mass: 24258.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#39: Protein uL2


Mass: 27343.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#44: Protein eL6


Mass: 25375.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#46: Protein 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E / Large ribosomal subunit protein uL10


Mass: 21507.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05388
#62: Protein uL23


Mass: 13727.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#64: Protein eL24


Mass: 13719.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#68: Protein eL29


Mass: 12643.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#79: Protein eL40


Mass: 6241.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#81: Protein Ribosomal protein L36a


Mass: 12358.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: J3KQN4
#86: Protein eIF5A1


Mass: 15716.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#87: Protein Elongation factor 1-alpha 1 / EF-1-alpha-1 / Elongation factor Tu / EF-Tu / Eukaryotic elongation factor 1 A-1 / eEF1A-1


Mass: 48519.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68105

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60S ribosomal protein ... , 36 types, 36 molecules LBLCLJLHLGLKLOLLLVLMLaLNLILDLQLRLSLTLPLULYLZLrLhLFLcLdLeLfLg...

#40: Protein 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3


Mass: 46092.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#41: Protein 60S ribosomal protein L4 / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 41747.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#42: Protein 60S ribosomal protein L11 / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5


Mass: 19342.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#43: Protein 60S ribosomal protein L9 / Large ribosomal subunit protein uL6


Mass: 21655.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#45: Protein 60S ribosomal protein L7a / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 27224.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#47: Protein 60S ribosomal protein L12 / Large ribosomal subunit protein uL11


Mass: 16003.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050
#48: Protein 60S ribosomal protein L13a / 23 kDa highly basic protein / Large ribosomal subunit protein uL13


Mass: 23431.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#49: Protein 60S ribosomal protein L13 / Breast basic conserved protein 1 / Large ribosomal subunit protein eL13


Mass: 23673.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#50: Protein 60S ribosomal protein L23 / 60S ribosomal protein L17 / Large ribosomal subunit protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#51: Protein 60S ribosomal protein L14 / CAG-ISL 7 / Large ribosomal subunit protein eL14


Mass: 15965.036 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#52: Protein 60S ribosomal protein L27a / Large ribosomal subunit protein uL15


Mass: 16488.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#53: Protein 60S ribosomal protein L15 / Large ribosomal subunit protein eL15


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#54: Protein 60S ribosomal protein L10 / Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein ...Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein L10 / Tumor suppressor QM


Mass: 23682.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27635
#55: Protein 60S ribosomal protein L5 / Large ribosomal subunit protein uL18


Mass: 34079.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#56: Protein 60S ribosomal protein L18 / Large ribosomal subunit protein eL18


Mass: 21556.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#57: Protein 60S ribosomal protein L19 / Large ribosomal subunit protein eL19


Mass: 22441.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#58: Protein 60S ribosomal protein L18a / Large ribosomal subunit protein eL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#59: Protein 60S ribosomal protein L21 / Large ribosomal subunit protein eL21


Mass: 18478.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#60: Protein 60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#61: Protein 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 / Large ribosomal subunit protein eL22


Mass: 11481.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#63: Protein 60S ribosomal protein L26 / Large ribosomal subunit protein uL24


Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#65: Protein 60S ribosomal protein L27 / Large ribosomal subunit protein eL27


Mass: 15704.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#66: Protein 60S ribosomal protein L28 / Large ribosomal subunit protein eL28


Mass: 14362.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#67: Protein 60S ribosomal protein L35 / Large ribosomal subunit protein uL29


Mass: 14462.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#69: Protein 60S ribosomal protein L7 / Large ribosomal subunit protein uL30


Mass: 26590.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#70: Protein 60S ribosomal protein L30 / Large ribosomal subunit protein eL30


Mass: 10954.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#71: Protein 60S ribosomal protein L31 / Large ribosomal subunit protein eL31


Mass: 12635.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#72: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 15022.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#73: Protein 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33


Mass: 12433.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#74: Protein 60S ribosomal protein L34 / Large ribosomal subunit protein eL34


Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#75: Protein 60S ribosomal protein L36 / Large ribosomal subunit protein eL36


Mass: 11915.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#76: Protein 60S ribosomal protein L37 / G1.16 / Large ribosomal subunit protein eL37


Mass: 10090.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#77: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#78: Protein/peptide 60S ribosomal protein L39 / Large ribosomal subunit protein eL39


Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#80: Protein/peptide 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#82: Protein 60S ribosomal protein L37a / Large ribosomal subunit protein eL43


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513

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Non-polymers , 12 types, 875 molecules

#88: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C7H19N3
#89: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: K
#90: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 433 / Source method: obtained synthetically / Formula: Mg
#91: Chemical ChemComp-ANM / ANISOMYCIN


Mass: 265.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#92: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H12N2
#93: Chemical ChemComp-3H3 / 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione


Mass: 457.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H35NO6 / Feature type: SUBJECT OF INVESTIGATION
#94: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#95: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#96: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#97: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#98: Chemical ChemComp-ZIY / plitidepsin


Mass: 1110.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C57H87N7O15 / Feature type: SUBJECT OF INVESTIGATION
#99: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Human ribosome 80S with P-site tRNA, A-site tRNA eEF1A and eIF5A1
Type: RIBOSOME / Entity ID: #1-#48, #50-#83, #86-#87 / Source: MULTIPLE SOURCES
Molecular weightValue: 5.5 MDa / Experimental value: YES
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 79 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19_4092: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20290 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004243179
ELECTRON MICROSCOPYf_angle_d0.594356403
ELECTRON MICROSCOPYf_dihedral_angle_d14.32184448
ELECTRON MICROSCOPYf_chiral_restr0.03744025
ELECTRON MICROSCOPYf_plane_restr0.00423411

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