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- PDB-7zjx: Rabbit 80S ribosome programmed with SECIS and SBP2 -

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Basic information

Entry
Database: PDB / ID: 7zjx
TitleRabbit 80S ribosome programmed with SECIS and SBP2
Components
  • (40S ribosomal protein ...) x 29
  • (60S ribosomal Protein ...) x 34
  • (Ribosomal protein ...) x 7
  • 18S rRNA18S ribosomal RNA
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • CrPV IRESCripavirus internal ribosome entry site
  • GPX4 SECIS element
  • Guanine nucleotide-binding protein subunit beta-2-like 1
  • Ribosomal protein
  • Ribosomal_L18_c domain-containing protein
  • Ribosomal_L23eN domain-containing protein
  • S10_plectin domain-containing protein
  • Selenocysteine insertion sequence-binding protein 2
  • Ubiquitin carboxyl extension protein 80
KeywordsRIBOSOME / Selenocysteine / recoding / 80S
Function / homology
Function and homology information


forebrain neuron development / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / selenocysteine incorporation / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / selenocysteine insertion sequence binding / L13a-mediated translational silencing of Ceruloplasmin expression ...forebrain neuron development / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / selenocysteine incorporation / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / selenocysteine insertion sequence binding / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / striatum development / ribosomal subunit / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / TOR signaling / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / organelle membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / gastrulation / rough endoplasmic reticulum / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribonucleoprotein complex binding / Nuclear events stimulated by ALK signaling in cancer / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / DNA-(apurinic or apyrimidinic site) lyase / small-subunit processome / cytosolic ribosome / mRNA 3'-UTR binding / ribosomal small subunit biogenesis / cytoplasmic ribonucleoprotein granule / rRNA processing / Regulation of expression of SLITs and ROBOs / cytosolic small ribosomal subunit / ribosome binding / large ribosomal subunit / glucose homeostasis / regulation of translation / heparin binding / cell body / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / SARS-CoV-2 modulates host translation machinery / postsynaptic density / rRNA binding / ribosome / structural constituent of ribosome / cadherin binding / ribonucleoprotein complex / translation / positive regulation of apoptotic process / focal adhesion / intracellular membrane-bounded organelle / dendrite / synapse / positive regulation of cell population proliferation / nucleolus / protein kinase binding / endoplasmic reticulum / mitochondrion / DNA binding / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Selenocysteine insertion sequence-binding protein 2 / Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily ...Selenocysteine insertion sequence-binding protein 2 / Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L27e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S27a / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S4, C-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L38e protein family / Ribosomal L22e protein family / 40S Ribosomal protein S10 / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Plectin/S10, N-terminal / Ribosomal protein L44 / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal L27e protein family / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / RS4NT (NUC023) domain / Ribosomal protein L1 signature. / Ribosomal protein L37ae / Ribosomal protein S27 / Ribosomal protein L19, eukaryotic / Ribosomal protein S17e signature. / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal L40e family / Ribosomal protein L36e / Ribosomal protein S28e / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal family S4e / Ribosomal protein L7A/L8 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein S7e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein S6e / Ribosomal L37ae protein family / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL13 ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL38 / 60S ribosomal protein L36 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL20 / Ribosomal protein L19 / 40S ribosomal protein S26 / Small ribosomal subunit protein RACK1 / 40S ribosomal protein S25 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL28 / Ribosomal protein S5 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS15 / 60S ribosomal protein L37a / 40S ribosomal protein S24 / Large ribosomal subunit protein eL42 / 40S ribosomal protein S27 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS11 / 60S ribosomal protein L27 / Large ribosomal subunit protein uL2 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Selenocysteine insertion sequence-binding protein 2 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Cricket paralysis virus
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHilal, T. / Simonovic, M. / Spahn, C.M.T.
Funding support Germany, United States, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB740, FOR1805 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097042, GM077073 United States
CitationJournal: Science / Year: 2022
Title: Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon.
Authors: Tarek Hilal / Benjamin Y Killam / Milica Grozdanović / Malgorzata Dobosz-Bartoszek / Justus Loerke / Jörg Bürger / Thorsten Mielke / Paul R Copeland / Miljan Simonović / Christian M T Spahn /
Abstract: The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec ...The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec UGA recoding in mammals. A complex between the noncoding Sec-insertion sequence (SECIS), SECIS-binding protein 2 (SBP2), and 40 ribosomal subunit enables Sec-specific elongation factor eEFSec to deliver Sec. eEFSec and SBP2 do not interact directly but rather deploy their carboxyl-terminal domains to engage with the opposite ends of the SECIS. By using its Lys-rich and carboxyl-terminal segments, the ribosomal protein eS31 simultaneously interacts with Sec-specific transfer RNA (tRNA) and SBP2, which further stabilizes the assembly. eEFSec is indiscriminate toward l-serine and facilitates its misincorporation at Sec UGA codons. Our results support a fundamentally distinct mechanism of Sec UGA recoding in eukaryotes from that in bacteria.
History
DepositionApr 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_entity_assembly / pdbx_initial_refinement_model / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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 / _em_entity_assembly.source / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Selenocysteine insertion sequence-binding protein 2
I: CrPV IRES
L5: 28S rRNA
L7: 5S rRNA
L8: 5.8S rRNA
LD: 60S ribosomal protein uL2
LE: 60S ribosomal protein uL3
LF: 60S ribosomal protein L4
LG: Ribosomal_L18_c domain-containing protein
LH: 60S ribosomal protein L6
LI: 60S ribosomal Protein uL30
LJ: 60S ribosomal protein eL8
LK: 60S ribosomal protein L9
LL: Ribosomal protein L10
LM: 60S ribosomal protein L11
LO: 60S ribosomal protein eL13
LP: 60S ribosomal protein L14
LQ: Ribosomal protein L15
LR: 60S ribosomal protein uL13
LS: 60S ribosomal protein uL22
LT: 60S ribosomal Protein eL18
LU: 60S ribosomal protein L19
LV: 60S ribosomal protein eL20
LW: 60S ribosomal protein L21
LX: 60S ribosomal protein eL22
LY: 60S ribosomal protein L23
LZ: Ribosomal protein L24
La: Ribosomal_L23eN domain-containing protein
Lb: Ribosomal protein L26
Lc: 60S ribosomal protein L27
Ld: 60S ribosomal protein L27a
Le: 60S ribosomal protein L29
Lf: 60S ribosomal protein L30
Lg: 60S ribosomal protein L31
Lh: Ribosomal protein L32
Li: 60S ribosomal protein L35a
Lj: 60S ribosomal protein L34
Lk: 60S ribosomal protein L35
Ll: 60S ribosomal protein L36
Lm: Ribosomal protein L37
Ln: 60S ribosomal protein L38
Lo: 60S ribosomal protein eL39
Lp: 60S ribosomal protein L40
Lq: 60S ribosomal protein eL42
Lr: 60S ribosomal protein eL43
Ls: 60S ribosomal protein eL28
Lx: Ribosomal protein
S: GPX4 SECIS element
S2: 18S rRNA
SB: 40S ribosomal protein S27
SC: 40S ribosomal protein S28
SD: Ubiquitin carboxyl extension protein 80
SE: 40S ribosomal protein S30
SF: 40S ribosomal protein eS26
SG: Guanine nucleotide-binding protein subunit beta-2-like 1
SH: 40S ribosomal protein S29
SL: 40S ribosomal protein SA
SM: 40S ribosomal protein S3a
SN: 40S ribosomal protein uS5
SO: 40S ribosomal protein S3
SP: 40S ribosomal protein S4
SQ: Ribosomal protein S5
SR: 40S ribosomal protein S6
SS: 40S ribosomal protein S7
ST: 40S ribosomal protein S8
SU: 40S ribosomal protein S9
SV: S10_plectin domain-containing protein
SW: 40S ribosomal protein S11
SX: 40S ribosomal protein S12
SY: 40S ribosomal protein S13
SZ: 40S ribosomal protein uS11
Sa: 40S ribosomal protein S15
Sb: 40S ribosomal protein uS9
Sc: 40S ribosomal protein S17
Sd: 40S ribosomal protein S18
Se: 40S Ribosomal protein eS19
Sf: 40S ribosomal protein S20
Sg: 40S ribosomal protein eS21
Sh: 40S ribosomal protein S15a
Si: 40S ribosomal protein S23
Sj: 40S ribosomal protein S24
Sk: 40S ribosomal protein S25
Sl: 60S ribosomal protein L41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,195,45291
Polymers4,194,92883
Non-polymers5238
Water0
1


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

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Components

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Protein , 7 types, 7 molecules BLGLaLxSDSGSV

#1: Protein Selenocysteine insertion sequence-binding protein 2 / SECIS-binding protein 2


Mass: 95640.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SECISBP2, SBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T21
#9: Protein Ribosomal_L18_c domain-containing protein


Mass: 34523.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#28: Protein Ribosomal_L23eN domain-containing protein


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#47: Protein Ribosomal protein /


Mass: 24875.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8
#52: Protein Ubiquitin carboxyl extension protein 80 / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8C0T835
#55: Protein Guanine nucleotide-binding protein subunit beta-2-like 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2K6K8B0
#67: Protein S10_plectin domain-containing protein


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3

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RNA chain , 6 types, 6 molecules IL5L7L8SS2

#2: RNA chain CrPV IRES / Cripavirus internal ribosome entry site


Mass: 52131.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cricket paralysis virus
#3: RNA chain 28S rRNA / 28S ribosomal RNA


Mass: 1557505.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38851.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 39
#5: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50809.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 57148
#48: RNA chain GPX4 SECIS element


Mass: 275721.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: GenBank: 25123295
#49: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 603814.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 37956930

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60S ribosomal Protein ... , 34 types, 34 molecules LDLELFLHLILJLKLMLOLPLRLSLTLULVLWLXLYLcLdLeLfLgLiLjLkLlLnLoLp...

#6: Protein 60S ribosomal protein uL2 /


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8B8VPA8
#7: Protein 60S ribosomal protein uL3 /


Mass: 46120.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#8: Protein 60S ribosomal protein L4 /


Mass: 46430.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#10: Protein 60S ribosomal protein L6 /


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#11: Protein 60S ribosomal Protein uL30 /


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A7J8C453
#12: Protein 60S ribosomal protein eL8 /


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P62424
#13: Protein 60S ribosomal protein L9 /


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#15: Protein 60S ribosomal protein L11 /


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#16: Protein 60S ribosomal protein eL13 /


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TKB3
#17: Protein 60S ribosomal protein L14 /


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#19: Protein 60S ribosomal protein uL13 /


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A0N8ETI8
#20: Protein 60S ribosomal protein uL22 /


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8J4KQ25
#21: Protein 60S ribosomal Protein eL18 /


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: F6QKI9
#22: Protein 60S ribosomal protein L19 /


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2J8KH59
#23: Protein 60S ribosomal protein eL20 /


Mass: 20749.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A1Z5LHJ5
#24: Protein 60S ribosomal protein L21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#25: Protein 60S ribosomal protein eL22 /


Mass: 14756.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q4R5I3
#26: Protein 60S ribosomal protein L23 /


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A3P9HH38
#30: Protein 60S ribosomal protein L27 /


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A851LWS6
#31: Protein 60S ribosomal protein L27a /


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#32: Protein 60S ribosomal protein L29 /


Mass: 26721.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#33: Protein 60S ribosomal protein L30 /


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#34: Protein 60S ribosomal protein L31 /


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#36: Protein 60S ribosomal protein L35a /


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#37: Protein 60S ribosomal protein L34 /


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5
#38: Protein 60S ribosomal protein L35 /


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#39: Protein 60S ribosomal protein L36 /


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A1S3FQR5
#41: Protein 60S ribosomal protein L38 /


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A1A7W9T9
#42: Protein 60S ribosomal protein eL39 /


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#43: Protein 60S ribosomal protein L40 /


Mass: 14800.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8C8Y9V5
#44: Protein 60S ribosomal protein eL42 /


Mass: 12489.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A7J7V6K8
#45: Protein 60S ribosomal protein eL43 /


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A6I9ZMF9
#46: Protein 60S ribosomal protein eL28 /


Mass: 15844.696 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A4U1EJN3
#83: Protein/peptide 60S ribosomal protein L41 /


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

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Ribosomal protein ... , 7 types, 7 molecules LLLQLZLbLhLmSQ

#14: Protein Ribosomal protein L10 /


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#18: Protein Ribosomal protein L15 /


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#27: Protein Ribosomal protein L24 /


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#29: Protein Ribosomal protein L26 /


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5N3X333
#35: Protein Ribosomal protein L32 /


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#40: Protein Ribosomal protein L37 /


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#62: Protein Ribosomal protein S5 /


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9DBR8

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40S ribosomal protein ... , 29 types, 29 molecules SBSCSESFSHSLSMSNSOSPSRSSSTSUSWSXSYSZSaSbScSdSeSfSgShSiSjSk

#50: Protein 40S ribosomal protein S27 /


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A7J8BG50
#51: Protein 40S ribosomal protein S28 /


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A3M0JHZ8
#53: Protein 40S ribosomal protein S30 /


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#54: Protein 40S ribosomal protein eS26 /


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2K5LQY6
#56: Protein 40S ribosomal protein S29 /


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#57: 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 / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32970.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#58: Protein 40S ribosomal protein S3a /


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#59: Protein 40S ribosomal protein uS5 /


Mass: 31285.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: O18789
#60: Protein 40S ribosomal protein S3 /


Mass: 31146.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase
#61: Protein 40S ribosomal protein S4 /


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q76N24
#63: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P62753
#64: Protein 40S ribosomal protein S7 /


Mass: 47356.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#65: Protein 40S ribosomal protein S8 /


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q5E958
#66: Protein 40S ribosomal protein S9 /


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#68: Protein 40S ribosomal protein S11 /


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#69: Protein 40S ribosomal protein S12 /


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#70: Protein 40S ribosomal protein S13 /


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A663F1C0
#71: Protein 40S ribosomal protein uS11 /


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A7L0BEC6
#72: Protein 40S ribosomal protein S15 /


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#73: Protein 40S ribosomal protein uS9 /


Mass: 19213.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#74: Protein 40S ribosomal protein S17 /


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#75: Protein 40S ribosomal protein S18 /


Mass: 17801.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: H0WTR0
#76: Protein 40S Ribosomal protein eS19 /


Mass: 16104.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2Y9E7Q1
#77: Protein 40S ribosomal protein S20 /


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#78: Protein 40S ribosomal protein eS21 /


Mass: 9181.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A1Z5KTU7
#79: Protein 40S ribosomal protein S15a /


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#80: Protein 40S ribosomal protein S23 /


Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#81: Protein 40S ribosomal protein S24 /


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A6J1UT65
#82: Protein 40S ribosomal protein S25 /


Mass: 13645.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2U4BVW1

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Non-polymers , 1 types, 8 molecules

#84: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY

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Experimental details

-
Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
180S-SBP2-SECISCOMPLEX#1-#830MULTIPLE SOURCES
2Selenocysteine insertion sequence-binding protein 2COMPLEX#11RECOMBINANT
380S RibosomeEukaryotic ribosomeRIBOSOME#3-#47, #49-#831NATURAL
4CrPV IRESCripavirus internal ribosome entry siteCOMPLEX#21RECOMBINANT
5GPX4 SECIS elementCOMPLEX#481RECOMBINANT
Molecular weightValue: 3.5 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
34Cricket paralysis virus12136
45Rattus norvegicus (Norway rat)10116
53Oryctolagus cuniculus (rabbit)9986
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
24Synthetic construct (others)32630
35Synthetic construct (others)32630
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 %

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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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6908

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4cryoSPARCCTF correction
7PHENIX1.19.2model fitting
9PHENIX1.19.2model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cisTEMclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 179421
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39295 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7O7Y

7o7y


Accession code: 7O7Y / Source name: PDB / Type: experimental model

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