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- PDB-8q87: Structure of the G. gallus 80S rotated ribosome in complex with e... -

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Basic information

Entry
Database: PDB / ID: 8q87
TitleStructure of the G. gallus 80S rotated ribosome in complex with eEF2 and SERBP1
Components
  • (40S ribosomal protein ...) x 14
  • (60S ribosomal protein ...) x 15
  • (Large ribosomal subunit protein ...) x 12
  • (Ribosomal protein ...) x 24
  • (Small ribosomal subunit protein ...) x 8
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • DNA-(apurinic or apyrimidinic site) lyase
  • Elongation factor 2
  • Phe tRNA
  • Ribosomal protei uL14
  • Ribosomal protein
  • SERPINE1 mRNA binding protein 1
  • Ubiquitin
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / translation / complex / eEF2 / SERBP1
Function / homology
Function and homology information


TNFR1-mediated ceramide production / Major pathway of rRNA processing in the nucleolus and cytosol / Protein hydroxylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling ...TNFR1-mediated ceramide production / Major pathway of rRNA processing in the nucleolus and cytosol / Protein hydroxylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / TCF dependent signaling in response to WNT / Downstream TCR signaling / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / FCERI mediated NF-kB activation / Regulation of innate immune responses to cytosolic DNA / Autodegradation of the E3 ubiquitin ligase COP1 / RAD18 and ubiquitinated PCNA-mediated recruitment of translesion polymerases / Nucleotide Excision Repair / Deactivation of the beta-catenin transactivating complex / TRAF6 mediated induction of proinflammatory cytokines / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / NFkB activation mediated by RIP1 complexed with activated TLR3 / Activated TAK1 mediates p38 MAP kinase phosphorylation / Activated TAK1 mediates Jun kinases (JNK) phosphorylation and activation / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of AXIN / Degradation of DVL / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Hedgehog ligand biogenesis / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / NFkB and MAPK activation mediated by TRAF6 upon TLR7 or TLR21 stimulation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Downregulation of ERBB2 signaling / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of PTEN localization / Regulation of PTEN stability and activity / Neddylation / ER Quality Control Compartment (ERQC) / NOTCH3 Activation and Transmission of Signal to the Nucleus / Peroxisomal protein import / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE)
Similarity search - Function
Glycerate/sugar phosphate transporter, conserved site / : / glpT family of transporters signature. / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Major facilitator superfamily ...Glycerate/sugar phosphate transporter, conserved site / : / glpT family of transporters signature. / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Major facilitator superfamily / Major Facilitator Superfamily / : / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Elongation Factor G, domain II / Ribosomal protein L6, N-terminal domain / Elongation Factor G, domain III / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Ribosomal protein L28e / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Ribosomal protein S26e signature. / MFS transporter superfamily / metallochaperone-like domain / Ribosomal protein L41 / Ribosomal protein L41 / TRASH domain / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein L1, conserved site / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L1 signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / S27a-like superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L10e, conserved site / Plectin/S10 domain / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / : / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L44e
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 ...GUANOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL34 / 40S ribosomal protein S27 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS14 / SERPINE1 mRNA binding protein 1 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein eL38 / 60S ribosomal protein L32 / Ribosomal protein S10 / Ribosomal protein L37 / 40S ribosomal protein S8 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL2 / 40S ribosomal protein S7 / DNA-(apurinic or apyrimidinic site) lyase / Ribosomal protein L15 / Large ribosomal subunit protein uL24 / Ribosomal protein / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS13 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL30 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL4 C-terminal domain-containing protein / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL3 / Ribosomal protein L19 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS15 / 60S ribosomal protein L6 / Elongation factor 2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S16 / 60S ribosomal protein L21
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsNurullina, L. / Jenner, L. / Yusupov, M.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM) France
CitationJournal: To Be Published
Title: Structural insights into inactive ribosome complexes derived from cold-treated chick embryo cells
Authors: Nurullina, L. / Terrosu, S. / Jenner, L. / Myasnikov, A. / Yusupov, M.
History
DepositionAug 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B5: 28S rRNA
B8: 5.8S rRNA
B7: 5S rRNA
Az: 60S ribosomal protein L41
BA: 60S ribosomal protein L8
BB: Ribosomal protein uL3
BC: 60S ribosomal protein L4 C-terminal domain-containing protein
BD: Large ribosomal subunit protein uL18
BE: 60S ribosomal protein L6
BF: Large ribosomal subunit protein uL30
BG: Large ribosomal subunit protein eL8
BH: 60S ribosomal protein L9
BI: Ribosomal protein uL16,Large ribosomal subunit protein uL16,Large ribosomal subunit protein uL16
BJ: 60S ribosomal protein L11
BL: Large ribosomal subunit protein eL13
BM: 60S ribosomal protein L14
BN: Ribosomal protein L15
BO: Ribosomal protein uL13
BP: 60S ribosomal protein L17
BQ: Ribosomal protein eL18
BR: Ribosomal protein L19
BS: Ribosomal protein eL20
BT: 60S ribosomal protein L21
BU: Large ribosomal subunit protein eL22
BV: Ribosomal protei uL14
BW: Ribosomal protein L24
BX: Ribosomal protein uL23
BY: Ribosomal protein L26 like 1
BZ: Large ribosomal subunit protein eL27
Ba: Ribosomal protein uL15
Bb: 60S ribosomal protein L29
Bc: Large ribosomal subunit protein eL30
Bd: 60S ribosomal protein L31
Be: Ribosomal protein L32
Bf: Ribosomal protein eL33
Bg: 60S ribosomal protein L34
Bh: Large ribosomal subunit protein uL29
Bi: Large ribosomal subunit protein eL36
Bj: Ribosomal protein L37
Bk: 60S ribosomal protein L38
Bl: Large ribosomal subunit protein eL39
Bm: Ubiquitin-60S ribosomal protein L40
Bo: Ribosomal protein L36a like
Bp: Large ribosomal subunit protein eL43
Br: 60S ribosomal protein L28
A2: 18S rRNA
Aa: Ribosomal protein eS1
AA: 40S ribosomal protein S27
AB: 40S ribosomal protein S28
Ab: 40S ribosomal protein S2
AC: Ubiquitin
Ac: DNA-(apurinic or apyrimidinic site) lyase
Ad: Small ribosomal subunit protein eS4
AD: Ribosomal protein eS30
AE: 40S ribosomal protein S26
Ae: Ribosomal protein S5
Af: Small ribosomal subunit protein eS6
AF: Small ribosomal subunit protein RACK1
Ag: 40S ribosomal protein S7
AG: 40S ribosomal protein S29
Ah: 40S ribosomal protein S8
Ai: 40S ribosomal protein S9
Aj: Ribosomal protein S10
Ak: 40S ribosomal protein S11
Al: Small ribosomal subunit protein eS12
Am: Small ribosomal subunit protein uS15
An: Ribosomal protein S14
Ao: Small ribosomal subunit protein uS19
Aq: Small ribosomal subunit protein eS17
Ar: 40S ribosomal protein S18
As: Ribosomal protein eS19
At: 40S ribosomal protein S20
Au: Ribosomal protein eS21
Av: 40S ribosomal protein S15a
Aw: Ribosomal protein uS12
Ax: 40S ribosomal protein S24
Ay: 40S ribosomal protein S25
AZ: Small ribosomal subunit protein uS2
Ap: Ribosomal protein S16
V: Phe tRNA
S: SERPINE1 mRNA binding protein 1
A: Elongation factor 2
Bs: Large ribosomal subunit protein uL10
Bt: 60S ribosomal protein L12
Bv: Ribosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,822,411586
Polymers3,809,48785
Non-polymers12,925501
Water70,1683895
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 5 molecules B5B8B7A2V

#1: RNA chain 28S rRNA


Mass: 1439489.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: KT445934.2
#2: RNA chain 5.8S rRNA


Mass: 50446.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: KT445934.2
#3: RNA chain 5S rRNA


Mass: 38322.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: 63782
#46: RNA chain 18S rRNA


Mass: 588288.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: KT445934.2
#80: RNA chain Phe tRNA


Mass: 24593.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo

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60S ribosomal protein ... , 15 types, 15 molecules AzBABCBEBHBJBMBPBTBbBdBgBkBrBt

#4: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus A0A087WNH4 sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A087WNH4
#5: Protein 60S ribosomal protein L8


Mass: 28086.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NIX0
#7: Protein 60S ribosomal protein L4 C-terminal domain-containing protein


Mass: 46853.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZII1
#9: Protein 60S ribosomal protein L6


Mass: 34014.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q8UWG7
#12: Protein 60S ribosomal protein L9


Mass: 21871.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1D5NVI1
#14: Protein 60S ribosomal protein L11


Mass: 20269.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1D5P3B1
#16: Protein 60S ribosomal protein L14


Mass: 15514.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF9
#19: Protein 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1D5PR40
#23: Protein 60S ribosomal protein L21


Mass: 18622.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: R4GIQ2
#31: Protein 60S ribosomal protein L29


Mass: 8433.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1L1RNZ2
#33: Protein 60S ribosomal protein L31


Mass: 19836.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1L1RT94
#36: Protein 60S ribosomal protein L34


Mass: 13340.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1L1S0X5
#40: Protein 60S ribosomal protein L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embtyo / References: UniProt: E1BU66
#45: Protein 60S ribosomal protein L28


Mass: 15920.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5F346
#84: Protein 60S ribosomal protein L12


Mass: 17766.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1BTG1

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Ribosomal protein ... , 24 types, 24 molecules BBBIBNBOBQBRBSBWBXBYBaBeBfBjBoAaADAeAjAnAsAuAwAp

#6: Protein Ribosomal protein uL3


Mass: 46201.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZJZ2
#13: Protein Ribosomal protein uL16,Large ribosomal subunit protein uL16,Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / Jun-binding protein JIF-1 / Ribosomal protein L10


Mass: 24506.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N terminal of the ...Details: The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q08200
#17: Protein Ribosomal protein L15


Mass: 24193.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NQG5
#18: Protein Ribosomal protein uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus sequence from PDB entry 7O7Z (XP_002723961.2 ) because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#20: Protein Ribosomal protein eL18


Mass: 21411.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#21: Protein Ribosomal protein L19


Mass: 23481.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZKK8
#22: Protein Ribosomal protein eL20


Mass: 20856.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#26: Protein Ribosomal protein L24


Mass: 17837.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0XRE7
#27: Protein Ribosomal protein uL23


Mass: 17701.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the E1BS06 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V1AGP8 and two more sequences
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#28: Protein Ribosomal protein L26 like 1


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F2Z4K6
#30: Protein Ribosomal protein uL15


Mass: 16851.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NBX4 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZL98 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#34: Protein Ribosomal protein L32


Mass: 15955.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1BVB1
#35: Protein Ribosomal protein eL33


Mass: 12609.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NQ35 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0YS49 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#39: Protein Ribosomal protein L37


Mass: 11103.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1C810
#43: Protein Ribosomal protein L36a like


Mass: 12335.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NIK4 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0YUB1 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0YUB1
#47: Protein Ribosomal protein eS1


Mass: 29923.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F2Z4K7 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XXX0 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#54: Protein Ribosomal protein eS30


Mass: 14536.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the A0A1D5PQV entry although it is an obsoleted entry, because no more entry in database.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#56: Protein Ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus G1TFM5 sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: G1TFM5
#63: Protein Ribosomal protein S10


Mass: 18945.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1C4N0
#67: Protein Ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZHW8
#71: Protein Ribosomal protein eS19


Mass: 16118.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the A0A1D5PDV6 entry although it is an obsoleted entry, because no more sequence in database.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#73: Protein Ribosomal protein eS21


Mass: 9173.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the E1BSJ2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZQ38 and A0A8V0ZC45 sequences.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#75: Protein Ribosomal protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NDC2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XRS9 sequence.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#79: Protein Ribosomal protein S16


Mass: 16445.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: R4GGJ0

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Large ribosomal subunit protein ... , 12 types, 12 molecules BDBFBGBLBUBZBcBhBiBlBpBs

#8: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34156.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P22451
#10: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 28844.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZJ56
#11: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a


Mass: 30064.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P32429
#15: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1


Mass: 24455.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P41125
#24: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 14754.892 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF8
#29: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P61355
#32: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12835.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P67883
#37: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF7
#38: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 12331.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF6
#41: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6398.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF5
#44: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10271.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P32046
#83: Protein Large ribosomal subunit protein uL10 / 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E


Mass: 34322.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P47826

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Protein , 7 types, 7 molecules BVBmACAcSABv

#25: Protein Ribosomal protei uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the E1BY89 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the other entries.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#42: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14769.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: O42388
#51: Protein Ubiquitin


Mass: 18018.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P79781
#52: Protein DNA-(apurinic or apyrimidinic site) lyase


Mass: 26760.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
References: UniProt: F1NPA9, DNA-(apurinic or apyrimidinic site) lyase
#81: Protein SERPINE1 mRNA binding protein 1


Mass: 43470.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0ZUK5
#82: Protein Elongation factor 2 / EF-2


Mass: 95645.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
References: UniProt: Q90705, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#85: Protein Ribosomal protein


Mass: 24755.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F6SU35

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40S ribosomal protein ... , 14 types, 14 molecules AAABAbAEAgAGAhAiAkArAtAvAxAy

#48: Protein 40S ribosomal protein S27


Mass: 9566.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A3Q2TV39
#49: Protein 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A3Q2U825
#50: Protein 40S ribosomal protein S2


Mass: 28875.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0Z891
#55: Protein 40S ribosomal protein S26


Mass: 13063.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZM66
#59: Protein 40S ribosomal protein S7


Mass: 22153.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NN16
#60: Protein 40S ribosomal protein S29


Mass: 18662.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0Z8V3
#61: Protein 40S ribosomal protein S8


Mass: 24112.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NB02
#62: Protein 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus B7NZS8 sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: B7NZS8
#64: Protein 40S ribosomal protein S11


Mass: 18384.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TH5
#70: Protein 40S ribosomal protein S18


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus G1TPG3 sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: G1TPG3
#72: Protein 40S ribosomal protein S20


Mass: 13399.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NH93
#74: Protein 40S ribosomal protein S15a


Mass: 14881.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A3Q3A7P6
#76: Protein 40S ribosomal protein S24


Mass: 15237.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NF89
#77: Protein 40S ribosomal protein S25


Mass: 13746.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NU56 entry although it is an obsoleted entry, because no more sequence in database.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V1A7V4

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Small ribosomal subunit protein ... , 8 types, 8 molecules AdAfAFAlAmAoAqAZ

#53: Protein Small ribosomal subunit protein eS4 / 40S ribosomal protein S4


Mass: 29652.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P47836
#57: Protein Small ribosomal subunit protein eS6 / 40S ribosomal protein S6


Mass: 28723.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P47838
#58: Protein Small ribosomal subunit protein RACK1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Receptor for activated C kinase ...Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Receptor for activated C kinase / Receptor of activated protein C kinase 1 / Receptor of activated protein kinase C 1 / RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P63247
#65: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 14569.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P84175
#66: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q6ITC7
#68: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P62846
#69: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 15566.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P08636
#78: Protein Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal protein SA / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 33093.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P50890

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Non-polymers , 4 types, 4396 molecules

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


Mass: 24.305 Da / Num. of mol.: 492 / Source method: obtained synthetically / Formula: Mg
#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#88: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#89: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3895 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

-
Sample preparation

ComponentName: 80S ribosome / Type: RIBOSOME / Details: Contains endogenous P/E tRNA, SERBP1 and eEF2 / Entity ID: #1-#85 / Source: NATURAL
Molecular weightValue: 4.2 MDa / Experimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 %

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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 magnification: 96000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19rc4_4035: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 100204 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Cross_correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003239958
ELECTRON MICROSCOPYf_angle_d0.545351384
ELECTRON MICROSCOPYf_dihedral_angle_d13.2383622
ELECTRON MICROSCOPYf_chiral_restr0.03643437
ELECTRON MICROSCOPYf_plane_restr0.00523929

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