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- PDB-9i78: Cryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 ... -

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Basic information

Entry
Database: PDB / ID: 9i78
TitleCryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon
Components
  • (60S ribosomal protein ...) x 30
  • (Putative 60S ribosomal ...) x 2
  • (Putative ribosomal ...) x 2
  • (Ribosomal protein ...) x 6
  • 26S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • CCDC47
  • Dolichyl-diphosphooligosaccharide--protein glycotransferase
  • Putative inorganic phosphate transporter protein
  • SEC61 beta subunit
  • SEC61 gamma subunit
  • Translocon Sec61/SecY plug domain-containing protein
  • Translocon-associated protein subunit alpha
KeywordsRIBOSOME / membrane protein biogenesis / SND3 / co-translation translocation / insertase
Function / homology
Function and homology information


dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / preribosome / protein targeting to ER / protein N-linked glycosylation via asparagine / endoplasmic reticulum calcium ion homeostasis / protein kinase regulator activity / protein transmembrane transporter activity / protein targeting / endomembrane system ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / preribosome / protein targeting to ER / protein N-linked glycosylation via asparagine / endoplasmic reticulum calcium ion homeostasis / protein kinase regulator activity / protein transmembrane transporter activity / protein targeting / endomembrane system / post-translational protein modification / cellular response to amino acid starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular protein transport / protein transport / ribosome biogenesis / large ribosomal subunit / regulation of translation / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / metal ion binding / membrane / cytosol
Similarity search - Function
SRP-independent targeting protein 3 / Phosphate transport (Pho88) / PAT complex subunit CCDC47 / PAT complex subunit CCDC47 / Translocon-associated protein (TRAP), alpha subunit / Translocon-associated protein (TRAP), alpha subunit / Gcn1, N-terminal / : / : / Generalcontrol nonderepressible 1 (Gcn1) N-terminal ...SRP-independent targeting protein 3 / Phosphate transport (Pho88) / PAT complex subunit CCDC47 / PAT complex subunit CCDC47 / Translocon-associated protein (TRAP), alpha subunit / Translocon-associated protein (TRAP), alpha subunit / Gcn1, N-terminal / : / : / Generalcontrol nonderepressible 1 (Gcn1) N-terminal / Stalled ribosome sensor GCN1-like, HEAT repeats / Fungal GCN1-like, HEAT repeats / Stalled ribosome sensor GCN1 N-terminal / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / Elongation factor 3/GNC1 HEAT repeat / EF3 N-terminal HEAT repeat / Centrosomal protein CEP104-like, TOG domain / : / STT3/PglB/AglB core domain / Parkin co-regulated protein / Parkin co-regulated protein / TOG domain / TOG / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / HEAT repeat profile. / HEAT, type 2 / Ribosomal protein L30e / Ribosomal protein L28e / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / : / Ribosomal protein L10e / Ribosomal protein L6e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L6e / : / Ribosomal protein L34Ae / Ribosomal protein L34e
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / 60S ribosomal protein L26-like protein / Putative inorganic phosphate transporter protein / Ribosomal protein L15 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL3 / 60S ribosomal protein L26-like protein / Putative inorganic phosphate transporter protein / Ribosomal protein L15 / 60S ribosomal protein L27 / 60S ribosomal protein L6 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3 / 60S ribosomal protein l9-like protein / 60S ribosomal protein l21-like protein / Ribosomal protein L37 / 60S ribosomal protein L14-like protein / 60S ribosomal protein L2-like protein / 60S ribosomal protein L25-like protein / Uncharacterized protein / 60S ribosomal protein L43-like protein / 60S ribosomal protein L32-like protein / 60S ribosomal protein L13 / Ribosomal protein L18-like protein / Ribosomal protein L19 / 60S ribosomal protein L8 / 60S ribosomal protein L36 / 60S ribosomal protein L44-like protein / 60S ribosomal protein L20 / 60S ribosomal protein l33-like protein / Putative 60S ribosomal protein / 60S ribosomal protein L22-like protein / Large ribosomal subunit protein uL18 / 60S ribosomal protein l30-like protein / 60S ribosomal protein L10-like protein / 60S ribosomal protein L4-like protein / Uncharacterized protein / 60S ribosomal protein l7-like protein / Ribosomal protein l34-like protein / Translocon-associated protein subunit alpha / Large ribosomal subunit protein uL22 / 60S ribosomal protein L16-like protein / Translocon Sec61/SecY plug domain-containing protein / Putative 60S ribosomal protein / Large ribosomal subunit protein uL5 / 60S ribosomal protein l23-like protein / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein eL39 / 60S ribosomal protein L29
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsYang, T.J. / McDowell, M.A.
Funding supportEuropean Union, Germany, 3items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionHORIZON-MSCA-2022-PF-01; Project ID: 101107937European Union
Max Planck Society Germany
German Research Foundation (DFG)SFB 1507/P16 (project-ID 450648163) Germany
CitationJournal: Nat Commun / Year: 2025
Title: SND3 is the membrane insertase within a distinct SEC61 translocon complex.
Authors: Tzu-Jing Yang / Saumyak Mukherjee / Julian D Langer / Gerhard Hummer / Melanie A McDowell /
Abstract: During the biogenesis of most eukaryotic integral membrane proteins (IMPs), transmembrane domains are inserted into the endoplasmic reticulum membrane by a dedicated insertase or the SEC61 translocon. ...During the biogenesis of most eukaryotic integral membrane proteins (IMPs), transmembrane domains are inserted into the endoplasmic reticulum membrane by a dedicated insertase or the SEC61 translocon. The SRP-independent (SND) pathway is the least understood route into the membrane, despite catering for a broad range of IMP types. Here, we show that Chaetomium thermophilum SND3 is a membrane insertase with an atypical fold. We further present a cryo-electron microscopy structure of a ribosome-associated SND3 translocon complex involved in co-translational IMP insertion. The structure reveals that the SND3 translocon additionally comprises the complete SEC61 translocon, CCDC47 and TRAPɑ. Here, the SEC61β N-terminus works together with CCDC47 to prevent substrate access to the translocon. Instead, molecular dynamics simulations show that SND3 disrupts the lipid bilayer to promote IMP insertion via its membrane-embedded hydrophilic groove. Structural and sequence comparisons indicate that the SND3 translocon is a distinct multipass translocon in fungi, euglenozoan parasites and other eukaryotic taxa.
History
DepositionJan 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Translocon Sec61/SecY plug domain-containing protein
2: SEC61 beta subunit
3: SEC61 gamma subunit
4: CCDC47
6: Putative inorganic phosphate transporter protein
7: Translocon-associated protein subunit alpha
LA: 60S ribosomal protein L2-like protein
LB: 60S ribosomal protein L3-like protein
LC: 60S ribosomal protein L4-like protein
LD: 60S ribosomal protein l5-like protein
LE: 60S ribosomal protein L6
LF: 60S ribosomal protein l7-like protein
LG: 60S ribosomal protein L8
LH: 60S ribosomal protein l9-like protein
LI: 60S ribosomal protein L10-like protein
LJ: Putative ribosomal protein
LL: 60S ribosomal protein L13
LM: 60S ribosomal protein L14-like protein
LN: Ribosomal protein L15
LO: 60S ribosomal protein L16-like protein
LP: 60S ribosomal protein l17-like protein
LQ: Ribosomal protein L18-like protein
LR: Ribosomal protein L19
LS: 60S ribosomal protein L20
LT: 60S ribosomal protein l21-like protein
LU: 60S ribosomal protein L22-like protein
LV: 60S ribosomal protein l23-like protein
LX: 60S ribosomal protein L25-like protein
LY: 60S ribosomal protein L26-like protein
LZ: 60S ribosomal protein L27
La: 60S ribosomal protein L28-like protein
Lb: 60S ribosomal protein L29
Lc: 60S ribosomal protein l30-like protein
Ld: Putative 60S ribosomal protein
Le: 60S ribosomal protein L32-like protein
Lf: 60S ribosomal protein l33-like protein
Lg: Ribosomal protein l34-like protein
Lh: Dolichyl-diphosphooligosaccharide--protein glycotransferase
Li: 60S ribosomal protein L36
Lj: Ribosomal protein L37
Lk: 60S ribosomal protein L38-like protein
Ll: Ribosomal protein eL39
Lm: Putative ribosomal protein
Ln: 60S ribosomal protein L41-A
Lo: 60S ribosomal protein L44-like protein
Lp: 60S ribosomal protein L43-like protein
Lq: Putative 60S ribosomal protein
L1: 26S rRNA
L2: 5.8S rRNA
L3: 5S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,121,455429
Polymers2,112,24350
Non-polymers9,212379
Water00
1


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

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Components

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Protein , 7 types, 7 molecules 123467Lh

#1: Protein Translocon Sec61/SecY plug domain-containing protein


Mass: 52322.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SHC8
#2: Protein SEC61 beta subunit


Mass: 12552.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#3: Protein SEC61 gamma subunit


Mass: 7818.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SFD9
#4: Protein CCDC47


Mass: 51723.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: genome engineered CCDC47 (internal FLAG-tag after the residue T60)
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0024800
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S5M5
#5: Protein Putative inorganic phosphate transporter protein


Mass: 24180.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Putative inorganic phosphate transporter protein with C-terminal TwinStrep-tag
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0007540
Production host: Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RYQ7
#6: Protein Translocon-associated protein subunit alpha


Mass: 29964.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SGC8
#38: Protein Dolichyl-diphosphooligosaccharide--protein glycotransferase


Mass: 14643.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase

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60S ribosomal protein ... , 30 types, 30 molecules LALBLCLDLELFLGLHLILLLMLOLPLSLTLULVLXLYLZLaLbLcLeLfLiLkLnLoLp

#7: Protein 60S ribosomal protein L2-like protein


Mass: 27598.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S4P8
#8: Protein 60S ribosomal protein L3-like protein


Mass: 44456.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RXW1
#9: Protein 60S ribosomal protein L4-like protein


Mass: 39439.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SFC3
#10: Protein 60S ribosomal protein l5-like protein


Mass: 35034.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SEG2
#11: Protein 60S ribosomal protein L6


Mass: 22132.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S0D6
#12: Protein 60S ribosomal protein l7-like protein


Mass: 28821.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SFL0
#13: Protein 60S ribosomal protein L8


Mass: 29744.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SAJ9
#14: Protein 60S ribosomal protein l9-like protein


Mass: 21582.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S0E5
#15: Protein 60S ribosomal protein L10-like protein


Mass: 25255.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SEI1
#17: Protein 60S ribosomal protein L13


Mass: 24191.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S992
#18: Protein 60S ribosomal protein L14-like protein


Mass: 16111.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S1R0
#20: Protein 60S ribosomal protein L16-like protein


Mass: 22888.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SH61
#21: Protein 60S ribosomal protein l17-like protein


Mass: 21072.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SGY1
#24: Protein 60S ribosomal protein L20


Mass: 20341.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SCE2
#25: Protein 60S ribosomal protein l21-like protein


Mass: 18159.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S0Z3
#26: Protein 60S ribosomal protein L22-like protein


Mass: 14302.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SDS8
#27: Protein 60S ribosomal protein l23-like protein


Mass: 14674.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SI44
#28: Protein 60S ribosomal protein L25-like protein


Mass: 17175.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S507
#29: Protein 60S ribosomal protein L26-like protein


Mass: 15565.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RYN9
#30: Protein 60S ribosomal protein L27


Mass: 15803.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RZE9
#31: Protein 60S ribosomal protein L28-like protein


Mass: 16848.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#32: Protein 60S ribosomal protein L29 / Ribosomal protein eL29


Mass: 7529.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: Q2H9W4
#33: Protein 60S ribosomal protein l30-like protein


Mass: 11602.616 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SEI0
#35: Protein 60S ribosomal protein L32-like protein


Mass: 15095.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S6V4
#36: Protein 60S ribosomal protein l33-like protein


Mass: 12330.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SCL3
#39: Protein 60S ribosomal protein L36


Mass: 12784.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SBN1
#41: Protein 60S ribosomal protein L38-like protein


Mass: 9537.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#44: Protein/peptide 60S ribosomal protein L41-A / Ribosomal protein eL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: P0CX86
#45: Protein 60S ribosomal protein L44-like protein


Mass: 12045.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SBZ6
#46: Protein 60S ribosomal protein L43-like protein


Mass: 10158.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S6B0

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Putative ribosomal ... , 2 types, 2 molecules LJLm

#16: Protein Putative ribosomal protein


Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SHQ2
#43: Protein Putative ribosomal protein


Mass: 14609.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)

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Ribosomal protein ... , 6 types, 6 molecules LNLQLRLgLjLl

#19: Protein Ribosomal protein L15


Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0RZ88
#22: Protein Ribosomal protein L18-like protein


Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S9B5
#23: Protein Ribosomal protein L19


Mass: 22409.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S9T3
#37: Protein Ribosomal protein l34-like protein


Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SFN0
#40: Protein Ribosomal protein L37


Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0S101
#42: Protein Ribosomal protein eL39


Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: Q2H9R2

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Putative 60S ribosomal ... , 2 types, 2 molecules LdLq

#34: Protein Putative 60S ribosomal protein


Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SD68
#47: Protein Putative 60S ribosomal protein


Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: UniProt: G0SHJ6

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RNA chain , 3 types, 3 molecules L1L2L3

#48: RNA chain 26S rRNA


Mass: 1078730.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
#49: RNA chain 5.8S rRNA


Mass: 50147.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: GenBank: XR_002966750.1
#50: RNA chain 5S rRNA


Mass: 38596.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus)
References: GenBank: 7OLC_3

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Non-polymers , 1 types, 379 molecules

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


Mass: 24.305 Da / Num. of mol.: 379 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: ribosome-bound SND3 translocon / Type: COMPLEX / Entity ID: #1-#50 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2100 mMPotassium acetateKOAc1
310 mMMagnesium acetateMg(OAc)21
40.25 %DigitoninDigitonin1
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: waiting time: 15 s blot force: 0

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4.0particle selectionblob picker
2EPU3.8image acquisition
4cryoSPARC4.4.0CTF correctionpatch-CTF
7UCSF ChimeraX1.7.0model fitting
8Coot0.9.8model fitting
9PHENIX1.2model fitting
11PHENIX1.2model refinement
12cryoSPARC4.4.0initial Euler assignmentab-initio reconstruction
13cryoSPARC4.4.0final Euler assignmentnon-uniform refinement
14cryoSPARC4.4.0classification3D classification without alignment
15cryoSPARC4.4.03D reconstructionnon-uniform refinement with CTF refinements
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2108591
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119533 / Details: non-uniform refinement with CTF refinements / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1

IDPDB-IDDetailsSource nameTypeAccession codeInitial refinement model-ID
1complex of CCDC47 and SND3AlphaFoldin silico model
2complex of SEC61 transloconAlphaFoldin silico model
3complex of SEC61 translocon and TRAP alpha subunitAlphaFoldin silico model
47OLC

7olc

ribosomePDBexperimental model7OLC2
RefinementCross valid method: NONE

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