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- EMDB-52829: Cryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52829
TitleCryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon complex with improved density for TRAP alpha luminal domain
Map dataCryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon complex with improved density for TRAP alpha subunit
Sample
  • Complex: ribosome-bound SND3 translocon
Keywordsmembrane protein biogenesis / SND3 / ribosome / co-translation translocation / insertase
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsYang TJ / McDowell MA
Funding supportEuropean Union, Germany, 3 items
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
DepositionFeb 14, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52829.png

Downloads & links

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Map

FileDownload / File: emd_52829.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Chaetomium thermophilum ribosome-bound SND3 translocon complex with improved density for TRAP alpha subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 535.68 Å		1.05 Å/pix.
x 512 pix.
= 535.68 Å		1.05 Å/pix.
x 512 pix.
= 535.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.9491446 - 2.7515569
Average (Standard dev.)0.00087780337 (±0.108483806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 535.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map (A) of Chaetomium thermophilum ribosome-bound SND3...

Fileemd_52829_half_map_1.map
AnnotationHalf map (A) of Chaetomium thermophilum ribosome-bound SND3 translocon complex with improved density for TRAP alpha subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (B) of Chaetomium thermophilum ribosome-bound SND3...

Fileemd_52829_half_map_2.map
AnnotationHalf map (B) of Chaetomium thermophilum ribosome-bound SND3 translocon complex with improved density for TRAP alpha subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ribosome-bound SND3 translocon

EntireName: ribosome-bound SND3 translocon
Components
  • Complex: ribosome-bound SND3 translocon

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Supramolecule #1: ribosome-bound SND3 translocon

SupramoleculeName: ribosome-bound SND3 translocon / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#50
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMKOAcPotassium acetate
10.0 mMMg(OAc)2Magnesium acetate
0.25 %DigitoninDigitonin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: waiting time: 15 s blot force: 0.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 14039 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2108591
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.0) / Software - details: patch-CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0)
Software - details: non-uniform refinement with CTF refinements
Number images used: 31235
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.4.0) / Software - details: ab-initio reconstruction
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.4.0) / Software - details: non-uniform refinement
Final 3D classificationNumber classes: 10 / Avg.num./class: 40000 / Software - Name: cryoSPARC (ver. 4.4.0) / Software - details: 3D classification without alignment

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