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- EMDB-24703: Metazoan pre-targeting GET complex cBUGG (C1) -

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Basic information

Entry
Database: EMDB / ID: EMD-24703
TitleMetazoan pre-targeting GET complex cBUGG (C1)
Map datasharpened cBUGG (C1)
Sample
  • Complex: metazoan pre-targeting GET complex cBUGG (C1)
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / NK T cell activation / GET complex / ubiquitin-like protein transferase activity / maintenance of unfolded protein / tail-anchored membrane protein insertion into ER membrane / protein carrier chaperone / positive regulation of ERAD pathway / synaptonemal complex assembly ...BAT3 complex / immune response-activating cell surface receptor signaling pathway / NK T cell activation / GET complex / ubiquitin-like protein transferase activity / maintenance of unfolded protein / tail-anchored membrane protein insertion into ER membrane / protein carrier chaperone / positive regulation of ERAD pathway / synaptonemal complex assembly / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding / endoplasmic reticulum stress-induced pre-emptive quality control / natural killer cell activation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / ubiquitin-specific protease binding / proteasome binding / regulation of embryonic development / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / polyubiquitin modification-dependent protein binding / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / proteasomal protein catabolic process / synapse assembly / ERAD pathway / negative regulation of proteolysis / Hsp70 protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / lung development / molecular function activator activity / kidney development / brain development / regulation of protein stability / protein modification process / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein-folding chaperone binding / ribosome binding / chromosome / chromatin organization / ubiquitin-dependent protein catabolic process / spermatogenesis / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein stabilization / receptor ligand activity / signaling receptor binding / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / apoptotic process / negative regulation of apoptotic process / nucleolus / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Ubl4, C-terminal TUGS domain / UBL4A-like, ubiquitin-like domain / Tethering Ubl4a to BAGS domain / Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / : ...Ubl4, C-terminal TUGS domain / UBL4A-like, ubiquitin-like domain / Tethering Ubl4a to BAGS domain / Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / : / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Ubiquitin domain signature. / Ubiquitin domain / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Tetratricopeptide-like helical domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ubiquitin-like protein 4A / Large proline-rich protein BAG6 / ATPase GET3 / Golgi to ER traffic protein 4 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKeszei AFA / Yip MCJ
Funding support United States, 5 items
OrganizationGrant numberCountry
Other privateSmith Family Foundation United States
Other privateVallee Scholars Program United States
David and Lucile Packard Foundation2019-69660 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137415 United States
American Heart Association287375208 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural insights into metazoan pretargeting GET complexes.
Authors: Alexander F A Keszei / Matthew C J Yip / Ta-Chien Hsieh / Sichen Shao /
Abstract: Close coordination between chaperones is essential for protein biosynthesis, including the delivery of tail-anchored (TA) proteins containing a single C-terminal transmembrane domain to the ...Close coordination between chaperones is essential for protein biosynthesis, including the delivery of tail-anchored (TA) proteins containing a single C-terminal transmembrane domain to the endoplasmic reticulum (ER) by the conserved GET pathway. For successful targeting, nascent TA proteins must be promptly chaperoned and loaded onto the cytosolic ATPase Get3 through a transfer reaction involving the chaperone SGTA and bridging factors Get4, Ubl4a and Bag6. Here, we report cryo-electron microscopy structures of metazoan pretargeting GET complexes at 3.3-3.6 Å. The structures reveal that Get3 helix 8 and the Get4 C terminus form a composite lid over the Get3 substrate-binding chamber that is opened by SGTA. Another interaction with Get4 prevents formation of Get3 helix 4, which links the substrate chamber and ATPase domain. Both interactions facilitate TA protein transfer from SGTA to Get3. Our findings show how the pretargeting complex primes Get3 for coordinated client loading and ER targeting.
History
DepositionAug 16, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24703.png

Downloads & links

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Map

FileDownload / File: emd_24703.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened cBUGG (C1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 364 pix.
= 300.3 Å		0.83 Å/pix.
x 364 pix.
= 300.3 Å		0.83 Å/pix.
x 364 pix.
= 300.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.031457677 - 0.06538608
Average (Standard dev.)7.8792815e-05 (±0.0011406344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions364364364
Spacing364364364
CellA=B=C: 300.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8250.8250.825
M x/y/z364364364
origin x/y/z0.0000.0000.000
length x/y/z300.300300.300300.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS364364364
D min/max/mean-0.0310.0650.000

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Supplemental data

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Additional map: masked cBUGG (C1)

Fileemd_24703_additional_1.map
Annotationmasked cBUGG (C1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened cBUGG (C1)

Fileemd_24703_additional_2.map
Annotationunsharpened cBUGG (C1)
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: cBUGG (C1) half1

Fileemd_24703_half_map_1.map
AnnotationcBUGG (C1) half1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cBUGG (C1) half2

Fileemd_24703_half_map_2.map
AnnotationcBUGG (C1) half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : metazoan pre-targeting GET complex cBUGG (C1)

EntireName: metazoan pre-targeting GET complex cBUGG (C1)
Components
  • Complex: metazoan pre-targeting GET complex cBUGG (C1)

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Supramolecule #1: metazoan pre-targeting GET complex cBUGG (C1)

SupramoleculeName: metazoan pre-targeting GET complex cBUGG (C1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 388455
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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