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- EMDB-24700: Metazoan pre-targeting GET complex (cBUGG-in) -

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Basic information

Entry
Database: EMDB / ID: EMD-24700
TitleMetazoan pre-targeting GET complex (cBUGG-in)
Map datasharpened cBUGG-in (C2)
Sample
  • Complex: metazoan pre-targeting GET complex cBUGG-in
    • Protein or peptide: ATPase GET3
    • Protein or peptide: Golgi to ER traffic protein 4 homolog
    • Protein or peptide: Large proline-rich protein BAG6
    • Protein or peptide: Ubiquitin-like protein 4A
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsATPase / complex / membrane protein chaperone / CHAPERONE
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / GET complex / ubiquitin-like protein transferase activity / TRC complex / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / cytoplasmic sequestering of protein / Hydrolases; Acting on acid anhydrides ...BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / GET complex / ubiquitin-like protein transferase activity / TRC complex / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / cytoplasmic sequestering of protein / Hydrolases; Acting on acid anhydrides / synaptonemal complex assembly / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding / natural killer cell activation / endoplasmic reticulum stress-induced pre-emptive quality control / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / proteasome binding / ubiquitin-specific protease binding / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / ERAD pathway / synapse assembly / Hsp70 protein binding / kidney development / molecular function activator activity / negative regulation of proteolysis / lung development / regulation of protein stability / protein modification process / brain development / ribosome binding / chromatin organization / chromosome / protein-folding chaperone binding / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / cell differentiation / protein stabilization / intracellular membrane-bounded organelle / signaling receptor binding / apoptotic process / ubiquitin protein ligase binding / nucleolus / negative regulation of apoptotic process / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ubl4, C-terminal TUGS domain / UBL4A-like, ubiquitin-like domain / Tethering Ubl4a to BAGS domain / Golgi to ER traffic protein 4 / Large proline-rich protein BAG6 / : / Golgi to ER traffic protein 4 / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Arsenical pump ATPase, ArsA/GET3, eukaryotic ...Ubl4, C-terminal TUGS domain / UBL4A-like, ubiquitin-like domain / Tethering Ubl4a to BAGS domain / Golgi to ER traffic protein 4 / Large proline-rich protein BAG6 / : / Golgi to ER traffic protein 4 / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / 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 speciesDanio rerio (zebrafish) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKeszei AFA / Yip MCJ
Funding support United States, 5 items
OrganizationGrant numberCountry
Other privateSmith Family Foundation
Other privateVallee Scholars Program United States
David and Lucile Packard Foundation2019-69660
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137415
American Heart Association287375208
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) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ru9
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24700.png

Downloads & links

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Map

FileDownload / File: emd_24700.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened cBUGG-in (C2)
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.017
Minimum - Maximum-0.051822446 - 0.10410803
Average (Standard dev.)0.000077275676 (±0.0017668096)
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-0.0520.1040.000

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Supplemental data

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Additional map: masked cBUGG-in (C2)

Fileemd_24700_additional_1.map
Annotationmasked cBUGG-in (C2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened cBUGG-in (C2)

Fileemd_24700_additional_2.map
Annotationunsharpened cBUGG-in (C2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cBUGG-in half1

Fileemd_24700_half_map_1.map
AnnotationcBUGG-in half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cBUGG-in half2

Fileemd_24700_half_map_2.map
AnnotationcBUGG-in 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-in

EntireName: metazoan pre-targeting GET complex cBUGG-in
Components
  • Complex: metazoan pre-targeting GET complex cBUGG-in
    • Protein or peptide: ATPase GET3
    • Protein or peptide: Golgi to ER traffic protein 4 homolog
    • Protein or peptide: Large proline-rich protein BAG6
    • Protein or peptide: Ubiquitin-like protein 4A
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: metazoan pre-targeting GET complex cBUGG-in

SupramoleculeName: metazoan pre-targeting GET complex cBUGG-in / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: ATPase GET3

MacromoleculeName: ATPase GET3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 38.574414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMAASVEDE FEDAPDVEPL EPTLKNIIEQ KSLKWIFVGG KGGVGKTTCS CSLAVQLAAV RESVLIISTN PAHNISDAFD QKFSKVPTK VKGYDNLFAM EIDPSLGVAE LPDEFFEEDN MLSMGKKMMQ EAMSAFPGID EAMSYAEVMR LVKGMNFSVV V FDTAPTGH ...String:
GHMAASVEDE FEDAPDVEPL EPTLKNIIEQ KSLKWIFVGG KGGVGKTTCS CSLAVQLAAV RESVLIISTN PAHNISDAFD QKFSKVPTK VKGYDNLFAM EIDPSLGVAE LPDEFFEEDN MLSMGKKMMQ EAMSAFPGID EAMSYAEVMR LVKGMNFSVV V FDTAPTGH TLRLLNFPTI VERGLGRLMQ IKNQISPFIS QMCNMLGLGD MNADQLASKL EETLPVIRSV SEQFKDPEQT TF ICVCIAE FLSLYETERL IQELAKCRID THNIIVNQLV FPDNERPCKM CEARHKIQSK YLDQMEDLYE DFHIVKLPLL PHE VRGADK VNTFSKQLLE PYSPPKK

UniProtKB: ATPase GET3

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Macromolecule #2: Golgi to ER traffic protein 4 homolog

MacromoleculeName: Golgi to ER traffic protein 4 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.054695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSTMAAA AAMAEQESAR NGGRNRGGVQ RVEGKLRASV EKGDYYEAHQ MYRTLFFRYM SQSKHTEARE LMYSGALLFF SHGQQNSAA DLSMLVLESL EKAEVEVADE LLENLAKVFS LMDPNSPERV TFVSRALKWS SGGSGKLGHP RLHQLLALTL W KEQNYCES ...String:
GPLGSTMAAA AAMAEQESAR NGGRNRGGVQ RVEGKLRASV EKGDYYEAHQ MYRTLFFRYM SQSKHTEARE LMYSGALLFF SHGQQNSAA DLSMLVLESL EKAEVEVADE LLENLAKVFS LMDPNSPERV TFVSRALKWS SGGSGKLGHP RLHQLLALTL W KEQNYCES RYHFLHSADG EGCANMLVEY STSRGFRSEV DMFVAQAVLQ FLCLKNKSSA SVVFTTYTQK HPSIEDGPPF VE PLLNFIW FLLLAVDGGK LTVFTVLCEQ YQPSLRRDPM YNEYLDRIGQ LFFGVPPKQT SSYGGLLGNL LTSLMGSSEQ EDG EESPSD GSPIELD

UniProtKB: Golgi to ER traffic protein 4 homolog

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Macromolecule #3: Large proline-rich protein BAG6

MacromoleculeName: Large proline-rich protein BAG6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.618276 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPGSAETEPW AAAVPPEWVP IIQQDIQSQR KVKPQPPLSD AYLSGMPAKR RKTMQGEGPQ LLLSEAVSRA AKAAGARPLT SPESLSRDL EAPEVQESYR QQLRSDIQKR LQEDPNYSPQ RFPNAQRAFA DDP

UniProtKB: Large proline-rich protein BAG6

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Macromolecule #4: Ubiquitin-like protein 4A

MacromoleculeName: Ubiquitin-like protein 4A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.74148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQLTVKALQG RECSLQVPED ELVSTLKQLV SEKLNVPVRQ QRLLFKGKAL ADGKRLSDYS IGPNSKLNLV VKPLEKVLLE EGEAQRLAD SPPPQVWQLI SKVLARHFSA ADASRVLEQL QRDYERSLSR LTLDDIERLA SRFLHPEVTE TMEKGFSKGS E NLYFQ

UniProtKB: Ubiquitin-like protein 4A

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28439
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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