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- PDB-7rua: Metazoan pre-targeting GET complex (cBUGG-out) -

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Basic information

Entry
Database: PDB / ID: 7rua
TitleMetazoan pre-targeting GET complex (cBUGG-out)
Components
  • ATPase GET3
  • Golgi to ER traffic protein 4 homolog
  • Large proline-rich protein BAG6
  • Ubiquitin-like protein 4A
KeywordsCHAPERONE / ATPase / complex / membrane protein chaperone
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / GET complex / maintenance of unfolded protein / ubiquitin-like protein transferase activity / tail-anchored membrane protein insertion into ER membrane / positive regulation of ERAD pathway / cytoplasmic sequestering of protein / Hydrolases; Acting on acid anhydrides / synaptonemal complex assembly ...BAT3 complex / immune response-activating cell surface receptor signaling pathway / GET complex / maintenance of unfolded protein / ubiquitin-like protein transferase activity / tail-anchored membrane protein insertion into ER membrane / positive regulation of ERAD pathway / 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 / misfolded protein binding / internal peptidyl-lysine acetylation / endoplasmic reticulum stress-induced pre-emptive quality control / natural killer cell activation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / proteasome binding / ubiquitin-specific protease binding / regulation of embryonic development / polyubiquitin modification-dependent protein binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / proteasomal protein catabolic process / ERAD pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / synapse assembly / Hsp70 protein binding / molecular function activator activity / kidney development / negative regulation of proteolysis / lung development / regulation of protein stability / brain development / protein modification process / 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 / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / apoptotic process / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
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
ADENOSINE-5'-TRIPHOSPHATE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKeszei, A.F.A. / Yip, M.C.J. / Shao, S.
Funding support United States, 5items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: ATPase GET3
B: ATPase GET3
C: Golgi to ER traffic protein 4 homolog
D: Large proline-rich protein BAG6
E: Ubiquitin-like protein 4A
F: Golgi to ER traffic protein 4 homolog
G: Large proline-rich protein BAG6
H: Ubiquitin-like protein 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,10613
Polymers217,9788
Non-polymers1,1285
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area24510 Å2
ΔGint-191 kcal/mol
Surface area64730 Å2

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Components

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Protein , 4 types, 8 molecules ABCFDGEH

#1: Protein ATPase GET3 / Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Guided entry of tail-anchored proteins ...Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Guided entry of tail-anchored proteins factor 3 / ATPase


Mass: 38574.414 Da / Num. of mol.: 2 / Mutation: D68N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: get3, asna1, si:dkey-121b10.2, zgc:86799 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6IQE5, Hydrolases; Acting on acid anhydrides
#2: Protein Golgi to ER traffic protein 4 homolog / Conserved edge-expressed protein / Transmembrane domain recognition complex 35 kDa subunit / TRC35


Mass: 37054.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GET4, C7orf20, CEE, TRC35, CGI-20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L5D6
#3: Protein Large proline-rich protein BAG6 / BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG-6 / HLA-B- ...BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG-6 / HLA-B-associated transcript 3 / Protein G3 / Protein Scythe


Mass: 14618.276 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG6, BAT3, G3 / Production host: Escherichia coli (E. coli) / References: UniProt: P46379
#4: Protein Ubiquitin-like protein 4A / Ubiquitin-like protein GDX


Mass: 18741.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBL4A, DXS254E, GDX, UBL4 / Production host: Escherichia coli (E. coli) / References: UniProt: P11441

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Non-polymers , 3 types, 5 molecules

#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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

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Sample preparation

ComponentName: metazoan pre-targeting GET complex cBUGG-out / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Danio rerio (zebrafish)7955
21Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35535 / Symmetry type: POINT

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