+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24701 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Metazoan pre-targeting GET complex (cBUGG-out) | ||||||||||||||||||
Map data | Sharpened cBUGG-out (C2) | ||||||||||||||||||
Sample |
| ||||||||||||||||||
Keywords | ATPase / complex / membrane protein chaperone / 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 / 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 / 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 / ERAD pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / synapse assembly / Hsp70 protein binding / kidney development / molecular function activator activity / negative regulation of proteolysis / lung development / brain development / protein modification process / regulation of protein stability / ribosome binding / chromatin organization / protein-folding chaperone binding / chromosome / 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 | ||||||||||||||||||
Biological species | Danio rerio (zebrafish) / Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||
Authors | Keszei AFA / Yip MCJ | ||||||||||||||||||
Funding support | United States, 5 items
| ||||||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24701.map.gz | 7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-24701-v30.xml emd-24701.xml | 23 KB 23 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24701_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_24701.png | 93.2 KB | ||
Filedesc metadata | emd-24701.cif.gz | 6.3 KB | ||
Others | emd_24701_additional_1.map.gz emd_24701_additional_2.map.gz emd_24701_half_map_1.map.gz emd_24701_half_map_2.map.gz | 159.7 MB 160.6 MB 164.3 MB 159.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24701 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24701 | HTTPS FTP |
-Validation report
Summary document | emd_24701_validation.pdf.gz | 838 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_24701_full_validation.pdf.gz | 837.5 KB | Display | |
Data in XML | emd_24701_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_24701_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24701 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24701 | HTTPS FTP |
-Related structure data
Related structure data | 7ruaMC 7ru9C 7rucC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_24701.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened cBUGG-out (C2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Masked cBUGG-out (C2)
File | emd_24701_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Masked cBUGG-out (C2) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Unsharpened cBUGG-out (C2)
File | emd_24701_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened cBUGG-out (C2) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: cBUGG-out half2
File | emd_24701_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | cBUGG-out half2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: cBUGG-out half1
File | emd_24701_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | cBUGG-out half1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : metazoan pre-targeting GET complex cBUGG-out
Entire | Name: metazoan pre-targeting GET complex cBUGG-out |
---|---|
Components |
|
-Supramolecule #1: metazoan pre-targeting GET complex cBUGG-out
Supramolecule | Name: metazoan pre-targeting GET complex cBUGG-out / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
---|---|
Source (natural) | Organism: Danio rerio (zebrafish) |
-Macromolecule #1: ATPase GET3
Macromolecule | Name: 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 weight | Theoretical: 38.574414 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: Golgi to ER traffic protein 4 homolog
Macromolecule | Name: 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 weight | Theoretical: 37.054695 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #3: Large proline-rich protein BAG6
Macromolecule | Name: Large proline-rich protein BAG6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.618276 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPGSAETEPW AAAVPPEWVP IIQQDIQSQR KVKPQPPLSD AYLSGMPAKR RKTMQGEGPQ LLLSEAVSRA AKAAGARPLT SPESLSRDL EAPEVQESYR QQLRSDIQKR LQEDPNYSPQ RFPNAQRAFA DDP UniProtKB: Large proline-rich protein BAG6 |
-Macromolecule #4: Ubiquitin-like protein 4A
Macromolecule | Name: Ubiquitin-like protein 4A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.74148 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQLTVKALQG RECSLQVPED ELVSTLKQLV SEKLNVPVRQ QRLLFKGKAL ADGKRLSDYS IGPNSKLNLV VKPLEKVLLE EGEAQRLAD SPPPQVWQLI SKVLARHFSA ADASRVLEQL QRDYERSLSR LTLDDIERLA SRFLHPEVTE TMEKGFSKGS E NLYFQ UniProtKB: Ubiquitin-like protein 4A |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ATP |
---|---|
Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |