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Yorodumi- EMDB-25373: Get3 bound to ADP and the transmembrane domain of the tail-anchor... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25373 | |||||||||
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Title | Get3 bound to ADP and the transmembrane domain of the tail-anchored protein Bos1 - nucleotide binding domain map | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Tail-anchored membrane protein targeting Deviant Walker A ATPase targeting factor / CHAPERONE | |||||||||
Function / homology | Function and homology information GET complex / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Giardia intestinalis (strain ATCC 50803 / WB clone C6) (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Fry MY / Maggiolo AO | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3. Authors: Michelle Y Fry / Vladimíra Najdrová / Ailiena O Maggiolo / Shyam M Saladi / Pavel Doležal / William M Clemons / Abstract: Tail-anchored (TA) membrane proteins, accounting for roughly 2% of proteomes, are primarily targeted posttranslationally to the endoplasmic reticulum membrane by the guided entry of TA proteins (GET) ...Tail-anchored (TA) membrane proteins, accounting for roughly 2% of proteomes, are primarily targeted posttranslationally to the endoplasmic reticulum membrane by the guided entry of TA proteins (GET) pathway. For this complicated process, it remains unknown how the central targeting factor Get3 uses nucleotide to facilitate large conformational changes to recognize then bind clients while also preventing exposure of hydrophobic surfaces. Here, we identify the GET pathway in Giardia intestinalis and present the structure of the Get3-client complex in the critical postnucleotide-hydrolysis state, demonstrating that Get3 reorganizes the client-binding domain (CBD) to accommodate and shield the client transmembrane helix. Four additional structures of GiGet3, spanning the nucleotide-free (apo) open to closed transition and the ATP-bound state, reveal the details of nucleotide stabilization and occluded CBD. This work resolves key conundrums and allows for a complete model of the dramatic conformational landscape of Get3. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25373.map.gz | 100.2 MB | EMDB map data format | |
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Header (meta data) | emd-25373-v30.xml emd-25373.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25373_fsc.xml | 10.9 KB | Display | FSC data file |
Images | emd_25373.png | 56.8 KB | ||
Masks | emd_25373_msk_1.map | 107.2 MB | Mask map | |
Filedesc metadata | emd-25373.cif.gz | 6.1 KB | ||
Others | emd_25373_half_map_1.map.gz emd_25373_half_map_2.map.gz | 82.7 MB 82.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25373 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25373 | HTTPS FTP |
-Validation report
Summary document | emd_25373_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_25373_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_25373_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_25373_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25373 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25373 | HTTPS FTP |
-Related structure data
Related structure data | 7sq0MC 7spyC 7spzC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25373.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.866 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25373_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: focused refined half map
File | emd_25373_half_map_1.map | ||||||||||||
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Annotation | focused refined half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: focused refined half map
File | emd_25373_half_map_2.map | ||||||||||||
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Annotation | focused refined half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The targeting factor Get3 bound to ADP and the TMD of the cargo t...
Entire | Name: The targeting factor Get3 bound to ADP and the TMD of the cargo tail-anchored protein Bos1 |
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Components |
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-Supramolecule #1: The targeting factor Get3 bound to ADP and the TMD of the cargo t...
Supramolecule | Name: The targeting factor Get3 bound to ADP and the TMD of the cargo tail-anchored protein Bos1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 157 KDa |
-Supramolecule #2: The TMD of the tail-anchored protein Bos1
Supramolecule | Name: The TMD of the tail-anchored protein Bos1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Supramolecule #3: The targeting factor Get3
Supramolecule | Name: The targeting factor Get3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Giardia intestinalis (strain ATCC 50803 / WB clone C6) (eukaryote) Strain: ATCC 50803 / WB clone C6 |
Molecular weight | Theoretical: 78 KDa |
-Macromolecule #1: ATPase ASNA1 homolog
Macromolecule | Name: ATPase ASNA1 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides |
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Source (natural) | Organism: Giardia intestinalis (strain ATCC 50803 / WB clone C6) (eukaryote) Strain: ATCC 50803 / WB clone C6 |
Molecular weight | Theoretical: 39.164922 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MLPSLHDILD QHTYKWIFFG GKGGVGKTTT SSSFSVLMAE TRPNEKFLLL STDPAHNISD AFDQKFGKAP TQVSGIPNLY AMEVDASNE MKSAVEAVQK ETGSAA(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK) ...String: MLPSLHDILD QHTYKWIFFG GKGGVGKTTT SSSFSVLMAE TRPNEKFLLL STDPAHNISD AFDQKFGKAP TQVSGIPNLY AMEVDASNE MKSAVEAVQK ETGSAA(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)ITCA SSFIKDGTFP GMDEMWSFIN LIKLIDTNEY STVIFD TAP TGHTLRFLEL PETVNKVLEI FTRLKDNMGG MLSMVMQTMG LSQNDIFGLI DKTYPKIDVV KRISAEFRDP SLCTFVG VC IPEFLSLYET ERLVQRLAVL DMDCHAIVIN FVLDANAATP CSMCRSRARM QNKYIDQINE LYDDFNIVLS PLRHDEVR G IANLRDYAET LIKPYRFCWS ANPDPSSAK UniProtKB: ATPase ASNA1 homolog, ATPase ASNA1 homolog |
-Macromolecule #2: TMD of the tail-anchored protein Bos1
Macromolecule | Name: TMD of the tail-anchored protein Bos1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 15.860031 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MDHHHHHHEN LYFQSADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDD ALKLANEGKV KEAQAAAEQL KTTRNAYIQK YLLVFWIALI LLIIGIYYVL |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.73 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 2732 / Average exposure time: 1.82 sec. / Average electron dose: 63.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |