+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21388 | |||||||||
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Title | Structure of G-alpha-i bound to its chaperone Ric-8A | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information cell-cell adhesion involved in gastrulation / cell migration involved in gastrulation / basement membrane organization / vasculature development / G-protein alpha-subunit binding / T cell migration / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding ...cell-cell adhesion involved in gastrulation / cell migration involved in gastrulation / basement membrane organization / vasculature development / G-protein alpha-subunit binding / T cell migration / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / guanyl-nucleotide exchange factor activity / Regulation of insulin secretion / G protein-coupled receptor binding / visual learning / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / response to peptide hormone / ADP signalling through P2Y purinoceptor 12 / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / GDP binding / heterotrimeric G-protein complex / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / in utero embryonic development / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / lysosomal membrane / cell division / GTPase activity / centrosome / GTP binding / nucleolus / magnesium ion binding / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus/Homo sapiens (Norway rat) / Rattus norvegicus (Norway rat) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.14 Å | |||||||||
Authors | Seven AB / Hilger D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Rep / Year: 2020 Title: Structures of Gα Proteins in Complex with Their Chaperone Reveal Quality Control Mechanisms. Authors: Alpay Burak Seven / Daniel Hilger / Makaía M Papasergi-Scott / Li Zhang / Qianhui Qu / Brian K Kobilka / Gregory G Tall / Georgios Skiniotis / Abstract: Many chaperones promote nascent polypeptide folding followed by substrate release through ATP-dependent conformational changes. Here we show cryoEM structures of Gα subunit folding intermediates in ...Many chaperones promote nascent polypeptide folding followed by substrate release through ATP-dependent conformational changes. Here we show cryoEM structures of Gα subunit folding intermediates in complex with full-length Ric-8A, a unique chaperone-client system in which substrate release is facilitated by guanine nucleotide binding to the client G protein. The structures of Ric-8A-Gα and Ric-8A-Gα complexes reveal that the chaperone employs its extended C-terminal region to cradle the Ras-like domain of Gα, positioning the Ras core in contact with the Ric-8A core while engaging its switch2 nucleotide binding region. The C-terminal α5 helix of Gα is held away from the Ras-like domain through Ric-8A core domain interactions, which critically depend on recognition of the Gα C terminus by the chaperone. The structures, complemented with biochemical and cellular chaperoning data, support a folding quality control mechanism that ensures proper formation of the C-terminal α5 helix before allowing GTP-gated release of Gα from Ric-8A. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21388.map.gz | 14.6 MB | EMDB map data format | |
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Header (meta data) | emd-21388-v30.xml emd-21388.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_21388.png | 134.6 KB | ||
Others | emd_21388_half_map_1.map.gz emd_21388_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21388 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21388 | HTTPS FTP |
-Validation report
Summary document | emd_21388_validation.pdf.gz | 663.3 KB | Display | EMDB validaton report |
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Full document | emd_21388_full_validation.pdf.gz | 662.9 KB | Display | |
Data in XML | emd_21388_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | emd_21388_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21388 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21388 | HTTPS FTP |
-Related structure data
Related structure data | 6vu8MC 6vu5C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21388.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_21388_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_21388_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Ric-8A with G alpha q
Entire | Name: Complex of Ric-8A with G alpha q |
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Components |
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-Supramolecule #1: Complex of Ric-8A with G alpha q
Supramolecule | Name: Complex of Ric-8A with G alpha q / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Rattus norvegicus/Homo sapiens (Norway rat) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-Macromolecule #1: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)
Macromolecule | Name: Resistance to inhibitors of cholinesterase 8 homolog A (C. elegans) type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 60.512094 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: QGEFMEPRAV ADALETGEED AVTEALRSFN REHSQSFTFD DAQQEDRKRL AKLLVSVLEQ GLSPKHRVTW LQTIRILSRD RSCLDSFAS RQSLHALACY ADIAISEEPI PQPPDMDVLL ESLKCLCNLV LSSPTAQMLA AEARLVVRLA ERVGLYRKRS Y PHEVQFFD ...String: QGEFMEPRAV ADALETGEED AVTEALRSFN REHSQSFTFD DAQQEDRKRL AKLLVSVLEQ GLSPKHRVTW LQTIRILSRD RSCLDSFAS RQSLHALACY ADIAISEEPI PQPPDMDVLL ESLKCLCNLV LSSPTAQMLA AEARLVVRLA ERVGLYRKRS Y PHEVQFFD LRLLFLLTAL RTDVRQQLFQ ELHGVRLLTD ALELTLGVAP KENPLVILPA QETERAMEIL KVLFNITFDS VK REVDEED AALYRYLGTL LRHCVMADAA GDRTEEFHGH TVNLLGNLPL KCLDVLLALE LHEGSLEFMG VNMDVINALL AFL EKRLHQ THRLKECVAP VLSVLTECAR MHRPARKFLK AQVLPPLRDV RTRPEVGDLL RNKLVRLMTH LDTDVKRVAA EFLF VLCSE SVPRFIKYTG YGNAAGLLAA RGLMAGGRPE GQY(SEP)EDED(TPO)D TEEYREAKAS INPVTGRVEE KPPNPME GM TEEQKEHEAM KLVNMFDKLS RHRLIQPMGM SPRGHLTSLQ DAMCETMEGQ LSSDPDSDPD |
-Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1
Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-1 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 41.112715 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GCTLSAEDKA AVERSKMIDR NLREDGEKAA REVKLLLLGA GESGKSTIVK QMKIIHEAGY SEEECKQYKA VVYSNTIQSI IAIIRAMGR LKIDFGDSAR ADDARQLFVL AGAAEEGFMH HHHHHTAELA GVIKRLWKDS GVQACFNRSR EYQLNDSAAY Y LNDLDRIA ...String: GCTLSAEDKA AVERSKMIDR NLREDGEKAA REVKLLLLGA GESGKSTIVK QMKIIHEAGY SEEECKQYKA VVYSNTIQSI IAIIRAMGR LKIDFGDSAR ADDARQLFVL AGAAEEGFMH HHHHHTAELA GVIKRLWKDS GVQACFNRSR EYQLNDSAAY Y LNDLDRIA QPNYIPTQQD VLRTRVKTTG IVETHFTFKD LHFKMFDVGG QRSERKKWIH CFEGVTAIIF CVALSDYDLV LA EDEEMNR MHESMKLFDS ICNNKWFTDT SIILFLNKKD LFEEKIKKSP LTICYPEYAG SNTYEEAAAY IQCQFEDLNK RKD TKEIYT HFTCATDTKN VQFVFDAVTD VIIKNNLKDC GLF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 153110 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |