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Yorodumi- EMDB-23003: Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23003 | |||||||||
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Title | Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to Fab-DH4 in lipid nanodiscs | |||||||||
Map data | sharpened EM map of yEMC in lipid nanodiscs | |||||||||
Sample |
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Function / homology | Function and homology information EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / protein folding in endoplasmic reticulum / phospholipid transport / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phospholipid metabolic process / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane ...EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / protein folding in endoplasmic reticulum / phospholipid transport / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phospholipid metabolic process / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Miller-Vedam LE / Schirle Oakdale NS / Braeuning B / Boydston EA / Sevillano N / Popova KD / Bonnar JL / Shurtleff MJ / Prabu JR / Stroud RM ...Miller-Vedam LE / Schirle Oakdale NS / Braeuning B / Boydston EA / Sevillano N / Popova KD / Bonnar JL / Shurtleff MJ / Prabu JR / Stroud RM / Craik CS / Schulman BA / Weissman JS / Frost A | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2020 Title: Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. Authors: Lakshmi E Miller-Vedam / Bastian Bräuning / Katerina D Popova / Nicole T Schirle Oakdale / Jessica L Bonnar / Jesuraj R Prabu / Elizabeth A Boydston / Natalia Sevillano / Matthew J ...Authors: Lakshmi E Miller-Vedam / Bastian Bräuning / Katerina D Popova / Nicole T Schirle Oakdale / Jessica L Bonnar / Jesuraj R Prabu / Elizabeth A Boydston / Natalia Sevillano / Matthew J Shurtleff / Robert M Stroud / Charles S Craik / Brenda A Schulman / Adam Frost / Jonathan S Weissman / Abstract: Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player ...Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes. | |||||||||
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_23003.map.gz | 378.8 MB | EMDB map data format | |
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Header (meta data) | emd-23003-v30.xml emd-23003.xml | 32.5 KB 32.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23003_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_23003.png | 94.2 KB | ||
Masks | emd_23003_msk_1.map | 421.9 MB | Mask map | |
Others | emd_23003_additional_1.map.gz emd_23003_additional_2.map.gz emd_23003_additional_3.map.gz | 337.9 MB 338.4 MB 338.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23003 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23003 | HTTPS FTP |
-Validation report
Summary document | emd_23003_validation.pdf.gz | 465.5 KB | Display | EMDB validaton report |
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Full document | emd_23003_full_validation.pdf.gz | 465 KB | Display | |
Data in XML | emd_23003_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_23003_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23003 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23003 | HTTPS FTP |
-Related structure data
Related structure data | 7kraMC 7adoC 7adpC 7ktxC 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_23003.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened EM map of yEMC in lipid nanodiscs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.853 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23003_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened EM map of yEMC in lipid nanodiscs
File | emd_23003_additional_1.map | ||||||||||||
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Annotation | unsharpened EM map of yEMC in lipid nanodiscs | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: half EM map 1 of yEMC in lipid nanodiscs
File | emd_23003_additional_2.map | ||||||||||||
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Annotation | half EM map 1 of yEMC in lipid nanodiscs | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: half EM map 2 of yEMC in lipid nanodiscs
File | emd_23003_additional_3.map | ||||||||||||
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Annotation | half EM map 2 of yEMC in lipid nanodiscs | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : S. cerevisiae endoplasmic reticulum membrane protein complex (EMC...
+Supramolecule #1: S. cerevisiae endoplasmic reticulum membrane protein complex (EMC...
+Supramolecule #2: endoplasmic reticulum membrane protein complex
+Supramolecule #3: Fab DH4
+Macromolecule #1: ER membrane protein complex subunit 1
+Macromolecule #2: ER membrane protein complex subunit 2
+Macromolecule #3: ER membrane protein complex subunit 3
+Macromolecule #4: ER membrane protein complex subunit 4
+Macromolecule #5: ER membrane protein complex subunit 5
+Macromolecule #6: ER membrane protein complex subunit 6
+Macromolecule #7: Protein SOP4
+Macromolecule #8: Endoplasmic reticulum membrane protein complex subunit 10
+Macromolecule #9: Fab DH4 heavy chain
+Macromolecule #10: Fab DH4 light chain
+Macromolecule #11: Unassigned helix
+Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #13: [(2~{R})-1-octanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)et...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Dataset 1 collected on FEI Titan Krios at UCSF on July 2nd, 2019. |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7kra: |