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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11058 | ||||||||||||
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Title | Human ER Membrane protein Complex (EMC)![]() | ||||||||||||
![]() | 3D reconstruction of the human ER-Membrane Complex produced by single particle cryo-electron microscopy. | ||||||||||||
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Function / homology | ![]() inorganic cation transmembrane transporter activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Phillips BP / O'Donnell JP | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The architecture of EMC reveals a path for membrane protein insertion. Authors: John P O'Donnell / Ben P Phillips / Yuichi Yagita / Szymon Juszkiewicz / Armin Wagner / Duccio Malinverni / Robert J Keenan / Elizabeth A Miller / Ramanujan S Hegde / ![]() ![]() Abstract: Approximately 25% of eukaryotic genes code for integral membrane proteins that are assembled at the endoplasmic reticulum. An abundant and widely conserved multi-protein complex termed EMC has been ...Approximately 25% of eukaryotic genes code for integral membrane proteins that are assembled at the endoplasmic reticulum. An abundant and widely conserved multi-protein complex termed EMC has been implicated in membrane protein biogenesis, but its mechanism of action is poorly understood. Here, we define the composition and architecture of human EMC using biochemical assays, crystallography of individual subunits, site-specific photocrosslinking, and cryo-EM reconstruction. Our results suggest that EMC's cytosolic domain contains a large, moderately hydrophobic vestibule that can bind a substrate's transmembrane domain (TMD). The cytosolic vestibule leads into a lumenally-sealed, lipid-exposed intramembrane groove large enough to accommodate a single substrate TMD. A gap between the cytosolic vestibule and intramembrane groove provides a potential path for substrate egress from EMC. These findings suggest how EMC facilitates energy-independent membrane insertion of TMDs, explain why only short lumenal domains are translocated by EMC, and constrain models of EMC's proposed chaperone function. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.5 KB 20.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.1 KB | Display | ![]() |
Images | ![]() | 35.7 KB | ||
Masks | ![]() | 42.9 MB | ![]() | |
Others | ![]() ![]() | 39.8 MB 39.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z3wMC ![]() 6y4lC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 3D reconstruction of the human ER-Membrane Complex produced by single particle cryo-electron microscopy. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half map A, produced during local resolution estimation...
File | emd_11058_half_map_1.map | ||||||||||||
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Annotation | Half map A, produced during local resolution estimation in CryoSPARC and used to calculate FSC for human ER-Membrane Complex 3D reconstruction. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B, produced during local resolution estimation...
File | emd_11058_half_map_2.map | ||||||||||||
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Annotation | Half map B, produced during local resolution estimation in CryoSPARC and used to calculate FSC for human ER-Membrane Complex 3D reconstruction. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human ER Membrane protein Complex (EMC)
Entire | Name: Human ER Membrane protein Complex (EMC)![]() |
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Components |
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-Supramolecule #1: Human ER Membrane protein Complex (EMC)
Supramolecule | Name: Human ER Membrane protein Complex (EMC) / type: complex / ID: 1 / Parent: 0 / Details: 9-subunit human ER Membrane protein Complex (EMC) |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Experimental: 330 KDa |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.85 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 4e-05 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: LEICA PLUNGER | |||||||||||||||
Details | This sample was purified from suspension adapted human HEK293 cells and was monodisperse on EM grids. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 84.0 K / Max: 93.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-44 / Number grids imaged: 5 / Number real images: 11626 / Average exposure time: 11.0 sec. / Average electron dose: 39.36 e/Å2 Details: Data collected across 5 independent sessions using two different FEI Titan Krios Microscopes, both equipped with a Gatan K2 Summit detector and volta phase plate. Volta phase plate used ...Details: Data collected across 5 independent sessions using two different FEI Titan Krios Microscopes, both equipped with a Gatan K2 Summit detector and volta phase plate. Volta phase plate used without charging between exposures. Phase plate evolution varied between different microscopes used to collect data but positions were shifted once phase evolution progressed past 120 degrees. |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |