+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40245 | |||||||||
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Title | Human ER membrane protein complex (EMC) in GDN, 9-subunit map | |||||||||
Map data | Full map file | |||||||||
Sample |
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Keywords | Insertase / endoplasmic reticulum / transmembrane chaperone / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity ...extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / protein folding in endoplasmic reticulum / copper ion transport / autophagosome assembly / RHOA GTPase cycle / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / early endosome membrane / carbohydrate binding / angiogenesis / early endosome / Golgi membrane / apoptotic process / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Tomaleri GP / Nguyen VN / Januszyk K / Voorhees RM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Cell Biol / Year: 2023 Title: A selectivity filter in the ER membrane protein complex limits protein misinsertion at the ER. Authors: Tino Pleiner / Masami Hazu / Giovani Pinton Tomaleri / Vy N Nguyen / Kurt Januszyk / Rebecca M Voorhees / Abstract: Tail-anchored (TA) proteins play essential roles in mammalian cells, and their accurate localization is critical for proteostasis. Biophysical similarities lead to mistargeting of mitochondrial TA ...Tail-anchored (TA) proteins play essential roles in mammalian cells, and their accurate localization is critical for proteostasis. Biophysical similarities lead to mistargeting of mitochondrial TA proteins to the ER, where they are delivered to the insertase, the ER membrane protein complex (EMC). Leveraging an improved structural model of the human EMC, we used mutagenesis and site-specific crosslinking to map the path of a TA protein from its cytosolic capture by methionine-rich loops to its membrane insertion through a hydrophilic vestibule. Positively charged residues at the entrance to the vestibule function as a selectivity filter that uses charge-repulsion to reject mitochondrial TA proteins. Similarly, this selectivity filter retains the positively charged soluble domains of multipass substrates in the cytosol, thereby ensuring they adopt the correct topology and enforcing the "positive-inside" rule. Substrate discrimination by the EMC provides a biochemical explanation for one role of charge in TA protein sorting and protects compartment integrity by limiting protein misinsertion. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40245.map.gz | 121.4 MB | EMDB map data format | |
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Header (meta data) | emd-40245-v30.xml emd-40245.xml | 29 KB 29 KB | Display Display | EMDB header |
Images | emd_40245.png | 110.1 KB | ||
Masks | emd_40245_msk_1.map | 244.1 MB | Mask map | |
Others | emd_40245_additional_1.map.gz emd_40245_half_map_1.map.gz emd_40245_half_map_2.map.gz | 124.8 MB 226.8 MB 226.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40245 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40245 | HTTPS FTP |
-Validation report
Summary document | emd_40245_validation.pdf.gz | 931.9 KB | Display | EMDB validaton report |
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Full document | emd_40245_full_validation.pdf.gz | 931.4 KB | Display | |
Data in XML | emd_40245_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_40245_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40245 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40245 | HTTPS FTP |
-Related structure data
Related structure data | 8s9sMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40245.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Full map file | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40245_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharped Full map file
File | emd_40245_additional_1.map | ||||||||||||
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Annotation | Sharped Full map file | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map A
File | emd_40245_half_map_1.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B
File | emd_40245_half_map_2.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human ER Membrane Protein Complex
+Supramolecule #1: Human ER Membrane Protein Complex
+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: Membrane magnesium transporter 1
+Macromolecule #6: ER membrane protein complex subunit 6
+Macromolecule #7: ER membrane protein complex subunit 7
+Macromolecule #8: ER membrane protein complex subunit 8
+Macromolecule #9: ER membrane protein complex subunit 10
+Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #12: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | Sample solubilized and purified in GDN |
-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 grids imaged: 2 / Number real images: 11822 / Average exposure time: 2.66 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8s9s: |