- EMDB-21929: Human ER membrane protein complex in a lipid nanodisc, overall map -
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Open data
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Basic information
Entry
Database: EMDB / ID: EMD-21929
Title
Human ER membrane protein complex in a lipid nanodisc, overall map
Map data
'Overall' human EMC post-processed, sharpened, and masked map.
Sample
Complex: Human ER Membrane Protein Complex
Protein or peptide: ER membrane protein complex subunit 1
Protein or peptide: ER membrane protein complex subunit 2
Protein or peptide: ER membrane protein complex subunit 3
Protein or peptide: ER Membrane Protein Complex Subunit 4
Protein or peptide: Membrane magnesium transporter 1
Protein or peptide: ER membrane protein complex subunit 6
Protein or peptide: ER membrane protein complex subunit 7
Protein or peptide: ER membrane protein complex subunit 8
Protein or peptide: ER membrane protein complex subunit 10
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function
ER membrane protein complex subunit 8/9 / Uncharacterised protein family (UPF0172) / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 ...ER membrane protein complex subunit 8/9 / Uncharacterised protein family (UPF0172) / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6-like / EMC6 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 2-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / Carbohydrate-binding-like fold / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Tetratricopeptide repeat / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat region circular profile. / TPR repeat profile. / MPN domain / MPN domain profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily Similarity search - Domain/homology
ER membrane protein complex subunit 8 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6 / Endoplasmic reticulum membrane protein complex subunit 7 / ER membrane protein complex subunit 3 Similarity search - Component
Biological species
Homo sapiens (human) / Human (human)
Method
single particle reconstruction / cryo EM / Resolution: 3.4 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
DP2GM137412
United States
Citation
Journal: Science / Year: 2020 Title: Structural basis for membrane insertion by the human ER membrane protein complex. Authors: Tino Pleiner / Giovani Pinton Tomaleri / Kurt Januszyk / Alison J Inglis / Masami Hazu / Rebecca M Voorhees / Abstract: A defining step in the biogenesis of a membrane protein is the insertion of its hydrophobic transmembrane helices into the lipid bilayer. The nine-subunit endoplasmic reticulum (ER) membrane protein ...A defining step in the biogenesis of a membrane protein is the insertion of its hydrophobic transmembrane helices into the lipid bilayer. The nine-subunit endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved co- and posttranslational insertase at the ER. We determined the structure of the human EMC in a lipid nanodisc to an overall resolution of 3.4 angstroms by cryo-electron microscopy, permitting building of a nearly complete atomic model. We used structure-guided mutagenesis to demonstrate that substrate insertion requires a methionine-rich cytosolic loop and occurs via an enclosed hydrophilic vestibule within the membrane formed by the subunits EMC3 and EMC6. We propose that the EMC uses local membrane thinning and a positively charged patch to decrease the energetic barrier for insertion into the bilayer.
History
Deposition
May 8, 2020
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Header (metadata) release
May 27, 2020
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Map release
May 27, 2020
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Update
Aug 5, 2020
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Current status
Aug 5, 2020
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Sample solubilized and purified in DDM, then reconstituted into lipid nanodisc.
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Electron microscopy
Microscope
FEI TITAN KRIOS
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: 10 / Number real images: 6345 / Average exposure time: 2.0 sec. / Average electron dose: 59.2 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Calibrated magnification: 59808 / Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal magnification: 130000
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