National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
1R01GM130051-01
United States
Citation
Journal: Elife / Year: 2020 Title: An ER translocon for multi-pass membrane protein biogenesis. Authors: Philip T McGilvray / S Andrei Anghel / Arunkumar Sundaram / Frank Zhong / Michael J Trnka / James R Fuller / Hong Hu / Alma L Burlingame / Robert J Keenan / Abstract: Membrane proteins with multiple transmembrane domains play critical roles in cell physiology, but little is known about the machinery coordinating their biogenesis at the endoplasmic reticulum. Here ...Membrane proteins with multiple transmembrane domains play critical roles in cell physiology, but little is known about the machinery coordinating their biogenesis at the endoplasmic reticulum. Here we describe a ~ 360 kDa ribosome-associated complex comprising the core Sec61 channel and five accessory factors: TMCO1, CCDC47 and the Nicalin-TMEM147-NOMO complex. Cryo-electron microscopy reveals a large assembly at the ribosome exit tunnel organized around a central membrane cavity. Similar to protein-conducting channels that facilitate movement of transmembrane segments, cytosolic and luminal funnels in TMCO1 and TMEM147, respectively, suggest routes into the central membrane cavity. High-throughput mRNA sequencing shows selective translocon engagement with hundreds of different multi-pass membrane proteins. Consistent with a role in multi-pass membrane protein biogenesis, cells lacking different accessory components show reduced levels of one such client, the glutamate transporter EAAT1. These results identify a new human translocon and provide a molecular framework for understanding its role in multi-pass membrane protein biogenesis.
History
Deposition
Feb 21, 2020
-
Header (metadata) release
Mar 25, 2020
-
Map release
Sep 2, 2020
-
Update
Sep 2, 2020
-
Current status
Sep 2, 2020
Processing site: RCSB / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Entire : Native complex of a translating ribosome and a novel translocon c...
Entire
Name: Native complex of a translating ribosome and a novel translocon containing the Sec61 complex, TMEM147, NOMO, Nicalin, CCDC47, and TMCO1
Components
Complex: Native complex of a translating ribosome and a novel translocon containing the Sec61 complex, TMEM147, NOMO, Nicalin, CCDC47, and TMCO1
Complex: Translocon
Complex: Sec61 Complex
Complex: Sec61 alpha
Complex: Sec61 beta
Complex: Sec61 gamma
Complex: TMCO1
Complex: NOMO-Nicalin-TMEM147 Complex
Complex: TMEM147
Complex: Nicalin
Complex: NOMO
Complex: CCDC47
+
Supramolecule #1: Native complex of a translating ribosome and a novel translocon c...
Supramolecule
Name: Native complex of a translating ribosome and a novel translocon containing the Sec61 complex, TMEM147, NOMO, Nicalin, CCDC47, and TMCO1 type: complex / ID: 1 / Parent: 0
Source (natural)
Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum
Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum
+
Supramolecule #12: NOMO
Supramolecule
Name: NOMO / type: complex / ID: 12 / Parent: 5
Source (natural)
Organism: Homo sapiens (human) / Organ: Kidney / Cell: HEK293 / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum
-
Experimental details
-
Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
-
Sample preparation
Concentration
0.4 mg/mL
Buffer
pH: 7.4 Component:
Concentration
Formula
Name
150.0 mM
C2H3KO2
potassium acetate
50.0 mM
C8H18N2O4S
HEPES, pH 7.4
5.0 mM
MgCl2
magnesium chloride
0.25 percent (w/v)
C56H92O29
digitonin
Grid
Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: Two filter papers were added to each arm, 2.5 microliters of sample were added to grids, samples were blotted for 11 seconds, and 0.5 second of drain time was allowed before vitrification..
Details
Sample was well-dispersed on a thin (~2 nm) carbon film.
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 5562 / Average exposure time: 3.8 sec. / Average electron dose: 50.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron optics
Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi