[English] 日本語
![](img/lk-miru.gif)
- PDB-7kat: Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 po... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7kat | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore ring and Sec63 FN3 double mutant, class without Sec62 | ||||||
![]() |
| ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() protein transmembrane import into intracellular organelle / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Itskanov, S. / Park, E. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62. Authors: Samuel Itskanov / Katie M Kuo / James C Gumbart / Eunyong Park / ![]() Abstract: Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their ...Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their functions are poorly defined. In the present study, we determined cryo-electron microscopy (cryo-EM) structures of several variants of Sec61-Sec62-Sec63 complexes from Saccharomyces cerevisiae and Thermomyces lanuginosus and show that Sec62 and Sec63 induce opening of the Sec61 channel. Without Sec62, the translocation pore of Sec61 remains closed by the plug domain, rendering the channel inactive. We further show that the lateral gate of Sec61 must first be partially opened by interactions between Sec61 and Sec63 in cytosolic and luminal domains, a simultaneous disruption of which completely closes the channel. The structures and molecular dynamics simulations suggest that Sec62 may also prevent lipids from invading the channel through the open lateral gate. Our study shows how Sec63 and Sec62 work together in a hierarchical manner to activate Sec61 for post-translational protein translocation. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 250.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 194.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 22783MC ![]() 7kahC ![]() 7kaiC ![]() 7kajC ![]() 7kakC ![]() 7kalC ![]() 7kamC ![]() 7kanC ![]() 7kaoC ![]() 7kapC ![]() 7kaqC ![]() 7karC ![]() 7kasC ![]() 7kauC ![]() 7kb5C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein transport protein ... , 3 types, 3 molecules ACB
#1: Protein | ![]() Mass: 52936.086 Da / Num. of mol.: 1 / Mutation: M90L/T185I/M294I/M450L / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() Plasmid details: Mutant SEC63 is tagged with TEV-GFP and recombinantly expressed Strain: ATCC 204508 / S288c / References: UniProt: P32915 |
---|---|
#2: Protein | ![]() Mass: 8958.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() Plasmid details: Mutant SEC63 is tagged with TEV-GFP and recombinantly expressed Strain: ATCC 204508 / S288c / References: UniProt: P35179 |
#3: Protein | ![]() Mass: 8723.155 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SBH1, SEB1, YER087C-B, YER087BC / Production host: ![]() ![]() ![]() |
-Protein , 1 types, 1 molecules D
#4: Protein | ![]() Mass: 76312.039 Da / Num. of mol.: 1 / Mutation: E440R/F481S/del(441-447) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SEC63, NPL1, PTL1, YOR254C / Production host: ![]() ![]() ![]() |
---|
-Translocation protein ... , 2 types, 2 molecules EF
#5: Protein | Mass: 24263.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() Plasmid details: Mutant SEC63 is tagged with TEV-GFP and recombinantly expressed Strain: ATCC 204508 / S288c / References: UniProt: P33754 |
---|---|
#6: Protein | Mass: 21631.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() Plasmid details: Mutant SEC63 is tagged with TEV-GFP and recombinantly expressed Strain: ATCC 204508 / S288c / References: UniProt: P39742 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
-
Sample preparation
Component | Name: Endoplasmic reticulum protein-transport machinery Sec complex from yeast![]() Type: COMPLEX Details: Sec63 has the following mutations: E440R/F481S/del(441-447) Sec61 has the following mutations: M90L/T185I/M294I/M450L Entity ID: all / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 48.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name![]() |
-
Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 267541 / Details: autopicked particles | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32704 / Algorithm: FOURIER SPACE / Details: Non-uniform refinement from cryoSPARC / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Refine LS restraints |
|