+
Open data
-
Basic information
Entry | Database: PDB / ID: 5mg3 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | EM fitted model of bacterial holo-translocon | ||||||||||||
![]() |
| ||||||||||||
![]() | CHAPERONE / holotranslocon / membrane protein insertion machinery / protein secretion | ||||||||||||
Function / homology | ![]() protein localization to chloroplast / protein insertion into membrane from inner side / membrane insertase activity / thylakoid membrane organization / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation ...protein localization to chloroplast / protein insertion into membrane from inner side / membrane insertase activity / thylakoid membrane organization / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / protein insertion into membrane / protein secretion / protein transmembrane transporter activity / protein targeting / intracellular protein transport / protein transport / protein folding / protein-containing complex assembly / membrane => GO:0016020 / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14 Å | ||||||||||||
![]() | Schaffitzel, C. / Botte, M. | ||||||||||||
Funding support | ![]() ![]() ![]()
| ||||||||||||
![]() | ![]() Title: A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion. Authors: Mathieu Botte / Nathan R Zaccai / Jelger Lycklama À Nijeholt / Remy Martin / Kèvin Knoops / Gabor Papai / Juan Zou / Aurélien Deniaud / Manikandan Karuppasamy / Qiyang Jiang / Abhishek ...Authors: Mathieu Botte / Nathan R Zaccai / Jelger Lycklama À Nijeholt / Remy Martin / Kèvin Knoops / Gabor Papai / Juan Zou / Aurélien Deniaud / Manikandan Karuppasamy / Qiyang Jiang / Abhishek Singha Roy / Klaus Schulten / Patrick Schultz / Juri Rappsilber / Giuseppe Zaccai / Imre Berger / Ian Collinson / Christiane Schaffitzel / ![]() ![]() ![]() ![]() Abstract: The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein ...The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an integrative approach combining small-angle neutron scattering (SANS), low-resolution electron microscopy and biophysical analyses we determined the arrangement of the proteins and lipids within the super-complex. The results guided the placement of X-ray structures of individual HTL components and allowed the proposal of a model of the functional translocon. Their arrangement around a central lipid-containing pool conveys an unexpected, but compelling mechanism for membrane-protein insertion. The periplasmic domains of YidC and SecD are poised at the protein-channel exit-site of SecY, presumably to aid the emergence of translocating polypeptides. The SecY lateral gate for membrane-insertion is adjacent to the membrane 'insertase' YidC. Absolute-scale SANS employing a novel contrast-match-point analysis revealed a dynamic complex adopting open and compact configurations around an adaptable central lipid-filled chamber, wherein polytopic membrane-proteins could fold, sheltered from aggregation and proteolysis. | ||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 572.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 449.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 744.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 804.9 KB | Display | |
Data in XML | ![]() | 54.1 KB | Display | |
Data in CIF | ![]() | 83 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3506MC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein translocase subunit ... , 4 types, 4 molecules YEDF
#1: Protein | Mass: 50410.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 15248.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 67687.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Protein | Mass: 35413.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein , 2 types, 2 molecules GC
#3: Protein | Mass: 14326.448 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#6: Protein | Mass: 62658.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: bacterial holo-translocon (HTL) / Type: COMPLEX Details: Membrane Protein Complex consisting of SecYEG-SecDFYajC-YidC Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.25 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 5 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k) |
-
Processing
EM software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 84732 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53648 / Symmetry type: POINT |