[English] 日本語
![](img/lk-miru.gif)
- PDB-8qox: Two-component assembly of SlaA and SlaB S-layer proteins of Sulfo... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8qox | ||||||
---|---|---|---|---|---|---|---|
Title | Two-component assembly of SlaA and SlaB S-layer proteins of Sulfolobus acidocaldarius | ||||||
![]() |
| ||||||
![]() | STRUCTURAL PROTEIN / S-layer / dimer / N-glycosylation | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 11.2 Å | ||||||
![]() | Gambelli, L. / McLaren, M. / Isupov, M. / Conners, R. / Daum, B. | ||||||
Funding support | European Union, 1items
| ||||||
![]() | ![]() Title: Structure of the two-component S-layer of the archaeon . Authors: Lavinia Gambelli / Mathew McLaren / Rebecca Conners / Kelly Sanders / Matthew C Gaines / Lewis Clark / Vicki A M Gold / Daniel Kattnig / Mateusz Sikora / Cyril Hanus / Michail N Isupov / Bertram Daum / ![]() ![]() ![]() ![]() Abstract: Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell ...Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single-particle cryo electron microscopy, cryo electron tomography, and Alphafold2 predictions to generate an atomic model of the two-component S-layer of . The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes in SlaA play important roles in S-layer assembly. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 182 KB | Display | |
Data in CIF | ![]() | 285 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18127MC ![]() 7zcxC ![]() 8an2C ![]() 8an3C ![]() 8qp0C C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 151078.406 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q4J6E5 #2: Protein | Mass: 49560.953 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q4J6E6 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging |
-
Sample preparation
Component | Name: Two component S-layer ofSulfolobus acidocaldarius. / Type: COMPLEX / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM imaging | Cryogen: NITROGEN / Electron source:
| |||||||||||||||
Image recording |
|
-
Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Image processing | Details: Datasets were combined after particle-extraction in Relion then refined in M. | ||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 11.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2771 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 86 / Num. of volumes extracted: 22950 | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|