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- PDB-8qp0: A hexamer pore in the S-layer of Sulfolobus acidocaldarius formed... -

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Basic information

Entry
Database: PDB / ID: 8qp0
TitleA hexamer pore in the S-layer of Sulfolobus acidocaldarius formed by SlaA protein
ComponentsS-layer protein A
KeywordsSTRUCTURAL PROTEIN / S-layer / dimer / N-glycosylation / archea
Function / homology: / S-layer / extracellular region / S-layer protein A
Function and homology information
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 11.2 Å
AuthorsGambelli, L. / McLaren, M. / Isupov, M. / Conners, R. / Daum, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)803894European Union
CitationJournal: Elife / Year: 2024
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
DepositionSep 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-layer protein A
D: S-layer protein A
E: S-layer protein A
F: S-layer protein A
G: S-layer protein A
H: S-layer protein A


Theoretical massNumber of molelcules
Total (without water)906,4706
Polymers906,4706
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
S-layer protein A / Surface layer large protein


Mass: 151078.406 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J6E5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: S-layer of Sulfolobus acidocaldarius / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Buffer solutionpH: 4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6000 nm / Nominal defocus min: 4000 nm / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1

IDAccelerating voltage (kV)Model
1300FEI TITAN KRIOS
2200TFS TALOS
Image recording
IDImaging-IDElectron dose (e/Å2)Avg electron dose per subtomogram (e/Å2)Film or detector model
112.0283TFS FALCON 4i (4k x 4k)
222.0283GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImaging-IDDetails
2FEI tomography4image acquisition1
4Warp1.0.9CTF correction
9FEI tomography4image acquisition2
11Warp1.0.9final Euler assignment
13Warp1.0.93D reconstructionRelion 3.1 followed by M
14PHENIX1.20.1_4487:model refinement
Image processingDetails: Datasets were combined after particle-extraction in Relion then refined in M.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 11.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2271 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 86 / Num. of volumes extracted: 22950
Atomic model buildingPDB-ID: 7ZCX

7zcx


Accession code: 7ZCX / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00264494
ELECTRON MICROSCOPYf_angle_d0.67688830
ELECTRON MICROSCOPYf_dihedral_angle_d5.2868976
ELECTRON MICROSCOPYf_chiral_restr0.04510812
ELECTRON MICROSCOPYf_plane_restr0.00511244

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