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- EMDB-18127: S-layer of archaeon Sulfolobus acidocaldarius by subtomogram averaging -

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Basic information

Entry
Database: EMDB / ID: EMD-18127
TitleS-layer of archaeon Sulfolobus acidocaldarius by subtomogram averaging
Map data
Sample
  • Organelle or cellular component: Exosome
    • Other: SlaA S-layer
KeywordsS-layer / protein-protein interactions / protein-membrane interactions / STRUCTURAL PROTEIN
Function / homology
Function and homology information


S-layer / extracellular region / membrane
Similarity search - Function
: / Carboxypeptidase regulatory-like domain / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Carboxypeptidase-like, regulatory domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
S-layer protein A / Conserved membrane protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
Methodsubtomogram averaging / cryo EM / Resolution: 11.2 Å
AuthorsGambelli L / McLaren MJ / Daum B
Funding supportEuropean Union, 1 items
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
DepositionAug 4, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18127.png

Downloads & links

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Map

FileDownload / File: emd_18127.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.5 Å/pix.
x 200 pix.
= 700. Å		3.5 Å/pix.
x 200 pix.
= 700. Å		3.5 Å/pix.
x 200 pix.
= 700. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00509
Minimum - Maximum-0.0101413345 - 0.029858418
Average (Standard dev.)0.00015929922 (±0.0021361394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 700.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18127_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18127_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Exosome

EntireName: Exosome
Components
  • Organelle or cellular component: Exosome
    • Other: SlaA S-layer

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Supramolecule #1: Exosome

SupramoleculeName: Exosome / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic) / Strain: MW001

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Macromolecule #1: SlaA S-layer

MacromoleculeName: SlaA S-layer / type: other / ID: 1 / Classification: other
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic) / Strain: MW001
SequenceString: MNKLVGLLVS SLFLASILIG IAPAITTTAL TPPVSAGGIQ AYLLTGSGAP ASGLVLFVVN VSNIQVSSS NVTNVISTVV SNIQINAKTE NAQTGATTGS VTVRFPTSGY NAYYDSVDKV V FVVVSFLY PYTTTSVNIP LSYLSKYLPG LLTAQPYDET GAQVTSVSST ...String:
MNKLVGLLVS SLFLASILIG IAPAITTTAL TPPVSAGGIQ AYLLTGSGAP ASGLVLFVVN VSNIQVSSS NVTNVISTVV SNIQINAKTE NAQTGATTGS VTVRFPTSGY NAYYDSVDKV V FVVVSFLY PYTTTSVNIP LSYLSKYLPG LLTAQPYDET GAQVTSVSST PFGSLIDTST GQ QILGTNP VLTSYNSYTT QANTNMQEGV VSGTLTSFTL GGQSFSGSTV PVILYAPFIF SNS PYQAGL YNPMQVNGNL GSLSSEAYYH PVIWGRALIN TTLIDTYASG SVPFTFQLNY SVPG PLTIN MAQLAWIASI NNLPTSFTYL SYKFSNGYES FLGIISNSTQ LTAGALTINP SGNFT INGK KFYVYLLVVG STNSTTPVEY VTKLVVEYPS STNFLPQGVT VTTSSNKYTL PVYEIG GPA GTTITLTGNW YSTPYTVQIT VGSTPTLTNY VSQILLKAVA YEGINVSTTQ SPYYSTA IL STPPSEISIT GSSTITAQGK LTATSASATV NLLTNATLTY ENIPLTQYSF NGIIVTPG Y AAINGTTAMA YVIGALYNKT SDYVLSFAGS QEPMQVMNNN LTEVTTLAPF GLTLLAPSV PATETGTSPL QLEFFTVPST SYIALVDFGL WGNLTSVTVS AYDTVNNKLS VNLGYFYGIV IPPSISTAP YNYQNFICPN NYVTVTIYDP DAVLDPYPSG SFTTSSLPLK YGNMNITGAV I FPGSSVYN PSGVFGYSNF NKGAAVTTFT YTAQSGPFSP VALTGNTNYL SQYADNNPTD NY YFIQTVN GMPVLMGGLS IVASPVSASL PSSTSSPGFM YLLPSAAQVP SPLPGMATPN YNL NIYITY KIDGATVGNN MINGLYVASQ NTLIYVVPNG SFVGSNIKLT YTTTDYAVLH YFYS TGQYK VFKTVSVPNV TANLYFPSST TPLYQLSVPL YLSEPYYGSP LPTYIGLGTN GTSLW NSPN YVLFGVSAVQ QYLGFIKSIS VTLSNGTTVV IPLTTSNMQT LFPQLVGQEL QACNGT FQF GISITGLEKL LNLNVQQLNN SILSVTYHDY VTGETLTATT KLVALSTLSL VAKGAGV VE FLLTAYPYTG NITFAPPWFI AENVVKQPFM TYSDLQFAKT NPSAILSLST VNITVVGL G GKASVYYNST SGQTVITNIY GQTVATLSGN VLPTLTELAA GNGTFTGSLQ FTIVPNNTV VQIPSSLTKT SFAVYTNGSL AIVLNGKAYS LGPAGLFLLP FVTYTGSAIG ANATAIITVS DGVGTSTTQ VPITAENFTP IRLAPFQVPA QVPLPNAPKL KYEYNGSIVI TPQQQVLKIY V TSILPYPQ EFQIQAFVYE ASQFNVHTGS PTAAPVYFSY SAVRAYPALG IGTSVPNLLV YV QLQGISN LPAGKYVIVL SAVPFAGGPV LSEYPAQLIF TNVTLTQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy #1

Microscopy ID1
MicroscopeTFS KRIOS
Image recordingImage recording ID: 1 / Film or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 2.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeTFS TALOS
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 2.02 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Image recording ID1
DetailsDatasets were combined after particle-extraction in Relion then refined in M.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.0.9) / Software - details: Relion 3.1 followed by M / Number subtomograms used: 2771
ExtractionNumber tomograms: 86 / Number images used: 22950
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: Warp (ver. 1.0.9)
FSC plot (resolution estimation)

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