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- EMDB-14635: S-layer protein SlaA from Sulfolobus acidocaldarius at pH 4.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-14635
TitleS-layer protein SlaA from Sulfolobus acidocaldarius at pH 4.0
Map data
Sample
  • Organelle or cellular component: Monomeric S-layer protein SlaA with N-glycosylation
    • Protein or peptide: S-layer protein A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 6-deoxy-6-sulfo-beta-D-glucopyranose
KeywordsS-layer / dimer / N-glycosylation / STRUCTURAL PROTEIN
Function / homologyS-layer / extracellular region / S-layer protein A
Function and homology information
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic) / Sulfolobus acidocaldarius (acidophilic)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGambelli L / Isupov MN / 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
DepositionMar 29, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14635.png

Downloads & links

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Map

FileDownload / File: emd_14635.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 224 pix.
= 235.2 Å		1.05 Å/pix.
x 224 pix.
= 235.2 Å		1.05 Å/pix.
x 224 pix.
= 235.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.001727358 - 1.7250183
Average (Standard dev.)0.0014962661 (±0.028229328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 235.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14635_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14635_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Monomeric S-layer protein SlaA with N-glycosylation

EntireName: Monomeric S-layer protein SlaA with N-glycosylation
Components
  • Organelle or cellular component: Monomeric S-layer protein SlaA with N-glycosylation
    • Protein or peptide: S-layer protein A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 6-deoxy-6-sulfo-beta-D-glucopyranose

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Supramolecule #1: Monomeric S-layer protein SlaA with N-glycosylation

SupramoleculeName: Monomeric S-layer protein SlaA with N-glycosylation / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic) / Location in cell: Surface layer

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Macromolecule #1: S-layer protein A

MacromoleculeName: S-layer protein A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Molecular weightTheoretical: 151.078406 KDa
Recombinant expressionOrganism: Sulfolobus acidocaldarius (acidophilic)
SequenceString: MNKLVGLLVS SLFLASILIG IAPAITTTAL TPPVSAGGIQ AYLLTGSGAP ASGLVLFVVN VSNIQVSSSN VTNVISTVVS NIQINAKTE NAQTGATTGS VTVRFPTSGY NAYYDSVDKV VFVVVSFLYP YTTTSVNIPL SYLSKYLPGL LTAQPYDETG A QVTSVSST ...String:
MNKLVGLLVS SLFLASILIG IAPAITTTAL TPPVSAGGIQ AYLLTGSGAP ASGLVLFVVN VSNIQVSSSN VTNVISTVVS NIQINAKTE NAQTGATTGS VTVRFPTSGY NAYYDSVDKV VFVVVSFLYP YTTTSVNIPL SYLSKYLPGL LTAQPYDETG A QVTSVSST PFGSLIDTST GQQILGTNPV LTSYNSYTTQ ANTNMQEGVV SGTLTSFTLG GQSFSGSTVP VILYAPFIFS NS PYQAGLY NPMQVNGNLG SLSSEAYYHP VIWGRALINT TLIDTYASGS VPFTFQLNYS VPGPLTINMA QLAWIASINN LPT SFTYLS YKFSNGYESF LGIISNSTQL TAGALTINPS GNFTINGKKF YVYLLVVGST NSTTPVEYVT KLVVEYPSST NFLP QGVTV TTSSNKYTLP VYEIGGPAGT TITLTGNWYS TPYTVQITVG STPTLTNYVS QILLKAVAYE GINVSTTQSP YYSTA ILST PPSEISITGS STITAQGKLT ATSASATVNL LTNATLTYEN IPLTQYSFNG IIVTPGYAAI NGTTAMAYVI GALYNK TSD YVLSFAGSQE PMQVMNNNLT EVTTLAPFGL TLLAPSVPAT ETGTSPLQLE FFTVPSTSYI ALVDFGLWGN LTSVTVS AY DTVNNKLSVN LGYFYGIVIP PSISTAPYNY QNFICPNNYV TVTIYDPDAV LDPYPSGSFT TSSLPLKYGN MNITGAVI F PGSSVYNPSG VFGYSNFNKG AAVTTFTYTA QSGPFSPVAL TGNTNYLSQY ADNNPTDNYY FIQTVNGMPV LMGGLSIVA SPVSASLPSS TSSPGFMYLL PSAAQVPSPL PGMATPNYNL NIYITYKIDG ATVGNNMING LYVASQNTLI YVVPNGSFVG SNIKLTYTT TDYAVLHYFY STGQYKVFKT VSVPNVTANL YFPSSTTPLY QLSVPLYLSE PYYGSPLPTY IGLGTNGTSL W NSPNYVLF GVSAVQQYLG FIKSISVTLS NGTTVVIPLT TSNMQTLFPQ LVGQELQACN GTFQFGISIT GLEKLLNLNV QQ LNNSILS VTYHDYVTGE TLTATTKLVA LSTLSLVAKG AGVVEFLLTA YPYTGNITFA PPWFIAENVV KQPFMTYSDL QFA KTNPSA ILSLSTVNIT VVGLGGKASV YYNSTSGQTV ITNIYGQTVA TLSGNVLPTL TELAAGNGTF TGSLQFTIVP NNTV VQIPS SLTKTSFAVY TNGSLAIVLN GKAYSLGPAG LFLLPFVTYT GSAIGANATA IITVSDGVGT STTQVPITAE NFTPI RLAP FQVPAQVPLP NAPKLKYEYN GSIVITPQQQ VLKIYVTSIL PYPQEFQIQA FVYEASQFNV HTGSPTAAPV YFSYSA VRA YPALGIGTSV PNLLVYVQLQ GISNLPAGKY VIVLSAVPFA GGPVLSEYPA QLIFTNVTLT Q

UniProtKB: S-layer protein A

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #9: 6-deoxy-6-sulfo-beta-D-glucopyranose

MacromoleculeName: 6-deoxy-6-sulfo-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 1 / Formula: YZT
Molecular weightTheoretical: 244.22 Da
Chemical component information

ChemComp-YZT:
6-deoxy-6-sulfo-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 3.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Grid type: lacey with graphene oxide Blotting paper: Whatman 597.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 59.12 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66040
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7zcx:
S-layer protein SlaA from Sulfolobus acidocaldarius at pH 4.0

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