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

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Basic information

Entry
Database: PDB / ID: 7zcx
TitleS-layer protein SlaA from Sulfolobus acidocaldarius at pH 4.0
ComponentsS-layer protein A
KeywordsSTRUCTURAL PROTEIN / S-layer / dimer / N-glycosylation
Function / homology: / S-layer / extracellular region / 6-deoxy-6-sulfo-beta-D-glucopyranose / S-layer protein A
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGambelli, L. / Isupov, M.N. / 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
DepositionMar 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 2.0Feb 21, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_branch_scheme / refine / struct_conn
Item: _atom_site.auth_asym_id / _citation.country ..._atom_site.auth_asym_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_branch_scheme.pdb_asym_id / _refine.ls_d_res_high / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id
Revision 2.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: S-layer protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,37621
Polymers151,0781
Non-polymers16,29820
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules AAA

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


Mass: 151078.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: slaA, slp1, Saci_2355 / Production host: Sulfolobus acidocaldarius (acidophilic) / References: UniProt: Q4J6E5

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Sugars , 8 types, 20 molecules

#2: Polysaccharide 6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D- ...6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 812.746 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_6*SO/2=O/2=O][a1122h-1a_1-5]/1-1-2-3/a4-b1_b3-c1_b6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Glcp6SH]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-glucopyranose-(1-4)-6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)] ...beta-D-glucopyranose-(1-4)-6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1137.028 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_6*SO/2=O/2=O][a2122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-4-4/a4-b1_b3-c1_b4-e1_b6-f1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Glcp6SH]{[(4+1)][b-D-Glcp]{}}[(4+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide
6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6) ...6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 974.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_6*SO/2=O/2=O][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b3-c1_b4-d1_b6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Glcp6SH]{}[(4+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4[DManpa1-6]DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_b6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-YZT / 6-deoxy-6-sulfo-beta-D-glucopyranose


Type: saccharide / Mass: 244.220 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O8S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Monomeric S-layer protein SlaA with N-glycosylation / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic) / Cellular location: Surface layer
Buffer solutionpH: 3.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Grid type: lacey with graphene oxide Blotting paper: Whatman 597

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 59.12 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
7Cootmodel fitting
8UCSF Chimeramodel fitting
9UCSF ChimeraXmodel fitting
10ISOLDEmodel fitting
12REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66040 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 3.1 Å
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0129183
ELECTRON MICROSCOPYr_angle_refined_deg1.7821.80212790
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.71451039
ELECTRON MICROSCOPYr_dihedral_angle_2_deg36.98125.345290
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.818151135
ELECTRON MICROSCOPYr_dihedral_angle_4_deg36.69152
ELECTRON MICROSCOPYr_chiral_restr0.1020.21623
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.026458
ELECTRON MICROSCOPYr_nbd_refined0.1860.24852
ELECTRON MICROSCOPYr_nbtor_refined0.3110.213050
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.0770.2172
ELECTRON MICROSCOPYr_mcbond_it7.3246.024159
ELECTRON MICROSCOPYr_mcangle_it12.0349.0615197
ELECTRON MICROSCOPYr_scbond_it13.94110.385024
ELECTRON MICROSCOPYr_scangle_it23.72515.1247592
ELECTRON MICROSCOPYr_lrange_it35.975153.84633247
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3-3.0780.496745010.496745010.5680.496
3.078-3.1620.483724940.483724940.5940.483
3.162-3.2540.479712120.479712120.620.479
3.254-3.3540.476685180.476685180.6470.476
3.354-3.4640.46673630.46673630.7010.46
3.464-3.5860.426636380.426636380.7610.426
3.586-3.7210.386621820.386621820.8080.386
3.721-3.8730.333603960.333603960.8550.333
3.873-4.0450.281572840.281572840.8970.281
4.045-4.2420.25549490.25549490.930.25
4.242-4.4720.235518330.235518330.9570.235
4.472-4.7430.224493550.224493550.970.224
4.743-5.070.214464630.214464630.9730.214
5.07-5.4760.202433160.202433160.9670.202
5.476-5.9990.198397070.198397070.9590.198
5.999-6.7060.218356230.218356230.9410.218
6.706-7.7430.239318090.239318090.9330.239
7.743-9.480.276266940.276266940.9210.276
9.48-13.3960.337206230.337206230.9310.337
13.396-235.20.505113680.505113680.9740.505

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