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- PDB-8an3: S-layer protein SlaA from Sulfolobus acidocaldarius at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 8an3
TitleS-layer protein SlaA from Sulfolobus acidocaldarius at pH 7.0
ComponentsS-layer protein A
KeywordsSTRUCTURAL PROTEIN / S-layer / dimer / N-glycosylation
Function / homologyS-layer / extracellular region / S-layer protein A
Function and homology information
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 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
DepositionAug 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: S-layer protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,73420
Polymers151,0781
Non-polymers13,65619
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15480 Å2
ΔGint197 kcal/mol
Surface area46260 Å2
MethodPISA

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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 DSM 639 (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 , 7 types, 19 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.: 5
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.: 4
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.: 2
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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 650.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_6*SO/2=O/2=O]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Glcp6SH]{}}}}LINUCSPDB-CARE
#6: 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.: 3
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
#7: 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.: 2
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
#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 / N-Acetylglucosamine


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

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Details

Has ligand of interestY

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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: 7
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 FIELDBright-field microscopy / 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
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
7Cootmodel fitting
8UCSF Chimeramodel fitting
9UCSF ChimeraXmodel fitting
10ISOLDEmodel fitting
12REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1016259
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90965 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementResolution: 3.9→3.9 Å / Cor.coef. Fo:Fc: 0.885 / WRfactor Rwork: 0.34 / SU B: 14.051 / SU ML: 0.187 / Average fsc overall: 0.8265 / Average fsc work: 0.8265 / ESU R: 0.183 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.34 470269 -
all0.34 --
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 191.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å26.113 Å2-5.075 Å2
2---1.229 Å2-4.114 Å2
3----0.401 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.0128995
ELECTRON MICROSCOPYr_angle_refined_deg1.9091.77812502
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.14351039
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.2925.345290
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.877151135
ELECTRON MICROSCOPYr_dihedral_angle_4_deg39.856152
ELECTRON MICROSCOPYr_chiral_restr0.1130.21481
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.026307
ELECTRON MICROSCOPYr_nbd_refined0.1980.24912
ELECTRON MICROSCOPYr_nbtor_refined0.310.212784
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1210.2154
ELECTRON MICROSCOPYr_mcbond_it21.86315.0514159
ELECTRON MICROSCOPYr_mcangle_it35.85322.5635197
ELECTRON MICROSCOPYr_scbond_it28.23121.8534836
ELECTRON MICROSCOPYr_scangle_it48.88431.2687303
ELECTRON MICROSCOPYr_lrange_it70.914332.54832912
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.801-3.8990.496346500.496346500.5770.496
3.899-4.0060.46342160.46342160.6350.46
4.006-4.1220.415330490.415330490.70.415
4.122-4.2490.379317920.379317920.7610.379
4.249-4.3880.339311440.339311440.8120.339
4.388-4.5420.3297340.3297340.860.3
4.542-4.7140.271294010.271294010.8910.271
4.714-4.9060.254277600.254277600.9070.254
4.906-5.1240.249267340.249267340.9110.249
5.124-5.3740.254255830.254255830.910.254
5.374-5.6650.275241780.275241780.9010.275
5.665-6.0080.293228640.293228640.8920.293
6.008-6.4230.31217490.31217490.8940.31
6.423-6.9370.327201460.327201460.8920.327
6.937-7.5980.32184610.32184610.8980.32
7.598-8.4940.328166850.328166850.8980.328
8.494-9.8060.323147260.323147260.910.323
9.806-12.0040.287124700.287124700.9170.287
12.004-16.9540.35996100.35996100.8940.359
16.954-2310.75753170.75753170.980.757

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