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- PDB-8an2: S-layer protein SlaA from Sulfolobus acidocaldarius at pH 10.0 -

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Basic information

Entry
Database: PDB / ID: 8an2
TitleS-layer protein SlaA from Sulfolobus acidocaldarius at pH 10.0
ComponentsS-layer protein A
KeywordsSTRUCTURAL PROTEIN / S-layer / dimer / N-glycosylation
Function / homology: / S-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: 3.2 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 / Refinement description / Category: citation / citation_author / em_3d_fitting_list
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 / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type
Revision 1.2Nov 13, 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

Downloads & links

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Assembly

Deposited unit
AAA: S-layer protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,77720
Polymers151,0781
Non-polymers12,69919
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area14630 Å2
ΔGint183 kcal/mol
Surface area46580 Å2

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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 DSM 639 (acidophilic)
References: UniProt: Q4J6E5

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Sugars , 7 types, 19 molecules

#2: 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
#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.: 1
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.: 3
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.: 6
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 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.: 1
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
#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.: 3
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
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
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Buffer solutionpH: 10
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 61 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
Particle selectionNum. of particles selected: 280004
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29819 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingPDB-ID: 7ZCX

7zcx


Accession code: 7ZCX / Source name: PDB / Type: experimental model
RefinementResolution: 3.2→269.824 Å / Cor.coef. Fo:Fc: 0.912 / WRfactor Rwork: 0.288 / SU B: 5.18 / SU ML: 0.083 / Average fsc overall: 0.8618 / Average fsc work: 0.8618 / ESU R: 0.078 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.288 1255606 -
all0.288 --
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 118.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.197 Å2-0.625 Å20.167 Å2
2--1.129 Å20.008 Å2
3----0.932 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.0128925
ELECTRON MICROSCOPYr_angle_refined_deg1.9031.76912398
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.43951039
ELECTRON MICROSCOPYr_dihedral_angle_2_deg36.70425.345290
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.989151135
ELECTRON MICROSCOPYr_dihedral_angle_4_deg33.646152
ELECTRON MICROSCOPYr_chiral_restr0.1080.21499
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.026450
ELECTRON MICROSCOPYr_nbd_refined0.1930.25084
ELECTRON MICROSCOPYr_nbtor_refined0.3060.212666
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.0750.2198
ELECTRON MICROSCOPYr_mcbond_it10.7119.0964159
ELECTRON MICROSCOPYr_mcangle_it18.04113.6545197
ELECTRON MICROSCOPYr_scbond_it16.46213.6694766
ELECTRON MICROSCOPYr_scangle_it28.45619.7917200
ELECTRON MICROSCOPYr_lrange_it44.532208.50332681
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
3.2-3.2830.447931640.447931640.6880.447
3.283-3.3730.43906370.43906370.7240.43
3.373-3.4710.409878180.409878180.7610.409
3.471-3.5780.383857080.383857080.7970.383
3.578-3.6950.362829370.362829370.820.362
3.695-3.8250.336802610.336802610.8420.336
3.825-3.9690.311772510.311772510.8650.311
3.969-4.1310.278744260.278744260.8950.278
4.131-4.3150.25709930.25709930.9250.25
4.315-4.5250.232683970.232683970.9420.232
4.525-4.770.216650630.216650630.9550.216
4.77-5.0590.211614090.211614090.9610.211
5.059-5.4090.216576320.216576320.9550.216
5.409-5.8420.221535550.221535550.9480.221
5.842-6.3990.232496910.232496910.9320.232
6.399-7.1540.253444790.253444790.9180.253
7.154-8.260.251394650.251394650.9170.251
8.26-10.1140.247333120.247333120.9230.247
10.114-14.2930.274256220.274256220.9280.274
14.293-269.8240.509141280.509141280.9640.509

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