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- PDB-9qbj: Legobody dimer -

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Basic information

Entry
Database: PDB / ID: 9qbj
TitleLegobody dimer
Components
  • (Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin ...) x 2
  • Fa antibody 8D3_2_L
  • Fab antibody 8D3_2_H-H6
  • Nanobody ALFA-H6
KeywordsBIOSYNTHETIC PROTEIN / legobody / dimer / anti-alfa
Function / homology
Function and homology information


IgG binding / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Lysin motif ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Immunoglobulin G-binding protein A / Maltose/maltodextrin-binding periplasmic protein / Immunoglobulin G-binding protein G / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Mus musculus (house mouse)
Escherichia coli (E. coli)
Staphylococcus aureus subsp. aureus N315 (bacteria)
Streptococcus sp. 'group G' (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPacesa, M. / Van Hall-Beauvais, A. / Marchand, A. / Georgeon, S. / Correia, B.E.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Structure of a cryoEM scaffold
Authors: Pacesa, M. / Van Hall-Beauvais, A. / Marchand, A. / Georgeon, S. / Correia, B.E.
History
DepositionMar 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Nanobody ALFA-H6
D: Nanobody ALFA-H6
E: Fab antibody 8D3_2_H-H6
F: Fa antibody 8D3_2_L
G: Fab antibody 8D3_2_H-H6
H: Fa antibody 8D3_2_L
I: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
J: Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,80610
Polymers247,1218
Non-polymers6852
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Antibody , 5 types, 8 molecules CDEGFHIJ

#1: Antibody Nanobody ALFA-H6


Mass: 14813.540 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)
#2: Antibody Fab antibody 8D3_2_H-H6


Mass: 25539.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody Fa antibody 8D3_2_L


Mass: 24095.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IgG-binding protein A / ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IgG-binding protein A / Staphylococcal protein A / SpA / IgG-binding protein G


Mass: 59047.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria), (gene. exp.) Streptococcus sp. 'group G' (bacteria)
Gene: malE, Z5632, ECs5017, spa, SAOUHSC_00069, spa, SA0107, spg
Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: P02976, UniProt: P99134, UniProt: P19909
#5: Antibody Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IgG-binding protein A / ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / IgG-binding protein A / Staphylococcal protein A / SpA / IgG-binding protein G


Mass: 59176.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria), (gene. exp.) Streptococcus sp. 'group G' (bacteria)
Gene: malE, Z5632, ECs5017, spa, SAOUHSC_00069, spa, SA0107, spg
Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: P02976, UniProt: P99134, UniProt: P19909

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Sugars , 1 types, 2 molecules

#6: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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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: Legobody dimer / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114803 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315969
ELECTRON MICROSCOPYf_angle_d0.74221672
ELECTRON MICROSCOPYf_dihedral_angle_d5.3622182
ELECTRON MICROSCOPYf_chiral_restr0.0452407
ELECTRON MICROSCOPYf_plane_restr0.0052779

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