9QBJ | pdb_00009qbj

Legobody dimer

• PDB DOI: https://doi.org/10.2210/pdb9QBJ/pdb
• EM Map EMD-53000: EMDB EMDataResource

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Vicugna pacos, Mus musculus, Escherichia coli, Staphylococcus aureus subsp. aureus N315, Streptococcus sp. 'group G
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-03 Released: 2025-06-11 
• Deposition Author(s): Pacesa, M., Van Hall-Beauvais, A., Marchand, A., Georgeon, S., Correia, B.E.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of a cryoEM scaffold

Pacesa, M., Van Hall-Beauvais, A., Marchand, A., Georgeon, S., Correia, B.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 8-mer - A4B2C2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 247.81 kDa 
• Atom Count: 15,600 
• Modeled Residue Count: 1,997 
• Deposited Residue Count: 2,265 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody ALFA-H6	A [auth C], B [auth D]	133	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab antibody 8D3_2_H-H6	C [auth E], E [auth G]	237	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fa antibody 8D3_2_L	D [auth F], F [auth H]	219	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G	G [auth I]	543	Escherichia coli, Staphylococcus aureus subsp. aureus N315, Streptococcus sp. 'group G	Mutation(s): 0  Gene Names: malE, Z5632, ECs5017, spa, SAOUHSC_00069, SA0107, spg
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976  Go to UniProtKB:  P02976
Find proteins for P19909 (Streptococcus sp. group G) Explore P19909  Go to UniProtKB:  P19909
UniProt Groups	P02976P19909

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,Immunoglobulin G-binding protein A,Immunoglobulin G-binding protein G	H [auth J]	544	Escherichia coli, Staphylococcus aureus subsp. aureus N315, Streptococcus sp. 'group G	Mutation(s): 0  Gene Names: malE, Z5632, ECs5017, spa, SAOUHSC_00069, SA0107, spg
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976  Go to UniProtKB:  P02976
Find proteins for P19909 (Streptococcus sp. group G) Explore P19909  Go to UniProtKB:  P19909
UniProt Groups	P02976P19909

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	I [auth A], J [auth B]	2		N/A
Glycosylation Resources
GlyTouCan:  G66120GK GlyCosmos:  G66120GK

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Pacesa, M., Van Hall-Beauvais, A., Marchand, A., Georgeon, S., Correia, B.E.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release