9JE3 | pdb_00009je3

Structure of #2-911 Fab in complex with MEDI8852 Fab

• PDB DOI: https://doi.org/10.2210/pdb9JE3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-09-02 Released: 2025-09-03 
• Deposition Author(s): Itou, H., Sano, K., Ainai, A., Suzuki, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.204 (DCC) 

Starting Models: experimental

Literature

Finding and mimicking a conserved structural motif hidden in influenza virus haemagglutinins using anti-idiotypic antibodies: A novel approach for universal vaccine antigen design.

Itou, H., Sano, K., Ainai, A., Otsuki, K., Inoue, T., Suzuki, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 189.05 kDa 
• Atom Count: 13,553 
• Modeled Residue Count: 1,739 
• Deposited Residue Count: 1,740 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
#2-911 Fab heavy chain	A [auth E], E [auth A]	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
#2-911 Fab light chain	B [auth F], F [auth B]	215	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MEDI8852 Fab heavy chain	C [auth G], G [auth C]	228	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MEDI8852 Fab light chain	D [auth H], H [auth D]	210	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose	I [auth X], J [auth I], K [auth J]	2		N/A
Glycosylation Resources
GlyTouCan:  G92130SN GlyCosmos:  G92130SN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	L [auth H], M [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900006	I, J, K [auth X]	trehalose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.204 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.283	α = 90
b = 151.111	β = 90
c = 176.368	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Itou, H., Sano, K., Ainai, A., Suzuki, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release