8IQS

Crystal structure of Anti-PEG antibody M11 Fv-clasp fragment with PEG (co-crystallization with PEG3350)

• PDB DOI: https://doi.org/10.2210/pdb8IQS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-17 Released: 2024-03-20 
• Deposition Author(s): Mori, T., Teramoto, T., Liu, Y., Mori, T., Kakuta, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.270 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

Literature

Comparation of structures and binding properties between two anti-polyethylene glycol antibodies induced via T cell-independent and T cell-dependent pathway

Liu, Y., Mori, T., Teramoto, T., Kakuta, Y., Mori, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84.98 kDa 
• Atom Count: 5,551 
• Modelled Residue Count: 672 
• Deposited Residue Count: 734 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M11 VL-SARAH	A [auth L], C [auth l]	179	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
M11 VH-SARAH	B [auth H], D [auth h]	188	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE8 (Subject of Investigation/LOI)	F [auth H], H [auth h]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)	E [auth H], G [auth h]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.270 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.33	α = 90
b = 103.46	β = 90
c = 174.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-20 
Deposition Author(s): Mori, T., Teramoto, T., Liu, Y., Mori, T., Kakuta, Y.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2024-03-20
  Type: Initial release