8IQS | pdb_00008iqs

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 
    0.270 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The strategy used by naive anti-PEG antibodies to capture flexible and featureless PEG chains.

Liu, Y.Mori, T.Ito, Y.Kuroki, K.Hayashi, S.Kohda, D.Shimizu, T.Ishida, T.Roffler, S.R.Kaneko, M.K.Kato, Y.Arimori, T.Teramoto, T.Takemura, K.Ishibashi, K.Katayama, Y.Maenaka, K.Kakuta, Y.Kitao, A.Mori, T.

(2025) J Control Release 380: 396-403

  • DOI: https://doi.org/10.1016/j.jconrel.2025.02.001
  • Primary Citation of Related Structures:  
    8IQP, 8IQQ, 8IQR, 8IQS

  • PubMed Abstract: 

    Polyethylene glycol (PEG) is widely used as a standard stealth polymer, although the induction of anti-PEG antibodies and consequent effects have drawn attention in recent years. To date, several anti-PEG antibodies induced by PEG-modified proteins via the T cell-dependent (TD) pathway, in which affinity maturation occurs, have been reported. In contrast, structures of the naïve anti-PEG antibodies before affinity maturation have not been described in the literature. Here, to understand the details of the naïve anti-PEG antibodies capturing PEG, we studied a naïve anti-PEG antibody induced by a PEG-modified liposome in the absence of affinity maturation via the T cell-independent (TI) pathway. The mutation levels, structures as well as in vitro and in silico binding properties of TI and TD anti-PEG antibodies were compared. The TI anti-PEG antibody showed no mutation and a low binding affinity toward PEG, meanwhile, it allowed PEG chain sliding and weak interaction with the terminal group. Furthermore, the naïve anti-PEG antibodies may obtain high affinities by forming tunnel structures via minimal mutations. This research provides new insights into polymer-antibody interactions, which can facilitate the development of novel stealth polymers that can avoid antibody induction.


  • Organizational Affiliation

    Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M11 VL-SARAHA [auth L],
C [auth l]
179Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
M11 VH-SARAHB [auth H],
D [auth h]
188Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free:  0.270 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.33α = 90
b = 103.46β = 90
c = 174.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Structure summary
  • Version 1.2: 2025-03-19
    Changes: Database references
  • Version 1.3: 2025-03-26
    Changes: Database references