9X1H | pdb_00009x1h

Cryo-EM Structure of human complement C1s CUB domain in complex with RAY121


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


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Literature

Long lasting complement neutralisation by RAY121, an engineered anti-C1s antibody with C1q displacement function.

Ho, A.W.S.Fukuzawa, T.Koga, H.Ohmine, K.Kawauchi, H.Muraoka, M.Ikuta, Y.Gupta, G.Okuda, M.Onami, I.Ayabe, M.Takeiri, A.Konishi, H.Sugawara, Y.Usami, S.Ito, E.Shibahara, N.Ozeki, K.Wada, Y.Hirako, A.Takahashi, N.Sampei, Z.Haraya, K.Murao, N.Fujii, T.Torizawa, T.Shimada, H.Igawa, T.

(2025) EBioMedicine 122: 106009-106009

  • DOI: https://doi.org/10.1016/j.ebiom.2025.106009
  • Primary Citation of Related Structures:  
    9X1H

  • PubMed Abstract: 

    Antibody drugs blocking the complement classical pathway (CP) often require frequent intravenous administration to overcome the high abundance or rapid turnover of complement proteins. This makes treatment compliance burdensome for patients. Screening was performed to identify anti-C1s antibodies specific for the CUB domain of C1s with CP neutralising function. Antibody engineering was performed on the anti-C1s antibody to prolong its half-life in circulation. The variable region was mutated to confer pH-dependent binding to C1s, and the antibody Fc was modified to lower its isoelectric point and to have enhanced binding to the neonatal Fc receptor. A combination of pH-dependent binding to C1s and optimisation of charge characteristics was required for the final engineered antibody, RAY121, to achieve a long half-life in circulation and long-lasting neutralisation of the CP. In male cynomolgus monkeys, a single subcutaneous injection suppressed CP activity for more than a month. RAY121 neutralises the CP by using a unique mechanism of displacing C1q from the C1 complex and blocking its reassembly. Structure analysis by cryo-electron microscopy revealed that the RAY121 epitope on C1s is distinct from the C1q binding site, and that C1q displacement is mediated by the Fab arm sterically obstructing C1q binding to C1s. RAY121 is able to neutralise the CP for an extended duration and is effective at doses that can be administered subcutaneously for convenient treatment. These data present RAY121 as a promising agent for the treatment of CP-driven autoimmune disorders. Chugai Pharmaceutical Co. Ltd.


  • Organizational Affiliation
    • Chugai Pharmabody Research, Singapore, 138623, Singapore. Electronic address: adrian.h@chugai-pharmabody.com.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RAY121 Fab Light chainA [auth L],
B [auth M]
220Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RAY121 Fab Heavy chainC [auth I],
E [auth H]
225Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C1s subcomponent heavy chainD [auth B],
F [auth A]
290Homo sapiensMutation(s): 0 
Gene Names: C1S
EC: 3.4.21.42
UniProt & NIH Common Fund Data Resources
Find proteins for P09871 (Homo sapiens)
Explore P09871 
Go to UniProtKB:  P09871
PHAROS:  P09871
GTEx:  ENSG00000182326 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09871
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.5

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release