4LLU

Structure of Pertuzumab Fab with light chain Clambda at 2.16A

• PDB DOI:  https://doi.org/10.2210/pdb4LLU/pdb

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


• Deposited: 2013-07-09 Released: 2014-01-29 
• Deposition Author(s): Pustilnik, A., Lewis, S.M., Wu, X., Sereno, A., Huang, F., Guntas, G., Leaver-Fay, A., Smith, E.M., Ho, C., Hansen-Estruch, C., Chamberlain, A.K., Truhlar, S.M., Kuhlman, B., Demarest, S.J., Atwell, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.273 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface.

Lewis, S.M., Wu, X., Pustilnik, A., Sereno, A., Huang, F., Rick, H.L., Guntas, G., Leaver-Fay, A., Smith, E.M., Ho, C., Hansen-Estruch, C., Chamberlain, A.K., Truhlar, S.M., Conner, E.M., Atwell, S., Kuhlman, B., Demarest, S.J.

(2014) Nat Biotechnol 32: 191-198

• PubMed: 24463572 
• DOI: https://doi.org/10.1038/nbt.2797
• Primary Citation of Related Structures:  
  4LLD, 4LLM, 4LLQ, 4LLU, 4LLW, 4LLY


• PubMed Abstract: 
  

Robust generation of IgG bispecific antibodies has been a long-standing challenge. Existing methods require extensive engineering of each individual antibody, discovery of common light chains, or complex and laborious biochemical processing. Here we combine computational and rational design approaches with experimental structural validation to generate antibody heavy and light chains with orthogonal Fab interfaces. Parental monoclonal antibodies incorporating these interfaces, when simultaneously co-expressed, assemble into bispecific IgG with improved heavy chain-light chain pairing. Bispecific IgGs generated with this approach exhibit pharmacokinetic and other desirable properties of native IgG, but bind target antigens monovalently. As such, these bispecific reagents may be useful in many biotechnological applications.

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Organizational Affiliation: 

Eli Lilly Biotechnology Center, San Diego, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 94.84 kDa 
• Atom Count: 6,706 
• Modelled Residue Count: 856 
• Deposited Residue Count: 878 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERTUZUMAB FAB Heavy chain	A, C	227	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6C4R2 (Homo sapiens) Explore S6C4R2  Go to UniProtKB:  S6C4R2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain CLAMBDA	B, D	212	Homo sapiens	Mutation(s): 0  Gene Names: IGLC2
UniProt
Find proteins for P0DOY2 (Homo sapiens) Explore P0DOY2  Go to UniProtKB:  P0DOY2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], G [auth C], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.273 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.024	α = 90
b = 69.739	β = 98.75
c = 70.828	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Pustilnik, A., Lewis, S.M., Wu, X., Sereno, A., Huang, F., Guntas, G., Leaver-Fay, A., Smith, E.M., Ho, C., Hansen-Estruch, C., Chamberlain, A.K., Truhlar, S.M., Kuhlman, B., Demarest, S.J., Atwell, S.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2014-02-12
  Changes: Database references
• Version 1.2: 2014-03-26
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description