6A79 | pdb_00006a79

Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the mutant scFv fragment (P103A) of murine monoclonal antibody B5209B

• PDB DOI: https://doi.org/10.2210/pdb6A79/pdb

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


• Deposited: 2018-07-02 Released: 2019-01-30 
• Deposition Author(s): Mizohata, E., Nakayama, T., Kado, Y., Yokota, Y., Inoue, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.295 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.273 (Depositor) 
• R-Value Observed: 
  0.274 (Depositor) 

Literature

Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface.

Yamashita, T., Mizohata, E., Nagatoishi, S., Watanabe, T., Nakakido, M., Iwanari, H., Mochizuki, Y., Nakayama, T., Kado, Y., Yokota, Y., Matsumura, H., Kawamura, T., Kodama, T., Hamakubo, T., Inoue, T., Fujitani, H., Tsumoto, K.

(2019) Structure 27: 519

• PubMed: 30595454 
• DOI: https://doi.org/10.1016/j.str.2018.11.002
• Primary Citation Related Structures: 
  6A76, 6A77, 6A78, 6A79


• PubMed Abstract: 
  

  To investigate favorable single amino acid substitutions that improve antigen-antibody interactions, alanine (Ala) mutagenesis scanning of the interfacial residues of a cancer-targeted antibody, B5209B, was performed based on X-ray crystallography analysis. Two substitutions were shown to significantly enhance the binding affinity for the antigen, by up to 30-fold. One substitution improved the affinity by a gain of binding enthalpy, whereas the other substitution improved the affinity by a gain of binding entropy. Molecular dynamics simulations showed that the enthalpic improvement could be attributed to the stabilization of distant salt bridges located at the periphery of the antigen-antibody interface. The entropic improvement was due to the release of water molecules that were stably trapped in the antigen-antibody interface of the wild-type antibody. Importantly, these effects of the Ala substitutions were caused by subtle adjustments of the binding interface. These results will be helpful to design high-affinity antibodies with avoiding entropy-enthalpy compensation.

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Organizational Affiliation: 
• Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan.
Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan.
Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. Electronic address: [e-mail].
Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan. Electronic address: [e-mail].
Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.44 kDa 
• Atom Count: 5,238 
• Modeled Residue Count: 641 
• Deposited Residue Count: 682 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Roundabout homolog 1	A, D [auth B]	91	Homo sapiens	Mutation(s): 0  Gene Names: ROBO1, DUTT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6N7 (Homo sapiens) Explore Q9Y6N7  Go to UniProtKB:  Q9Y6N7
PHAROS:  Q9Y6N7 GTEx:  ENSG00000169855

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain region of the anti-human Robo1 antibody B5209B scFv	B [auth L], E [auth M]	112	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of the anti-human Robo1 antibody B5209B scFv	C [auth H], F [auth I]	138	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth L], H [auth M]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.295 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.273 (Depositor) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.766	α = 90
b = 150.219	β = 90
c = 66.852	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Mizohata, E., Nakayama, T., Kado, Y., Yokota, Y., Inoue, T.

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Funding Organization	Location	Grant Number
	Japan	FIRST Program (MDADD)

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary