9KLU | pdb_00009klu

Crystal structure of a Streptococcal protein G B1 mutant

• PDB DOI: https://doi.org/10.2210/pdb9KLU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Finegoldia magna
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-11-15 Released: 2026-01-28 
• Deposition Author(s): Shiga, S., Watanabe, H., Honda, S.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Regulating the orientation of homobivalent small binders through 3D domain-swapping design.

Shiga, S., Watanabe, H., Makabe, K., Honda, S.

(2025) J Biological Chem 302: 111053-111053

• PubMed: 41391770 
• DOI: https://doi.org/10.1016/j.jbc.2025.111053
• Primary Citation Related Structures: 
  9KL7, 9KLS, 9KLT, 9KLU


• PubMed Abstract: 
  

  Homobivalent small binders represent bioactive dimeric proteins constructed by linking nanobodies or other small binders. As binding domain orientation in these dimeric binders affects binding affinity, expanding the orientation regulation techniques is crucial for optimizing their performance. Here, we report a 3D domain-swapping design as a genetic engineering approach to regulate the orientation of homobivalent small binders. We aimed to regulate B1 domain orientation of protein G as a model binder. By inserting single cysteine-containing polyproline sequences into loops located at the C- and N-terminal sides of the tertiary structure, we successfully designed 3D domain-swapped dimers with tail-to-tail and head-to-head orientations. Notably, the head-to-head-oriented dimer demonstrated potential as a functional homobivalent small binder. Our results highlight the applicability of the 3D domain-swapping design for regulating the orientation of homobivalent small binders and establish a foundation for developing 3D domain-swapped dimers.

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Organizational Affiliation: 
• Molecular Biosystems Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan; Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, Japan.
Molecular Biosystems Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata, Japan.
Molecular Biosystems Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.73 kDa 
• Atom Count: 980 
• Modeled Residue Count: 126 
• Deposited Residue Count: 134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein LG	A, B	67	Finegoldia magna	Mutation(s): 4
UniProt
Find proteins for Q53291 (Finegoldia magna) Explore Q53291  Go to UniProtKB:  Q53291

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.506	α = 90
b = 75.058	β = 90
c = 96.925	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-28 
Deposition Author(s): Shiga, S., Watanabe, H., Honda, S.

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Funding Organization	Location	Grant Number
Other government	Japan	--

Revision History  

• Version 1.0: 2026-01-28
  Type: Initial release