Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 262.27 kDa 
• Atom Count: 18219 
• Modelled Residue Count: 2226 
• Deposited Residue Count: 2266 
• Unique protein chains: 5

5GS0

Crystal structure of the complex of TLR3 and bi-specific diabody

• PDB DOI: 10.2210/pdb5GS0/pdb

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


• Deposited: 2016-08-13 Released: 2016-10-12 
• Deposition Author(s): Kim, J.H., Song, D.H., Youn, S.J., Kim, J.W., Cho, G., Lee, H., Lee, J.O.
• Funding Organization(s): Ministry of Science, ICT and Future Planning, Ministry of Health & Welfare

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.27 Å
• R-Value Free: 0.248 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Crystal structure of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface.

Kim, J.H., Song, D.H., Youn, S.J., Kim, J.W., Cho, G., Kim, S.C., Lee, H., Jin, M.S., Lee, J.O.

(2016) Sci Rep 6: 34515-34515

• PubMed: 27682821 
• DOI: 10.1038/srep34515
• Primary Citation of Related Structures:  
  5GRU, 5GRV, 5GRW, 5GRX, 5GRY, 5GRZ, 5GS0, 5GS1, 5GS2, 5GS3


• PubMed Abstract: 
  

Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Diabodies are engineered antibody fragments that are composed of two Fv domains connected by short peptide linkers. They are attractive candidates for mediators in assembling protein nano-structures because they can simultaneously bind to two different proteins and are rigid enough to be crystallized. However, comparison of previous crystal structures demonstrates that there is substantial structural diversity in the Fv interface region of diabodies and, therefore, reliable prediction of its structure is not trivial. Here, we present the crystal structures of ten mono- and bi-specific diabodies. We found that changing an arginine residue in the Fv interface to threonine greatly reduced the structural diversity of diabodies. We also found that one of the bispecific diabodies underwent an unexpected process of chain swapping yielding a non-functional monospecific diabody. In order to further reduce structural flexibility and prevent chain shuffling, we introduced disulfide bridges in the Fv interface regions. The disulfide-bridged diabodies have rigid and predictable structures and may have applications in crystallizing proteins, analyzing cryo-electron microscopic images and building protein nano-assemblies.

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Organizational Affiliation: 

Department of Chemistry, KAIST, Daejeon, Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 3	A, D [auth B]	671	Homo sapiens	Mutation(s): 0  Gene Names: TLR3
UniProt & NIH Common Fund Data Resources
Find proteins for O15455 (Homo sapiens) Explore O15455  Go to UniProtKB:  O15455
PHAROS:  O15455 GTEx:  ENSG00000164342

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain (anti-TLR3)	B [auth C], E	107	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain (anti-TLR3)	C [auth D], F	127	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain (anti-Lid)	I [auth H], G [auth X]	121	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain (anti-Lid)	J [auth L], H [auth Y]	107	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth A], BA [auth A], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], Y [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	DA [auth A], EA [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	CA [auth A], UA [auth B], XA [auth B], Z [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.27 Å
• R-Value Free: 0.248 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.519	α = 90
b = 141.329	β = 106.88
c = 150.831	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-08-13 
• Released Date: 2016-10-12 
Deposition Author(s): Kim, J.H., Song, D.H., Youn, S.J., Kim, J.W., Cho, G., Lee, H., Lee, J.O.

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Funding Organization	Location	Grant Number
Ministry of Science, ICT and Future Planning	Korea, Republic Of	NRF-2014R1A2A1A10050436
Ministry of Health & Welfare	Korea, Republic Of	HI15C1886

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary