Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 48.31 kDa 
• Atom Count: 3713 
• Residue Count: 435 
• Unique protein chains: 2

6C5I

Unliganded S25-5 Fab

• DOI: 10.2210/pdb6C5I/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2018-01-16 Released: 2019-01-09 
• Deposition Author(s): Evans, S.V., Haji-Ghassemi, O.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.231 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Subtle Changes in the Combining Site of the Chlamydiaceae-Specific mAb S25-23 Increase the Antibody-Carbohydrate Binding Affinity by an Order of Magnitude.

Haji-Ghassemi, O., Muller-Loennies, S., Brooks, C.L., MacKenzie, C.R., Caveney, N., Van Petegem, F., Brade, L., Kosma, P., Brade, H., Evans, S.V.

(2019) Biochemistry 58: 714-726

• PubMed: 30571096 
• DOI: 10.1021/acs.biochem.8b00318
• Primary Citation of Related Structures:  
  6C5I, 6C5H, 6C5K, 6C5J


• PubMed Abstract: 
  

Murine antibodies S25-23, S25-26, and S25-5 derive from a common germ-line origin, and all bind the Chlamydiaceae family-specific epitope αKdo(2→8)αKdo(2→4)αKdo (where Kdo is 3-deoxy-α-d- manno-oct-2-ulosonic acid) with high affinity and specificity. These antibodies recognize the entire trisaccharide antigen in a linkage-dependent manner via a groove composed largely of germ-line residues. Despite sharing identical heavy and light chain genes, S25-23 binds the family-specific epitope with nanomolar affinity, which is an order of magnitude higher than that of S25-26, while S25-5 displays an affinity between those of S25-23 and S25-26. We determined the high-resolution crystal structures of S25-23 and S25-5 antigen binding fragments in complex with a pentasaccharide derived from the LPS of Chlamydia and measured the affinity of S25-5 for chlamydial LPS antigens using isothermal titration microcalorimetry. The 1.75 Å resolution structure of S25-23 shows how subtle conservative mutations Arg(L)-27E to lysine and Ser(H)-56 to threonine lead to an order of magnitude increase in affinity. Importantly, comparison between previous S25-26 structures and the 1.99 and 2.05 Å resolution liganded and unliganded structures of S25-5, respectively, shows how a Ser(L)-27E mutation results in an intermediate affinity due to the reduced enthalpic penalty associated with complex formation that would otherwise be required for arginine in this position. This strategy allows for subtle adjustments in the combining site via affinity maturation that have dramatic consequences for the affinity of an antibody for its antigen.

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Organizational Affiliation: 

Department of Biochemistry and Microbiology , University of Victoria , P.O. Box 3055 STN CSC, Victoria , British Columbia , Canada V8P 3P6.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab IgG1 Heavy Chain	H	218	Mus musculus	Mutation(s): 0  Gene Names: Igh
Find proteins for Q99LC4 (Mus musculus) Explore Q99LC4  Go to UniProtKB:  Q99LC4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab IgG1 (kappa) Light Chain	L	219	Mus musculus	Mutation(s): 0  Gene Names: LC
Find proteins for A0A0F7R5U8 (Mus musculus) Explore A0A0F7R5U8  Go to UniProtKB:  A0A0F7R5U8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG0	L	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
NI	L	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	H	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.231 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.635	α = 90
b = 72.877	β = 90
c = 109.015	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-01-16 
• Released Date: 2019-01-09 
Deposition Author(s): Evans, S.V., Haji-Ghassemi, O.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	Discovery Grant 171356-2013

Revision History 

• Version 1.0: 2019-01-09
  Type: Initial release
  
• Version 1.1: 2019-02-27
  Changes: Data collection, Database references
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary