Biological Assembly 1  

 3D View: Structure

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

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

Macromolecule Content

• Total Structure Weight: 48.08 kDa 
• Atom Count: 3549 
• Residue Count: 435 
• Unique protein chains: 2

1M7I

CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXNERI Y LIPOPOLYSACCHARIDE COMPLEXED WITH A PENTASACCHARIDE

• DOI: 10.2210/pdb1M7I/pdb

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


• Deposited: 2002-07-19 Released: 2003-07-22 
• Deposition Author(s): Vyas, N.K., Vyas, M.N., Chervenak, M.C., Johnson, M.A., Pinto, B.M., Bundle, D.R., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.282 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodynamics

Vyas, N.K., Vyas, M.N., Chervenak, M.C., Johnson, M.A., Pinto, B.M., Bundle, D.R., Quiocho, F.A.

(2002) Biochemistry 41: 13575-13586

• PubMed: 12427018 
• DOI: 10.1021/bi0261387
• Primary Citation of Related Structures:  
  1M71, 1M7I, 1M7D


• PubMed Abstract: 
  

The antigenic recognition of Shigella flexneri O-polysaccharide, which consists of a repeating unit ABCD [-->2)-alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->3)-beta-D-GlcpNAc-(1-->], by the monoclonal antibody SYA/J6 (IgG3, kappa) has been investigated by crystallographic analysis of the Fab domain and its two complexes with two antigen segments (a pentasaccharide Rha A-Rha B-Rha C-GlcNAc D-Rha A' and a modified trisaccharide Rha B-Rha C-GlcNAc D in which Rha C* is missing a C2-OH group). These complex structures, the first for a Fab specific for a periodic linear heteropolysaccharide, reveal a binding site groove (between the V(H) and V(L) domains) that makes polar and nonpolar contacts with all the sugar residues of the pentasaccharide. Both main-chain and side-chain atoms of the Fab are used in ligand binding. The charged side chain of Glu H50 of CDR H2 forms crucial hydrogen bonds to GlcNAc of the oligosaccharides. The modified trisaccharide is more buried and fits more snugly than the pentasaccharide. It also makes as many contacts (approximately 75) with the Fab as the pentasaccharide, including the same number of hydrogen bonds (eight, with four being identical). It is further engaged in more hydrophobic interactions than the pentasaccharide. These three features favorable to trisaccharide binding are consistent with the observation of a tighter complex with the trisaccharide than the pentasaccharide. Thermodynamic data demonstrate that the native tri- to pentasaccharides have free energies of binding in the range of 6.8-7.4 kcal mol(-1), and all but one of the hydrogen bonds to individual hydroxyl groups provide no more than approximately 0.7 kcal mol(-1). They further indicate that hydrophobic interactions make significant contributions to binding and, as the native epitope becomes larger across the tri-, tetra-, pentasaccharide series, entropy contributions to the free energy become dominant.

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Related Citations: 

• Preliminary Crystallographic Analysis of a Fab Specific for the O-antigen of Shigella flexneri Cell Surface Lipoplysacharide with and and without Bound Saccharides
  Vyas, N.K., Vyas, M.N., Chervenak, M.C., Johnson, M.A., Pinto, B.M., Bundle, D.R., Quiocho, F.A.
  (1993) J Mol Biol 231: 133

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Organizational Affiliation: 

Verna and Marrs Mclean Department of Biochemistry and Molecular Biology and Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of the monoclonal antibody Fab SYA/J6	A	215	Mus musculus	Mutation(s): 0  Gene Names: Igkc, Igk-C
Find proteins for A2NHM3 (Mus musculus) Explore A2NHM3  Go to UniProtKB:  A2NHM3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of the monoclonal antibody Fab SYA/J6	B	220	Mus musculus	Mutation(s): 0
Find proteins for P01801 (Mus musculus) Explore P01801  Go to UniProtKB:  P01801

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-methyl 6-deoxy-alpha-L-rhamnopyranoside	C	5		N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.282 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.51	α = 90
b = 70.51	β = 90
c = 203.1	γ = 90

Software Package:

Software Name	Purpose
Weissenberg	data collection
WEIS	data reduction
Protein	data reduction
MERLOT	phasing
CNS	refinement
WEISSENBERG	data reduction
WEIS	data scaling
PROTEIN	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-19 
• Released Date: 2003-07-22 
Deposition Author(s): Vyas, N.K., Vyas, M.N., Chervenak, M.C., Johnson, M.A., Pinto, B.M., Bundle, D.R., Quiocho, F.A.

Revision History 

• Version 1.0: 2003-07-22
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary