Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 78.58 kDa 
• Atom Count: 5094 
• Modelled Residue Count: 648 
• Deposited Residue Count: 704 
• Unique protein chains: 3

3MJ9

Crystal structure of JAML in complex with the stimulatory antibody HL4E10

• PDB DOI: 10.2210/pdb3MJ9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Cricetulus migratorius
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2010-04-12 Released: 2011-02-23 
• Deposition Author(s): Verdino, P., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.287 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Molecular insights into gamma delta T cell costimulation by an anti-JAML antibody.

Verdino, P., Witherden, D.A., Ferguson, M.S., Corper, A.L., Schiefner, A., Havran, W.L., Wilson, I.A.

(2011) Structure 19: 80-89

• PubMed: 21220118 
• DOI: 10.1016/j.str.2010.10.007
• Primary Citation of Related Structures:  
  3MJ9


• PubMed Abstract: 
  

γδ T cells bridge innate and adaptive immunity and function in immunosurveillance, immunoregulation, tumor cell recognition, and as first line of defense against microbial infection. Costimulation of epithelial γδ T cell activation by the JAML receptor can be induced by interaction with its endogenous ligand CAR or by binding of the stimulatory antibody HL4E10. We, therefore, determined the crystal structure of the JAML-HL4E10 Fab complex at 2.95 Å resolution. HL4E10 binds the membrane-proximal domain of JAML through hydrophobic interactions that account for nanomolar affinity and long half-life, contrasting with the fast kinetics and micromolar affinity of the hydrophilic CAR interaction with the membrane-distal JAML domain. Thus, despite different binding sites and mechanisms, JAML interaction with these two disparate ligands leads to the same functional outcome, namely JAML triggering and induction of cell signaling. Several characteristics of the HL4E10 antibody might then be harnessed in therapeutic applications, such as promoting healing of acute or chronic wounds.

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Organizational Affiliation: 

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Junctional adhesion molecule-like	A	268	Mus musculus	Mutation(s): 2  Gene Names: Amica1, Gm638, Jaml
UniProt
Find proteins for Q80UL9 (Mus musculus) Explore Q80UL9  Go to UniProtKB:  Q80UL9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN	B [auth L]	213	Cricetulus migratorius	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN	C [auth H]	223	Cricetulus migratorius	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.287 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.02	α = 90
b = 125.02	β = 90
c = 107.839	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-12 
• Released Date: 2011-02-23 
Deposition Author(s): Verdino, P., Wilson, I.A.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary