Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 152.29 kDa 
• Atom Count: 11253 
• Modelled Residue Count: 1358 
• Deposited Residue Count: 1358 
• Unique protein chains: 3

5LDN

A viral capsid:antibody complex

• PDB DOI: 10.2210/pdb5LDN/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human adenovirus 5, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-06-27 Released: 2017-07-12 
• Deposition Author(s): James, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 

Literature

Antibody-antigen kinetics constrain intracellular humoral immunity.

Bottermann, M., Lode, H.E., Watkinson, R.E., Foss, S., Sandlie, I., Andersen, J.T., James, L.C.

(2016) Sci Rep 6: 37457-37457

• PubMed: 27881870 
• DOI: 10.1038/srep37457
• Primary Citation of Related Structures:  
  5LDN


• PubMed Abstract: 
  

During infection with non-enveloped viruses, antibodies stimulate immunity from inside cells by activating the cytosolic Fc receptor TRIM21. This intracellular humoral response relies on opsonized viral particles reaching the cytosol intact but the antigenic and kinetic constraints involved are unknown. We have solved the structure of a potent TRIM21-dependent neutralizing antibody in complex with human adenovirus 5 hexon and show how these properties influence immune activity. Structure-guided mutagenesis was used to generate antibodies with 20,000-fold variation in affinity, on-rates that differ by ~50-fold and off-rates by >175-fold. Characterization of these variants during infection revealed that TRIM21-dependent neutralization and NFκB activation was largely unaffected by on-rate kinetics. In contrast, TRIM21 antiviral activity was exquisitely dependent upon off-rate, with sub-μM affinity antibodies nevertheless unable to stimulate signaling because of fast dissociation kinetics. These results define the antibody properties required to elicit an efficient intracellular immune response during viral infection.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexon protein,hexon capsid	A	927	Human adenovirus 5	Mutation(s): 0  Gene Names: L3
UniProt
Find proteins for P04133 (Human adenovirus C serotype 5) Explore P04133  Go to UniProtKB:  P04133

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody	B [auth L]	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody	C [auth H]	218	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.999	α = 90
b = 156.999	β = 90
c = 144.891	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-06-27 
• Released Date: 2017-07-12 
Deposition Author(s): James, L.

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Database references