Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 47252.73 
• Atom Count: 3299 
• Residue Count: 439 
• Unique protein chains: 2

1U6A

Crystal Structure of the Broadly Neutralizing Anti-HIV Fab F105

• DOI: 10.2210/pdb1U6A/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens


• Deposited: 2004-07-29 Released: 2005-08-09 
• Deposition Author(s): Wilkinson, R.A., Piscitelli, C., Teintze, M., Lawrence, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.251 
• R-Value Work: 0.210 

Literature

Structure of the Fab fragment of F105, a broadly reactive anti-human immunodeficiency virus (HIV) antibody that recognizes the CD4 binding site of HIV type 1 gp120.

Wilkinson, R.A., Piscitelli, C., Teintze, M., Cavacini, L.A., Posner, M.R., Lawrence, C.M.

(2005) J.Virol. 79: 13060-13069

• PubMed: 16189008 
• DOI: 10.1128/JVI.79.20.13060-13069.2005


• PubMed Abstract: 
  

We have determined the crystal structure of the Fab fragment from F105, a broadly reactive human antibody with limited potency that recognizes the CD4 binding site of gp120. The structure reveals an extended CDR H3 loop with a phenylalanine residue at the apex and shows a striking pattern of serine and tyrosine residues. Modeling the interaction between gp120 and F105 suggests that the phenylalanine may recognize the binding pocket of gp120 used by Phe(43) of CD4 and that numerous tyrosine and serine residues form hydrogen bonds with the main chain atoms of gp120. A comparison of the F105 structure to that of immunoglobulin G1 b12, a much more potent and broadly neutralizing antibody with an overlapping epitope, suggests similarities that contribute to the broad recognition of human immunodeficiency virus by both antibodies. While the putative epitope for F105 shows significant overlap with that predicted for b12, it appears to differ from the b12 epitope in extending across the interface between the inner and outer domains of gp120. In contrast, the CDR loops of b12 appear to interact predominantly with the outer domain of gp120. The difference between the predicted epitopes for b12 and F105 suggests that the unique potency of b12 may arise from its ability to avoid the interface between the inner and outer domains of gp120.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Montana State University, Bozeman, 59717, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
F105 LIGHT CHAIN	L	215	Homo sapiens	Mutation(s): 0  Gene Names: IGK@
Find proteins for Q6PIL8 (Homo sapiens) Go to UniProtKB:  Q6PIL8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
F105 HEAVY CHAIN	H	224	Homo sapiens	Mutation(s): 0  Gene Names: DKFZp686P15220
Find proteins for Q6N089 (Homo sapiens) Go to UniProtKB:  Q6N089

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.251 
• R-Value Work: 0.210 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 120.403	α = 90.00
b = 120.403	β = 90.00
c = 72.977	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
DENZO	data reduction
COMO	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-29 
• Released Date: 2005-08-09 
• Deposition Author(s): Wilkinson, R.A., Piscitelli, C., Teintze, M., Lawrence, C.M.

Revision History 

• Version 1.0: 2005-08-09
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance