Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 51327.79 
• Atom Count: 3582 
• Residue Count: 469 
• Unique protein chains: 3

1TJI

Crystal Structure of the broadly neutralizing anti-HIV-1 antibody 2F5 in complex with a gp41 17mer epitope

• DOI: 10.2210/pdb1TJI/pdb

• Classification: Viral protein/Immune system
• Organism(s): Human immunodeficiency virus type 1 group M subtype D
• Expression System: Cricetulus griseus


• Deposited: 2004-06-04 Released: 2004-10-05 
• Deposition Author(s): Ofek, G., Tang, M., Sambor, A., Katinger, H., Mascola, J.R., Wyatt, R., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.221 
• R-Value Work: 0.183 

Literature

Structure and mechanistic analysis of the Anti-Human Immunodeficiency Virus type 1 antibody 2F5 in complex with its gp41 epitope

Ofek, G., Tang, M., Sambor, A., Katinger, H., Mascola, J.R., Wyatt, R., Kwong, P.D.

(2004) J.Virol. 78: 10724-10737

• PubMed: 15367639 
• DOI: 10.1128/JVI.78.19.10724-10737.2004
• Primary Citation of Related Structures:  
  1TJH, 1TJG


• PubMed Abstract: 
  

The membrane-proximal region of the ectodomain of the gp41 envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) is the target of three of the five broadly neutralizing anti-HIV-1 antibodies thus far isolated. We have determined crystal structures of the antigen-binding fragment for one of these antibodies, 2F5, in complex with 7-mer, 11-mer, and 17-mer peptides of the gp41 membrane-proximal region, at 2.0-, 2.1-, and 2.2-A resolutions, respectively. The structures reveal an extended gp41 conformation, which stretches over 30 A in length. Contacts are made with five complementarity-determining regions of the antibody as well as with nonpolymorphic regions. Only one exclusive charged face of the gp41 epitope is bound by 2F5, while the nonbound face, which is hydrophobic, may be hidden due to occlusion by other portions of the ectodomain. The structures reveal that the 2F5 antibody is uniquely built to bind to an epitope that is proximal to a membrane surface and in a manner mostly unaffected by large-scale steric hindrance. Biochemical studies with proteoliposomes confirm the importance of lipid membrane and hydrophobic context in the binding of 2F5 as well as in the binding of 4E10, another broadly neutralizing antibody that recognizes the membrane-proximal region of gp41. Based on these structural and biochemical results, immunization strategies for eliciting 2F5- and 4E10-like broadly neutralizing anti-HIV-1 antibodies are proposed.

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Organizational Affiliation: 

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Instiutes of Health, Bethesda, MD 20892, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
anti-HIV-1 antibody 2F5 Light Chain	L	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
anti-HIV-1 antibody 2F5 Heavy Chain	H	237	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Envelope Glycoprotein GP41	P	18	Human immunodeficiency virus type 1 group M subtype D	Mutation(s): 0  Gene Names: env
Find proteins for P04580 (Human immunodeficiency virus type 1 group M subtype D) Go to UniProtKB:  P04580

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	H, L	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	H, L	ISOPROPYL ALCOHOL 2-PROPANOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NH2	P	NON-POLYMER	H2 N		--
YCM	H, L	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.221 
• R-Value Work: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 58.660	α = 90.00
b = 63.684	β = 90.00
c = 178.375	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-06-04 
• Released Date: 2004-10-05 
• Deposition Author(s): Ofek, G., Tang, M., Sambor, A., Katinger, H., Mascola, J.R., Wyatt, R., Kwong, P.D.

Revision History 

• Version 1.0: 2004-10-05
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance