Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2BC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2BC1D 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2BC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2BC1D 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.13 kDa 
• Atom Count: 7728 
• Residue Count: 946 
• Unique protein chains: 3

4G6F

Crystal Structure of 10E8 Fab in Complex with an HIV-1 gp41 Peptide

• DOI: 10.2210/pdb4G6F/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-07-19 Released: 2012-09-26 
• Deposition Author(s): Ofek, G., Huang, J., Connors, M., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

Broad and potent neutralization of HIV-1 by a gp41-specific human antibody.

Huang, J., Ofek, G., Laub, L., Louder, M.K., Doria-Rose, N.A., Longo, N.S., Imamichi, H., Bailer, R.T., Chakrabarti, B., Sharma, S.K., Alam, S.M., Wang, T., Yang, Y., Zhang, B., Migueles, S.A., Wyatt, R., Haynes, B.F., Kwong, P.D., Mascola, J.R., Connors, M.

(2012) Nature 491: 406-412

• PubMed: 23151583 
• DOI: 10.1038/nature11544
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Characterization of human monoclonal antibodies is providing considerable insight into mechanisms of broad HIV-1 neutralization. Here we report an HIV-1 gp41 membrane-proximal external region (MPER)-specific antibody, named 10E8, which neutralizes ∼98% of tested viruses. An analysis of sera from 78 healthy HIV-1-infected donors demonstrated that 27% contained MPER-specific antibodies and 8% contained 10E8-like specificities. In contrast to other neutralizing MPER antibodies, 10E8 did not bind phospholipids, was not autoreactive, and bound cell-surface envelope. The structure of 10E8 in complex with the complete MPER revealed a site of vulnerability comprising a narrow stretch of highly conserved gp41-hydrophobic residues and a critical arginine or lysine just before the transmembrane region. Analysis of resistant HIV-1 variants confirmed the importance of these residues for neutralization. The highly conserved MPER is a target of potent, non-self-reactive neutralizing antibodies, suggesting that HIV-1 vaccines should aim to induce antibodies to this region of HIV-1 envelope glycoprotein.

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Organizational Affiliation: 

HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
10E8 Heavy Chain	B, H	236	Homo sapiens	Mutation(s): 0  Gene Names: IGHV3-15*05
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
10E8 Light Chain	D, L	215	Homo sapiens	Mutation(s): 0  Gene Names: IGLV3-19*01
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
gp41 MPER Peptide	F, P	34	Human immunodeficiency virus 1	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.021	α = 90
b = 71.432	β = 104.5
c = 129.236	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-19 
• Released Date: 2012-09-26 
Deposition Author(s): Ofek, G., Huang, J., Connors, M., Kwong, P.D.

Revision History 

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Database references
• Version 1.2: 2015-09-16
  Changes: Refinement description
• Version 1.3: 2017-11-15
  Changes: Refinement description