Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

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

Macromolecule Content

• Total Structure Weight: 71.02 kDa 
• Atom Count: 4963 
• Residue Count: 607 
• Unique protein chains: 3

2CMR

Crystal structure of the HIV-1 neutralizing antibody D5 Fab bound to the gp41 inner-core mimetic 5-helix

• DOI: 10.2210/pdb2CMR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2006-05-11 Released: 2006-10-16 
• Deposition Author(s): Luftig, M.A., Mattu, M., Di Giovine, P., Geleziunas, R., Hrin, R., Barbato, G., Bianchi, E., Miller, M.D., Pessi, A., Carfi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

Structural Basis for HIV-1 Neutralization by a Gp41 Fusion Intermediate-Directed Antibody

Luftig, M.A., Mattu, M., Di Giovine, P., Geleziunas, R., Hrin, R., Barbato, G., Bianchi, E., Miller, M.D., Pessi, A., Carfi, A.

(2006) Nat Struct Mol Biol 13: 740

• PubMed: 16862157 
• DOI: 10.1038/nsmb1127
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Elicitation of potent and broadly neutralizing antibodies is an important goal in designing an effective human immunodeficiency virus-1 (HIV-1) vaccine. The HIV-1 gp41 inner-core trimer represents a functionally and structurally conserved target for therapeutics. Here we report the 2.0-A-resolution crystal structure of the complex between the antigen-binding fragment of D5, an HIV-1 cross-neutralizing antibody, and 5-helix, a gp41 inner-core mimetic. Both binding and neutralization depend on residues in the D5 CDR H2 loop protruding into the conserved gp41 hydrophobic pocket, as well as a large pocket in D5 surrounding core gp41 residues. Kinetic analysis of D5 mutants with perturbed D5-gp41 interactions suggests that D5 persistence at the fusion intermediate is crucial for neutralization. Thus, our data validate the gp41 N-peptide trimer fusion intermediate as a target for neutralizing antibodies and provide a template for identification of more potent and broadly neutralizing molecules.

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Organizational Affiliation: 

Istituto di Ricerche di Biologia Molecolare P. Angeletti, Via Pontina Km 30,600, I-00040 Pomezia (Rome), Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRANSMEMBRANE GLYCOPROTEIN	A	226	Human immunodeficiency virus 1	Mutation(s): 0
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Go to UniProtKB:  P04578

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
D5	H	217	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
D5	L	208	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.644	α = 90
b = 41.618	β = 110.55
c = 90.726	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-11 
• Released Date: 2006-10-16 
Deposition Author(s): Luftig, M.A., Mattu, M., Di Giovine, P., Geleziunas, R., Hrin, R., Barbato, G., Bianchi, E., Miller, M.D., Pessi, A., Carfi, A.

Revision History 

• Version 1.0: 2006-10-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-08
  Changes: Source and taxonomy