Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Macromolecule Content

• Total Structure Weight: 49.65 kDa 
• Atom Count: 3786 
• Residue Count: 447 
• Unique protein chains: 3

4WY7

Crystal structure of recombinant 4E10 expressed in Escherichia coli with epitope bound

• DOI: 10.2210/pdb4WY7/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human immunodeficiency virus type 1 (WMJ2 ISOLATE)
• Expression System: Escherichia coli BL21(DE3), synthetic construct
• Mutation(s): No 


• Deposited: 2014-11-16 Released: 2015-03-25 
• Deposition Author(s): Rujas, E., Morante, K., Tsumoto, K., Nieva, J.L., Caaveiro, J.M.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.207 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region.

Apellaniz, B., Rujas, E., Serrano, S., Morante, K., Tsumoto, K., Caaveiro, J.M., Jimenez, M.A., Nieva, J.L.

(2015) J Biol Chem 290: 12999-13015

• PubMed: 25787074 
• DOI: 10.1074/jbc.M115.644351
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The membrane-proximal external region (MPER) C-terminal segment and the transmembrane domain (TMD) of gp41 are involved in HIV-1 envelope glycoprotein-mediated fusion and modulation of immune responses during viral infection. However, the atomic structure of this functional region remains unsolved. Here, based on the high resolution NMR data obtained for peptides spanning the C-terminal segment of MPER and the TMD, we report two main findings: (i) the conformational variability of the TMD helix at a membrane-buried position; and (ii) the existence of an uninterrupted α-helix spanning MPER and the N-terminal region of the TMD. Thus, our structural data provide evidence for the bipartite organization of TMD predicted by previous molecular dynamics simulations and functional studies, but they do not support the breaking of the helix at Lys-683, as was suggested by some models to mark the initiation of the TMD anchor. Antibody binding energetics examined with isothermal titration calorimetry and humoral responses elicited in rabbits by peptide-based vaccines further support the relevance of a continuous MPER-TMD helix for immune recognition. We conclude that the transmembrane anchor of HIV-1 envelope is composed of two distinct subdomains: 1) an immunogenic helix at the N terminus also involved in promoting membrane fusion; and 2) an immunosuppressive helix at the C terminus, which might also contribute to the late stages of the fusion process. The unprecedented high resolution structural data reported here may guide future vaccine and inhibitor developments.

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Organizational Affiliation: 

From the Biophysics Unit (Consejo Superior de Investigaciones Científicas, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fab 4E10 Heavy chain	H	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab 4E10Light chain	L	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Envelope glycoprotein gp160	P	16	Human immunodeficiency virus type 1 (WMJ2 ISOLATE)	Mutation(s): 0  Gene Names: env
Find proteins for P05880 (Human immunodeficiency virus type 1 group M subtype B (isolate WMJ22)) Explore P05880  Go to UniProtKB:  P05880

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.207 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.3	α = 90
b = 44.58	β = 113.8
c = 85.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-11-16 
• Released Date: 2015-03-25 
Deposition Author(s): Rujas, E., Morante, K., Tsumoto, K., Nieva, J.L., Caaveiro, J.M.M.

Revision History 

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Database references
• Version 1.2: 2015-06-03
  Changes: Database references