1AIK

HIV GP41 CORE STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1AIK/pdb

• Classification: VIRAL PROTEIN
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-04-20 Released: 1997-06-16 
• Deposition Author(s): Chan, D.C., Fass, D., Berger, J.M., Kim, P.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.266 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 

Literature

Core structure of gp41 from the HIV envelope glycoprotein.

Chan, D.C., Fass, D., Berger, J.M., Kim, P.S.

(1997) Cell 89: 263-273

• PubMed: 9108481 
• DOI: https://doi.org/10.1016/s0092-8674(00)80205-6
• Primary Citation of Related Structures:  
  1AIK


• PubMed Abstract: 
  

  The envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) consists of a complex of gp120 and gp41. gp120 determines viral tropism by binding to target-cell receptors, while gp41 mediates fusion between viral and cellular membranes. Previous studies identified an alpha-helical domain within gp41 composed of a trimer of two interacting peptides. The crystal structure of this complex, composed of the peptides N36 and C34, is a six-helical bundle. Three N36 helices form an interior, parallel coiled-coil trimer, while three C34 helices pack in an oblique, antiparallel manner into highly conserved, hydrophobic grooves on the surface of this trimer. This structure shows striking similarity to the low-pH-induced conformation of influenza hemagglutinin and likely represents the core of fusion-active gp41. Avenues for the design/discovery of small-molecule inhibitors of HIV infection are directly suggested by this structure.

---

Organizational Affiliation: 

Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Dihedral - D3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 8.43 kDa 
• Atom Count: 637 
• Modelled Residue Count: 72 
• Deposited Residue Count: 72 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 GP41 GLYCOPROTEIN	A [auth N]	37	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: GP41
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04578  Go to UniProtKB:  P04578

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 GP41 GLYCOPROTEIN	B [auth C]	35	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: GP41
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04578  Go to UniProtKB:  P04578

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.266 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.5	α = 90
b = 49.5	β = 90
c = 55.3	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-06-16 
Deposition Author(s): Chan, D.C., Fass, D., Berger, J.M., Kim, P.S.

Revision History  

• Version 1.0: 1997-06-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-16
  Changes: Structure summary