gp41 - ENV Glycoprotein 41

gp41 is a transmembrane glycoprotein that transverses the lipid bilayer of the virion

Homology Model created using PDB structures: 1envA.pdb, 2ezpB.pdb, 2ezrA.pdb, 2ezpC.pdb, 2ezrC.pdb
[animated gif: 320x240 ]
ViralZone:HIV-1
PDB: 1ENV-A, 2EZP-B/C, 2ERZ-A/C (HIV-1 gp41)
SwissProt: P04578 (HIV-1 HXB2 ENV)
Chime Tutorial: not available
Los Alamos HIV structure DB: HIV ENV
EMBL: K03455 [EMBL/GenBank/DDBJ]
BioAfrica: Env Protein Data Mining Tool


Isoforms:

  • gp41 - transmembrane glycoprotein (345 amino acids)

Localization:

  • Cell plasma membrane
  • Virion envelope

Function:

  • Non-covalently bound to gp120
  • Mediates the fusion of viral and cellular membranes
    (Ref. #3)

Additional Information:

  • the gp120-gp41 complex occurs as a trimer on the surface of the virion
  • contains an N-terminal fusogenic domain, which mediates the fusion of viral and cellular membranes (Ref. #3)
  • the interaction between gp120 with cellular receptors trigger gp41 to extend (forming a prehairpin intermediate), which interacts with the plasma membrane of the target cell
  • the extended prehairpin intermediate collapses into a trimer-of-hairpins structure that brings the amino- and carboxyl-terminal regions of the gp41 extracellular domain into close proximity
  • bringing the amino- and carboxyl-terminal regions of the extracellular domain together forces the membranes together in a manner that facilitates membrane fusion

Genomic Location: [TOP]

Reference Sequences:

HIV-1 (HXB2): 

          10         20         30         40         50         60         70
           |          |          |          |          |          |          |
  AVGIGALFLG FLGAAGSTMG AASMTLTVQA RQLLSGIVQQ QNNLLRAIEA QQHLLQLTVW GIKQLQARIL
          80         90        100        110        120        130        140
           |          |          |          |          |          |          |
  AVERYLKDQQ LLGIWGCSGK LICTTAVPWN ASWSNKSLEQ IWNHTTWMEW DREINNYTSL IHSLIEESQN 
         150        160        170        180        190        200        210
           |          |          |          |          |          |          |
  QQEKNEQELL ELDKWASLWN WFNITNWLWY IKLFIMIVGG LVGLRIVFAV LSIVNRVRQG YSPLSFQTHL 
         220        230        240        250        260        270        280
           |          |          |          |          |          |          |
  PTPRGPDRPE GIEEEGGERD RDRSIRLVNG SLALIWDDLR SLCLFSYHRL RDLLLIVTRI VELLGRRGWE 
         290        300        310        320        330        340 
           |          |          |          |          |          | 
  ALKYWWNLLQ YWSQELKNSA VSLLNATAIA VAEGTDRVIE VVQGACRAIR HIPRRIRQGL ERILL 
      [download in fasta format]

Length: 345 amino acids
Molecular Weight: 39558 Da
Theoretical pI: 8.92
Protein Domains/Folds/Motifs: [TOP]

InterPro signature for Envelope Polyprotein gp41 - IPR000328

Contains an N-terminal fusogenic domain, which mediates the fusion of viral and cellular membranes (Ref. #3)


Secondary Structure prediction:

Transmembrane Regions - tmhmm:


Low Complexity Regions - seg:


Coiled-coil Region - ncoils:


Antigenic Sites - EMBOSS:
Predicted Motifs: Printer-friendly version
N-glycosylation:
N-myristoylation:
Amidation:
Protein kinase C:
Casein kinase II:
Tyrosine kinase:
cAMP / cGMP kinase:
Cell attachment motif:
Asp Protease motif:
Asp Prot Retro motif:
Cysteine-rich Region:
Tryptophan-rich Region:
Zinc-finger CCHC motif:
Leucine Zipper motif:

Protein-Protein Interactions: [TOP]

  • HIV gp41 interacts with the HIV Gag polyprotein prior to its incorporation into nascent virions
  • HIV gp41 interacts non-covalently with gp120
  • HIV gp41 interacts with the host cellular membrane
Primary and Secondary Database Entries: [TOP]

Identifiers:

ViralZone: HIV-1
PDB/MMDB: Search for HIV-1 & gp41

SwissProt: P04578 (HIV-1 HXB2 ENV)
EMBL: K03455; AAB50262.1 [EMBL/GenBank/DDBJ]

PIR: UNKNOWN
HIV: K03455; UNKNOWN$HXB2
InterPro: IPR000328 - gp41 family
Pfam: PF00517 - gp41 family
Prints: none
ProDom: PD000125 (31 - 80) / PD001599 (41 - 168) / PD605682 (81 - 107) / PD460876 (82 - 129)
PD628734 (108 - 129) / PD657031 (109 - 128) / PD553288 (153 - 204) / PD000116 (159 - 205)
PD653931 (159 - 205)/ PD000205 (206 - 284) / PD000745 (285 - 345) / PD000212 (286 - 332)
SCOP: SSF56349 - DNA breaking-rejoining enzymes / SSF56425 - Succinate dehydrogenase catalytic domain
BLOCKS: P04578
Prosite: P04578
ProtoNet: P04578
ProtoMap: P04578
PRESAGE: P04578
Database of Interacting Proteins: P04578
ModBase: P04578
Swiss-2DPAGE: 2D gel

BioAfrica Tools:
- Env Protein Data Mining Tool provides real-time analysis of HIV-1 Env isolates
- HIV Structure BLAST searches for similar HIV sequences that have known structures
- HIV Proteomics Resource contains protein sequence and structure analysis tools
Reviews and References: [TOP]

Cite the resource by citing the following paper:
Doherty R et al. BioAfrica's HIV-1 Proteomics Resource: Combining protein data with bioinformatics tools. Retrovirology (2005), 9;2(1):18.

1 - HIV Sequence Compendium 2000
Kuiken CL, Foley B, Hahn B, Korber B, Marx PA, McCutchan F, Mellors JW, Mullins JI, Sodroski J, Wolinksy S.
Theoretical Biol. & Biophys. Group, Los Alamos Nat Lab, LA-UR 01-3860 [Read it online: Compendium]
2 - Retroviruses
Coffin JM, Hughes SH, Varmus HE.
CD-ROM ed. (2002) Cold Spring Harbor Laboratory Press [Read it online: NCBI Bookshelf]
3 - A CD4 domain important for HIV-mediated syncytium formation lies outside the virus binding site.
Camerini D, Seed B.
Cell 60: 747-754 (1990) [pubmed: 2107024]
4 - [viral/plasma membrane fusion activity of gp41 core domain] The crystal structure of the SIV gp41
ectodomain at 1.47 A resolution.
Yang ZN, Mueser TC, Kaufman J, Stahl SJ, Wingfield PT, Hyde CC.
J Struct Biol 126(2): 131-144 (1999) [pubmed: 10388624]



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