Annotations for this protein have been verified by the authors of the corresponding papers


DP00048: Protein NefFASTA viewXML view

General information
DisProt:DP00048
Name:Protein Nef
Synonym(s):NEF_HV1BR
Negative factor
F-protein
3'ORF
C-terminal core protein [cleavage product 1]
First appeared in release:Release 1.0 (08/01/2003)
UniProt:P03406
UniGene: 
SwissProt: NEF_HV1BR
TrEMBL:  
NCBI (GI): 128023
Source organism:Human immunodeficiency virus type 1 (isolate BRU/LAI group M subtype B) (HIV-1)
Sequence length:206
Percent disordered:52%
Homologues: 


Native sequence

        10         20         30         40         50         60
         |          |          |          |          |          |
MGGKWSKSSV VGWPTVRERM RRAEPAADGV GAASRDLEKH GAITSSNTAA TNAACAWLEA - 60
QEEEEVGFPV TPQVPLRPMT YKAAVDLSHF LKEKGGLEGL IHSQRRQDIL DLWIYHTQGY - 120
FPDWQNYTPG PGVRYPLTFG WCYKLVPVEP DKVEEANKGE NTSLLHPVSL HGMDDPEREV - 180
LEWRFDSRLA FHHVARELHP EYFKNC



Functional narrative    

Human immunodeficiency virus (HIV) Nef protein accelerates virulent progression of acquired immunodeficiency syndrome (AIDS) by its interaction with specific cellular proteins (Src family proteins) involved in signal transduction and host cell activation. Nef is a regulatory myristoylated protein of HIV that has a two-domain structure comprising of an anchor domain and a core domain separated by the specific cleavage site of the HIV proteases. This small, ~27kDa protein is expressed in the early stages of viral replication and is postranslationaly modified by phosphorylation and an irreversible attachment of myristic acid to the N-terminus, which targets Nef to the cellular membrane. The unstructured regions comprise ~70 residues at the N-terminus, 30 amino acid loop, and a small (3 residue) flexible region at the C-terminus. These regions reveal an accessible surface that can be used to connect to other molecules and interact simultaneously to orchestrate quaternary assemblies.

Region 4: 1-70 Region 1: 1-73 Region 6: 71-147 Region 5: 148-178 Region 2: 149-178 Region 7: 179-203 Region 3: 204-206

Map of ordered and disordered regions







Note: 'Mouse' over a region to see the start and stop residues. Click on a region to see detailed information.


Region 1
Type:Disordered - Extended
Name: 
Location:1 - 73
Length:73
Region sequence:

MGGKWSKSSVVGWPTVRERMRRAEPAADGVGAASRDLEKHGAITSSNTAATNAACAWLEA
QEEEEVGFPVTPQ

Modification type:  
PDB: 1AVV:A, 1AVZ:A, 1EFN:A, 1QA4:A
Structural/functional type: Function arises from the disordered state
Function arises via a disorder to order transition
Functional classes: Molecular assembly
Entropic chain
Functional subclasses: Regulation of proteolysis in vivo
Protein-protein binding
Protein-lipid interaction
Flexible linkers/spacers
Phosphorylation
Fatty acylation (myristolation and palmitoylation)
Detection methods:
  1. Nuclear magnetic resonance (NMR)

  2. X-ray crystallography
References:
  1. Arold S, Franken P, Strub MP, Hoh F, Benichou S, Benarous R, Dumas C. "The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling." Structure. 1997; 5(10): 1361-72. PubMed: 9351809
Comments:
This region was disordered according to the PDB files.


Region 2
Type:Disordered - Extended
Name: 
Location:149 - 178
Length:30
Region sequence:

EPDKVEEANKGENTSLLHPVSLHGMDDPER

Modification type:  
PDB: 1AVV:A, 1AVZ:A, 1EFN:A, 1QA4:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Protein-protein binding
Detection methods:
  1. Nuclear magnetic resonance (NMR)

  2. X-ray crystallography
References:
  1. Arold S, Franken P, Strub MP, Hoh F, Benichou S, Benarous R, Dumas C. "The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling." Structure. 1997; 5(10): 1361-72. PubMed: 9351809
Comments:
This region was disordered according to the PDB files.


Region 3
Type:Disordered - Extended
Name: 
Location:204 - 206
Length:3
Region sequence:

KNC

Modification type:  
PDB: 1AVV:A, 1AVZ:A, 1EFN:A, 1QA4:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Unknown
Detection methods:
  1. Nuclear magnetic resonance (NMR)

  2. X-ray crystallography
References:
  1. Arold S, Franken P, Strub MP, Hoh F, Benichou S, Benarous R, Dumas C. "The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling." Structure. 1997; 5(10): 1361-72. PubMed: 9351809
Comments:
This region was disordered according to the PDB files.


Region 4
Type:Disordered - Extended
Name: 
Location:1 - 70
Length:70
Region sequence:

MGGKWSKSSVVGWPTVRERMRRAEPAADGVGAASRDLEKHGAITSSNTAATNAACAWLEA
QEEEEVGFPV

Modification type:  
PDB: 1AVV:A, 1AVZ:A, 1EFN:A, 1QA4:A
Structural/functional type: Function arises from the disordered state
Function arises via a disorder to order transition
Functional classes: Molecular assembly
Entropic chain
Functional subclasses: Fatty acylation (myristolation and palmitoylation)
Regulation of proteolysis in vivo
Protein-protein binding
Protein-lipid interaction
Flexible linkers/spacers
Phosphorylation
Detection methods:
  1. Nuclear magnetic resonance (NMR)

  2. X-ray crystallography
References:
  1. Arold ST, Baur AS. "Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein." Trends Biochem Sci. 2001; 26(6): 356-63. PubMed: 11406408
Comments:
 



Region 5
Type:Disordered - Extended
Name: 
Location:148 - 178
Length:31
Region sequence:

VEPDKVEEANKGENTSLLHPVSLHGMDDPER

Modification type:  
PDB: 1AVV:A, 1AVZ:A, 1EFN:A, 1QA4:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Unknown
Detection methods:
  1. Nuclear magnetic resonance (NMR)

  2. X-ray crystallography
References:
  1. Arold ST, Baur AS. "Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein." Trends Biochem Sci. 2001; 26(6): 356-63. PubMed: 11406408
Comments:
 



Region 6
Type:Ordered
Name: 
Location:71 - 147
Length:77
Region sequence:

TPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPG
PGVRYPLTFGWCYKLVP

Modification type:  
PDB: 1AVV:A
Structural/functional type:  
Functional classes:  
Functional subclasses:  
Detection methods:
  1. Nuclear magnetic resonance (NMR)

  2. X-ray crystallography
References:
  1. Arold ST, Baur AS. "Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein." Trends Biochem Sci. 2001; 26(6): 356-63. PubMed: 11406408
Comments:
 



Region 7
Type:Ordered
Name: 
Location:179 - 203
Length:25
Region sequence:

EVLEWRFDSRLAFHHVARELHPEYF

Modification type:  
PDB: 1AVV:A
Structural/functional type:  
Functional classes:  
Functional subclasses:  
Detection methods:
  1. Nuclear magnetic resonance (NMR)

  2. X-ray crystallography
References:
  1. Arold ST, Baur AS. "Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein." Trends Biochem Sci. 2001; 26(6): 356-63. PubMed: 11406408
Comments:
 



Comments


Additional UniProt ID: Q71VG3


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