9H1P | pdb_00009h1p

Mature HIV-1 matrix from MA-SP1 cleavage mutant


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The conserved HIV-1 spacer peptide 2 triggers matrix lattice maturation.

Stacey, J.C.V.Hrebik, D.Nand, E.Shetty, S.D.Qu, K.Boicu, M.Anders-Osswein, M.Uchil, P.D.Dick, R.A.Mothes, W.Krausslich, H.G.Muller, B.Briggs, J.A.G.

(2025) Nature 640: 258-264

  • DOI: https://doi.org/10.1038/s41586-025-08624-9
  • Primary Citation of Related Structures:  
    9H1P

  • PubMed Abstract: 

    The virus particles of human immunodeficiency virus type 1 (HIV-1) are released in an immature, non-infectious form. Proteolytic cleavage of the main structural polyprotein Gag into functional domains induces rearrangement into mature, infectious virions. In immature virus particles, the Gag membrane-binding domain, MA, forms a hexameric protein lattice that undergoes structural transition, following cleavage, into a distinct, mature MA lattice 1 . The mechanism of MA lattice maturation is unknown. Here we show that released spacer peptide 2 (SP2), a conserved peptide of unknown function situated about 300 residues downstream of MA, binds MA to induce structural maturation. By high-resolution in-virus structure determination of MA, we show that MA does not bind lipid into a side pocket as previously thought 1 , but instead binds SP2 as an integral part of the protein-protein interfaces that stabilize the mature lattice. Analysis of Gag cleavage site mutants showed that SP2 release is required for MA maturation, and we demonstrate that SP2 is sufficient to induce maturation of purified MA on lipid monolayers in vitro. SP2-triggered MA maturation correlated with faster fusion of virus with target cells. Our results reveal a new, unexpected interaction between two HIV-1 components, provide a high-resolution structure of mature MA, establish the trigger of MA structural maturation and assign function to the SP2 peptide.


  • Organizational Affiliation
    • Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag polyprotein
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
131Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 0 
Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12493 
Go to UniProtKB:  P12493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12493
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gag polyprotein
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
16Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 0 
Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12493 
Go to UniProtKB:  P12493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12493
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.3
MODEL REFINEMENTPHENIX1.21

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany240245660 - SFB 1129 (project 5 HGK, project 6 BM, project 931 21 JAGB)
German Research Foundation (DFG)GermanyDFG KR 906/7-1 (HGK)
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesT32 AI055403
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-12
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.3: 2025-04-16
    Changes: Data collection, Database references