9EK3 | pdb_00009ek3

HIV-1 immature WT matrix protein p17 lattice


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9EK3

This is version 1.1 of the entry. See complete history

Literature

Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity.

Chen, L.Hikichi, Y.Rey, J.S.Akil, C.Zhu, Y.Veler, H.Shen, Y.Perilla, J.R.Freed, E.O.Zhang, P.

(2025) Sci Adv 11: eadv4356-eadv4356

  • DOI: https://doi.org/10.1126/sciadv.adv4356
  • Primary Citation Related Structures: 
    9EK1, 9EK2, 9EK3

  • PubMed Abstract: 

    During HIV-1 maturation, the matrix (MA) lattice underlying the viral membrane undergoes a structural rearrangement, and the newly released capsid (CA) protein forms a mature CA. While it is well established that CA formation is essential for particle infectivity, the functional role of MA structural maturation remains unclear. Here, we examine maturation of an MA triple mutant, L20K/E73K/A82T, which, despite replicating similarly to wild-type (WT) in some cell lines, exhibits distinct biochemical behaviors that suggest altered MA-MA interactions. Cryo-electron tomography with subtomogram averaging reveals that, although the MA lattice in immature L20K/E73K/A82T virions closely resembles that of the WT, mature L20K/E73K/A82T virions lack a detectable MA lattice. All-atom molecular dynamics simulations suggest that this absence results from destabilized inter-trimer MA interactions in mature L20K/E73K/A82T mutant virions. These findings suggest that an ordered, membrane-associated mature MA lattice is not essential for HIV-1 infectivity, providing insights into the structural requirements for HIV-1 particle maturation and generation of infectious particles.


  • Organizational Affiliation
    • Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

Macromolecule Content 

  • Total Structure Weight: 519.22 kDa 
  • Atom Count: 36,387 
  • Modeled Residue Count: 4,485 
  • Deposited Residue Count: 4,485 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Matrix protein p17115Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYR

Query on MYR



Download:Ideal Coordinates CCD File
AB [auth N]
BB [auth O]
CB [auth P]
DB [auth Q]
EB [auth R]
AB [auth N],
BB [auth O],
CB [auth P],
DB [auth Q],
EB [auth R],
FB [auth S],
GB [auth T],
HB [auth U],
IB [auth V],
JB [auth W],
KB [auth X],
LB [auth Y],
MB [auth Z],
NA [auth A],
NB [auth a],
OA [auth B],
OB [auth b],
PA [auth C],
PB [auth c],
QA [auth D],
QB [auth d],
RA [auth E],
RB [auth e],
SA [auth F],
SB [auth f],
TA [auth G],
TB [auth g],
UA [auth H],
UB [auth h],
VA [auth I],
VB [auth i],
WA [auth J],
WB [auth j],
XA [auth K],
XB [auth k],
YA [auth L],
YB [auth l],
ZA [auth M],
ZB [auth m]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTNAMD3.0
MODEL REFINEMENTRosetta3.14

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI178846
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI150560
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI184080

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references