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 9SLY | pdb_00009sly

CryoEM Structure of HIV-1 CA hexamer from Mxb1-35/CA-NC tube complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

MxB N-Terminus Adopts a Stable alpha-Helix to Engage the HIV-1 Capsid Trimer Interface.

Zhu, Y., Rey, J.S., Shen, J., Perilla, J.R., Zhang, P.

(2026) bioRxiv 

  • DOI: https://doi.org/10.64898/2026.09.03.749210
  • Primary Citation Related Structures: 
    9SLY

  • PubMed Abstract: 

    The HIV-1 capsid, composed of capsid (CA) proteins arranged into a conical surface lattice, serves as a critical platform for host-pathogen interactions. Many host cofactors regulate HIV-1 infection by selectively recognizing the higher-order CA lattice rather than individual monomers or capsomers. Among these, Myxovirus resistance protein B (MxB) is a key cellular restriction factor that binds the capsid via its N-terminal fragment containing an arginine-rich motif (RRR), blocking HIV-1 infection at early infection stages. However, the structural basis of this interaction has remained elusive. Here, we present a structural characterization of the CA lattice in complex with the MxB N-terminal fragment using cryo-electron tomography and subtomogram averaging. Combining cryoEM structures with EM-guided all-atom molecular dynamics simulations, we identify residue-specific interactions between MxB and the CA trimer interfaces. Notably, residues 10-20 of the MxB N-terminus adopt an α-helical conformation that stabilizes binding at the CA trimer interface, revealing a previously unrecognized mode of capsid engagement. These findings provide new insight into arginine-rich motif-mediated recognition by MxB and other host factors and establish a structural framework for the development of capsid-targeting antiviral therapeutics.


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

Macromolecule Content 

  • Total Structure Weight: 154.57 kDa 
  • Atom Count: 10,350 
  • Modeled Residue Count: 1,326 
  • Deposited Residue Count: 1,392 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gag polyprotein
A, B, C, D, E
A, B, C, D, E, F
232Homo sapiensMutation(s): 0 
Gene Names: gag
UniProt
Find proteins for T2CI25 (Human immunodeficiency virus type 1)
Explore T2CI25 
Go to UniProtKB:  T2CI25
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2CI25
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2026-10-14
    Changes: Data collection, Database references