Evidence map›Paper›PMID 40890096›Full record

ArticleNature communications2025

Structural basis for HIV-1 capsid adaption to a deficiency in IP6 packaging.

Yanan Zhu, Alex B Kleinpeter, Juan S Rey, Juan Shen, Yao Shen, Jialu Xu, Nathan Hardenbrook, Long Chen, Anka Lucic, Juan R Perilla and 2 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. MX2 Mediates Collapse of the HIV-1 Capsid.bioRxiv : the preprint server for biology · 2026
    Article
  4. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Yanan Zhu *Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0003-1025-7929
Alex B Kleinpeter *Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.ORCID http://orcid.org/0000-0001-5630-1345
Juan S Rey *Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.ORCID http://orcid.org/0000-0003-2274-3748
Juan ShenDivision of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
Yao ShenDivision of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-0278-0771
Jialu XuDivision of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
Nathan HardenbrookDivision of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
Long ChenDivision of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-5595-3026
Anka LucicDivision of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
Juan R PerillaDepartment of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA. jperilla@udel.edu.ORCID http://orcid.org/0000-0003-1171-6816
Eric O FreedVirus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA. efreed@nih.gov.ORCID http://orcid.org/0000-0003-3345-022X
Peijun ZhangDivision of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. peijun.zhang@strubi.ox.ac.uk.ORCID http://orcid.org/0000-0003-1803-691X

Funding

Project 3. IntegrationU54AI170791 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Christopher R Aiken · 2022 to 2026
$30.6M
Technology Development 2: MAS NMR and dynamic nuclear polarization for HIV-1 structural biologyP50AI150481 · NIAID · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI XIONG, YONG · 2019 to 2021
$14.1M
Determining the molecular mechanisms of HIV-1 maturationR01AI178846 · NIAID · UNIVERSITY OF DELAWARE · PI Juan Roberto Perilla Jimenez · 2023 to 2026
$2.3M
EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council) 101021133NIAID NIH HHS K99 AI174891NIAID NIH HHS P50 AI150481NIAID NIH HHS R01 AI178846NIAID NIH HHS U54 AI170791RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) BB/S003339/1U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) P50AI150481Wellcome TrustWellcome Trust (Wellcome) 206422/Z/17/ZWellcome Trust (Wellcome) 311427/Z/24/Z
6 · The paper itself

Abstract

Inositol hexakisphosphate (IP6) promotes HIV-1 assembly by stabilizing the immature Gag lattice and becomes enriched within virions, where it is required for mature capsid assembly. Previously, we identified Gag mutants that package little IP6 yet assemble particles, though they are non-infectious due to defective capsid formation. Here, we report a compensatory mutation, G225R, in the C-terminus of capsid protein (CA) that restores capsid assembly and infectivity in these IP6-deficient mutants. G225R also enhances in vitro assembly of CA into capsid-like particles at far lower IP6 concentrations than required for wild-type CA. CryoEM structures of G225R CA hexamers and lattices at 2.7 Å resolution reveal that the otherwise disordered C-terminus becomes structured, stabilizing hexamer-hexamer interfaces. Molecular dynamics simulations support this mechanism. These findings uncover how HIV-1 can adapt to IP6 deficiency and highlight a previously unrecognized structural role of the CA C-terminus, while offering tools for capsid-related studies.

Indexed as

CapsidCapsid ProteinsHIV-1Phytic AcidVirus AssemblyCryoelectron Microscopygag Gene Products, Human Immunodeficiency VirusHumansMolecular Dynamics SimulationMutationVirionCapsid Proteinsgag Gene Products, Human Immunodeficiency VirusPhytic Acid

Identifiers

PMID40890096
PMCPMC12402280

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.