[English] 日本語
Yorodumi
- EMDB-57891: HIV-1 CA tri-hexamer interface -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-57891
TitleHIV-1 CA tri-hexamer interface
Map data
Sample
  • Complex: HIV-1 CA tri-hexamer interface
    • Protein or peptide: HIV-1 CA
KeywordsHIV-1 CA / VIRAL PROTEIN
Biological speciesHIV-1 group M (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsGoodale A / DiMaio F / Bergeron JRC
Funding support France, United Kingdom, 2 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGY0080/2021 France
Medical Research Council (MRC, United Kingdom)MR/W006820/1 United Kingdom
CitationJournal: bioRxiv / Year: 2026
Title: MX2 Mediates Collapse of the HIV-1 Capsid.
Authors: Andrew Goodale / Szu-Wei Huang / Nathalia Almeida / Dave J Williamson / Nikoloz Shkriabai / Gilberto Betancor / Luis Apolonia / Frank DiMaio / Sergi Padilla-Parra / Mamuka Kvaratskhelia / ...Authors: Andrew Goodale / Szu-Wei Huang / Nathalia Almeida / Dave J Williamson / Nikoloz Shkriabai / Gilberto Betancor / Luis Apolonia / Frank DiMaio / Sergi Padilla-Parra / Mamuka Kvaratskhelia / Julien R C Bergeron / Michael H Malim /
Abstract: The HIV-1 capsid core encapsulates the viral genome and mediates its delivery into the host cell's nucleus. It is composed of multiple copies of the Capsid (CA, p24) protein, assembled into hexamers ...The HIV-1 capsid core encapsulates the viral genome and mediates its delivery into the host cell's nucleus. It is composed of multiple copies of the Capsid (CA, p24) protein, assembled into hexamers and pentamers to create a lattice that forms a fullerene-like cone. Myxovirus resistance 2 (MX2) is an HIV-1 restriction factor that binds to the capsid core and blocks nuclear import of the viral genome. Here, we define a minimal region of MX2 required for HIV-1 restriction and produce a corresponding functional recombinant protein. We have used cryo-electron microscopy to determine the structure of this MX2 fragment bound to the tri-hexamer interface of the capsid lattice, revealing a large, buried interface combining electrostatic and hydrophobic interactions. This structure, together with assays that measure capsid core destabilisation, shows that MX2 binding induces conformational rearrangements in the capsid lattice that culminate in a loss of integrity. These results support a model whereby MX2 exerts its antiviral activity by disrupting the capsid lattice, inducing premature fragmentation and preventing HIV-1 nuclear import. By revealing the structural basis for MX2-mediated restriction, this work also provides the framework for the development of anti-HIV molecules that mimic MX2 restriction.
History
DepositionMay 5, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_57891.png

Downloads & links

-
Map

FileDownload / File: emd_57891.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 252 pix.
= 277.2 Å		1.1 Å/pix.
x 252 pix.
= 277.2 Å		1.1 Å/pix.
x 252 pix.
= 277.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.7293459 - 0.7821351
Average (Standard dev.)0.0037731256 (±0.03296133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions252252252
Spacing252252252
CellA=B=C: 277.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_57891_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_57891_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HIV-1 CA tri-hexamer interface

EntireName: HIV-1 CA tri-hexamer interface
Components
  • Complex: HIV-1 CA tri-hexamer interface
    • Protein or peptide: HIV-1 CA

-
Supramolecule #1: HIV-1 CA tri-hexamer interface

SupramoleculeName: HIV-1 CA tri-hexamer interface / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: HIV-1 group M (virus)

-
Macromolecule #1: HIV-1 CA

MacromoleculeName: HIV-1 CA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: HIV-1 group M (virus)
Molecular weightTheoretical: 25.761623 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPIVQNLQGQ MVHQAISPRT LNAWVKVVEE KAFSPEVIPM FSALSEGATP QDLNTMLNTV GGHQAAMQML KETINEEAAE WDRLHPVHA GPIAPGQMRE PRGSDIAGTT STLQEQIGWM THNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK E PFRDYVDR ...String:
MPIVQNLQGQ MVHQAISPRT LNAWVKVVEE KAFSPEVIPM FSALSEGATP QDLNTMLNTV GGHQAAMQML KETINEEAAE WDRLHPVHA GPIAPGQMRE PRGSDIAGTT STLQEQIGWM THNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK E PFRDYVDR FYKTLRAEQA SQEVKNWMTE TLLVQNANPD CKTILKALGP GATLEEMMTA CQGVGGPGHK ARVL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3j34

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 458221
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more