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- EMDB-43634: HIV-1 CA R18A tetramer-of-pentamers -

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Basic information

Entry
Database: EMDB / ID: EMD-43634
TitleHIV-1 CA R18A tetramer-of-pentamers
Map dataMain map
Sample
  • Complex: Capsid-like particle of HIV-1 CA R18A assembled in 1 M NaCl
    • Protein or peptide: HIV-1 CA R18A
Keywordscapsid / VIRUS LIKE PARTICLE
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsSchirra RT / Pornillos O / Ganser-Pornillos BK
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI167756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54-AI170856 United States
CitationJournal: Viruses / Year: 2024
Title: Arg18 Substitutions Reveal the Capacity of the HIV-1 Capsid Protein for Non-Fullerene Assembly.
Authors: Randall T Schirra / Nayara F B Dos Santos / Barbie K Ganser-Pornillos / Owen Pornillos /
Abstract: In the fullerene cone HIV-1 capsid, the central channels of the hexameric and pentameric capsomers each contain a ring of arginine (Arg18) residues that perform essential roles in capsid assembly and ...In the fullerene cone HIV-1 capsid, the central channels of the hexameric and pentameric capsomers each contain a ring of arginine (Arg18) residues that perform essential roles in capsid assembly and function. In both the hexamer and pentamer, the Arg18 rings coordinate inositol hexakisphosphate, an assembly and stability factor for the capsid. Previously, it was shown that amino-acid substitutions of Arg18 can promote pentamer incorporation into capsid-like particles (CLPs) that spontaneously assemble in vitro under high-salt conditions. Here, we show that these Arg18 mutant CLPs contain a non-canonical pentamer conformation and distinct lattice characteristics that do not follow the fullerene geometry of retroviral capsids. The Arg18 mutant pentamers resemble the hexamer in intra-oligomeric contacts and form a unique tetramer-of-pentamers that allows for incorporation of an octahedral vertex with a cross-shaped opening in the hexagonal capsid lattice. Our findings highlight an unexpected degree of structural plasticity in HIV-1 capsid assembly.
History
DepositionFeb 6, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43634.png

Downloads & links

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Map

FileDownload / File: emd_43634.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 332 pix.
= 717.12 Å		2.16 Å/pix.
x 332 pix.
= 717.12 Å		2.16 Å/pix.
x 332 pix.
= 717.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-0.34275016 - 1.6014689
Average (Standard dev.)0.003028575 (±0.061793253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions332332332
Spacing332332332
CellA=B=C: 717.12006 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map

Fileemd_43634_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_43634_half_map_2.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Capsid-like particle of HIV-1 CA R18A assembled in 1 M NaCl

EntireName: Capsid-like particle of HIV-1 CA R18A assembled in 1 M NaCl
Components
  • Complex: Capsid-like particle of HIV-1 CA R18A assembled in 1 M NaCl
    • Protein or peptide: HIV-1 CA R18A

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Supramolecule #1: Capsid-like particle of HIV-1 CA R18A assembled in 1 M NaCl

SupramoleculeName: Capsid-like particle of HIV-1 CA R18A assembled in 1 M NaCl
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 CA R18A

MacromoleculeName: HIV-1 CA R18A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PIVQNLQGQM VHQAISPATL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF ...String:
PIVQNLQGQM VHQAISPATL NAWVKVVEEK AFSPEVIPMF SALSEGATPQ DLNTMLNTVG GHQAAMQMLK ETINEEAAEW DRLHPVHAG PIAPGQMREP RGSDIAGTTS TLQEQIGWMT HNPPIPVGEI YKRWIILGLN KIVRMYSPTS ILDIRQGPKE P FRDYVDRF YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPG ATLEEMMTAC QGVGGPGHKA RVL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 50 mM Tris, pH 8, 1 M NaCl, 5 mM 2-mercaptoethanol
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 43954
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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