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- EMDB-55019: CryoEM Structure of HIV-1 CA hexamer from Mxb1-35/CA-NC tube complex -

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Basic information

Entry
Database: EMDB / ID: EMD-55019
TitleCryoEM Structure of HIV-1 CA hexamer from Mxb1-35/CA-NC tube complex
Map datamerged map
Sample
  • Complex: HIV-1 CA hexamer from Mxb1-35/CA-NC tube complex
    • Protein or peptide: Gag polyprotein
KeywordsMxb / HIV-1 CA-NC structure / VIRUS
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / virion membrane / structural molecule activity / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsZhu Y / Shen J / Zhang P / Perilla RJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: MxB N-Terminus Adopts a Stable alpha-Helix to Engage the HIV-1 Capsid Trimer Interface
Authors: Zhu Y / Rey SJ / Shen J / Perilla RJ / Zhang P
History
DepositionSep 5, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55019.png

Downloads & links

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Map

FileDownload / File: emd_55019.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmerged map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 256 pix.
= 343.04 Å		1.34 Å/pix.
x 256 pix.
= 343.04 Å		1.34 Å/pix.
x 256 pix.
= 343.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.239
Minimum - Maximum-0.001809411 - 1.8707321
Average (Standard dev.)0.002314366 (±0.02935256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 343.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55019_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1

Fileemd_55019_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_55019_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 CA hexamer from Mxb1-35/CA-NC tube complex

EntireName: HIV-1 CA hexamer from Mxb1-35/CA-NC tube complex
Components
  • Complex: HIV-1 CA hexamer from Mxb1-35/CA-NC tube complex
    • Protein or peptide: Gag polyprotein

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Supramolecule #1: HIV-1 CA hexamer from Mxb1-35/CA-NC tube complex

SupramoleculeName: HIV-1 CA hexamer from Mxb1-35/CA-NC tube complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gag polyprotein

MacromoleculeName: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.761623 KDa
Recombinant expressionOrganism: Escherichia (bacteria)
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

UniProtKB: Gag polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2845984
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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