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- EMDB-54044: STA structure of CA-MxB complex from HIV-1 CA-NC tube incubated w... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-54044
TitleSTA structure of CA-MxB complex from HIV-1 CA-NC tube incubated with MxB C-terminal tail
Map datamap
Sample
  • Complex: in vitro assembled HIV-1 CA-NC tube
KeywordsHIV-1 / hexamer / CA-NC tube / MxB / VIRUS
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 5.3 Å
AuthorsZhu Y / Shen J / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: MxB N-terminal tail adopts a stable alpha-helical conformation at the HIV-1 CA tri-hexamer interface
Authors: Zhu Y / Rey SJ / Shen J / Perilla RJ / Zhang P
History
DepositionJun 17, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54044.png

Downloads & links

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Map

FileDownload / File: emd_54044.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 192 pix.
= 257.28 Å		1.34 Å/pix.
x 192 pix.
= 257.28 Å		1.34 Å/pix.
x 192 pix.
= 257.28 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: 0.0159
Minimum - Maximum-0.048318055 - 0.06145525
Average (Standard dev.)0.000000000000011 (±0.00501717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 257.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half2

Fileemd_54044_half_map_1.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1

Fileemd_54044_half_map_2.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : in vitro assembled HIV-1 CA-NC tube

EntireName: in vitro assembled HIV-1 CA-NC tube
Components
  • Complex: in vitro assembled HIV-1 CA-NC tube

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Supramolecule #1: in vitro assembled HIV-1 CA-NC tube

SupramoleculeName: in vitro assembled HIV-1 CA-NC tube / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 21392
ExtractionNumber tomograms: 53 / Number images used: 129046 / Software - Name: emClarity
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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