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- EMDB-55015: CryoET STA structure of Class2 from Mxb1-35/CA-NC complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-55015
TitleCryoET STA structure of Class2 from Mxb1-35/CA-NC complex
Map datamerged map
Sample
  • Complex: Mxb1-35/CA-NC tube complex
KeywordsMxb / HIV-1 CA-NC structure / VIRUS
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 4.5 Å
AuthorsZhu Y / Rey SJ / Shen J / Perilla RJ / Zhang P
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_55015.png

Downloads & links

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Map

FileDownload / File: emd_55015.map.gz / Format: CCP4 / Size: 27 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 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: 0.015
Minimum - Maximum-0.030440617 - 0.051998742
Average (Standard dev.)-0.000000000000107 (±0.004577838)
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_55015_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_55015_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 : Mxb1-35/CA-NC tube complex

EntireName: Mxb1-35/CA-NC tube complex
Components
  • Complex: Mxb1-35/CA-NC tube complex

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

SupramoleculeName: Mxb1-35/CA-NC tube complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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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: 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: 5.5 µm / Nominal defocus min: 1.5 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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 107654
ExtractionNumber tomograms: 53 / Number images used: 129046 / Software - Name: RELION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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