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- EMDB-55102: Structure of cis-basal conformer of human CBS induced by non-acti... -

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Basic information

Entry
Database: EMDB / ID: EMD-55102
TitleStructure of cis-basal conformer of human CBS induced by non-activating allosteric SAO ligand - C1 symmetry -by single particle approach.
Map data
Sample
  • Complex: human CBS protein complex
Keywordstranssulfuration pathway / L-serine hydro-lyase / heme-binding protein / CBS domain / CYTOSOLIC PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsInayathulla M / Tomas M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_177195 Switzerland
CitationJournal: To Be Published
Title: Structure of cis-basal conformer of human CBS induced by non-activating allosteric SAO ligand - C1 symmetry -by single particle approach.
Authors: Inayathulla M / Tomas M
History
DepositionSep 18, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55102.png

Downloads & links

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Map

FileDownload / File: emd_55102.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-0.18849352 - 0.58821994
Average (Standard dev.)0.0010220496 (±0.014028563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55102_msk_1.map
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AxesZYX

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Additional map: unsharpened map

Fileemd_55102_additional_1.map
Annotationunsharpened map
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Half map: #1

Fileemd_55102_half_map_1.map
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Half map: #2

Fileemd_55102_half_map_2.map
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Sample components

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Entire : human CBS protein complex

EntireName: human CBS protein complex
Components
  • Complex: human CBS protein complex

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Supramolecule #1: human CBS protein complex

SupramoleculeName: human CBS protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
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: 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: 1.2 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: OTHER / Details: ab-initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 120136
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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