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- EMDB-55097: focused structure of regulatory domains of cis-basal conformer of... -

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Basic information

Entry
Database: EMDB / ID: EMD-55097
Titlefocused structure of regulatory domains of cis-basal conformer of human CBS induced by non-activating allosteric SAO ligand - by Helical approach
Map data
Sample
  • Complex: human Cystathionine beta-synthase Oligomeric complex
    • Protein or peptide: Cystathionine beta-synthase
  • Ligand: SINEFUNGIN
Keywordstranssulfuration pathway / L-serine hydro-lyase / heme-binding protein / CBS domain / LYASE
Function / homology
Function and homology information


Cysteine formation from homocysteine / L-homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / L-serine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / : / carbon monoxide binding / hydrogen sulfide biosynthetic process ...Cysteine formation from homocysteine / L-homocysteine catabolic process / modified amino acid binding / cystathionine beta-synthase / cystathionine beta-synthase activity / L-serine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / : / carbon monoxide binding / hydrogen sulfide biosynthetic process / L-serine metabolic process / homocysteine metabolic process / L-cysteine catabolic process / L-cysteine biosynthetic process / transsulfuration / nitric oxide binding / : / DNA protection / S-adenosyl-L-methionine binding / nitrite reductase (NO-forming) activity / oxygen binding / response to nutrient levels / pyridoxal phosphate binding / cellular response to hypoxia / heme binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily ...Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Cystathionine beta-synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.04 Å
AuthorsInayathulla M / Tomas M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation10.001.133 Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for a filamentous morpheein model of human cystathionine beta-synthase
Authors: Mohammed I / Mijatovic E / Philipp TM / Janickova L / Ascencao K / Asturias FJ / Martinez-Cruz LA / Szabo C / Stahlberg H / Majtan T
History
DepositionSep 18, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55097.png

Downloads & links

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Map

FileDownload / File: emd_55097.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.3450922 - 0.58194363
Average (Standard dev.)0.00069201994 (±0.018631041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55097_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_55097_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55097_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55097_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human Cystathionine beta-synthase Oligomeric complex

EntireName: human Cystathionine beta-synthase Oligomeric complex
Components
  • Complex: human Cystathionine beta-synthase Oligomeric complex
    • Protein or peptide: Cystathionine beta-synthase
  • Ligand: SINEFUNGIN

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Supramolecule #1: human Cystathionine beta-synthase Oligomeric complex

SupramoleculeName: human Cystathionine beta-synthase Oligomeric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cystathionine beta-synthase

MacromoleculeName: Cystathionine beta-synthase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: cystathionine beta-synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.665375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPM VRINKIGKKF GLKCELLAKC EFFNAGGSVK DRISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLALAAA V RGYRCIIV ...String:
MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPM VRINKIGKKF GLKCELLAKC EFFNAGGSVK DRISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLALAAA V RGYRCIIV MPEKMSSEKV DVLRALGAEI VRTPTNARFD SPESHVGVAW RLKNEIPNSH ILDQYRNASN PLAHYDTTAD EI LQQCDGK LDMLVASVGT GGTITGIARK LKEKCPGCRI IGVDPEGSIL AEPEELNQTE QTTYEVEGIG YDFIPTVLDR TVV DKWFKS NDEEAFTFAR MLIAQEGLLC GGSAGSTVAV AVKAAQELQE GQRCVVILPD SVRNYMTKFL SDRWMLQKGF LKEE DLTEK KPWWWHLRVQ ELGLSAPLTV LPTITCGHTI EILREKGFDQ APVVDEAGVI LGMVTLGNML SSLLAGKVQP SDQVG KVIY KQFKQIRLTD TLGRLSHILE MDHFALVVHE QIQYHSTGKS SQRQMVFGVV TAIDLLNFVA AQERDQK

UniProtKB: Cystathionine beta-synthase

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Macromolecule #2: SINEFUNGIN

MacromoleculeName: SINEFUNGIN / type: ligand / ID: 2 / Number of copies: 8 / Formula: SFG
Molecular weightTheoretical: 381.387 Da
Chemical component information

ChemComp-SFG:
SINEFUNGIN

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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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

Final reconstructionApplied symmetry - Helical parameters - Δz: 50.297 Å
Applied symmetry - Helical parameters - Δ&Phi: -172.188 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 4.04 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: cryoSPARC / Number images used: 211125
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-initio
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9spv:
focused structure of regulatory domains of cis-basal conformer of human CBS induced by non-activating allosteric SAO ligand - by Helical approach

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