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- EMDB-55115: Structure of trans-basal conformer of wild-type human CBS enzyme ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55115
TitleStructure of trans-basal conformer of wild-type human CBS enzyme in absence of substrate and allosteric activators- by Helical approach
Map dataunsharpened map
Sample
  • Complex: oligomeric assembly of human CBS enzyme
    • Protein or peptide: Cystathionine beta-synthase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
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: 3.0 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 23, 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_55115.png

Downloads & links

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Map

FileDownload / File: emd_55115.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 368.64 Å		0.72 Å/pix.
x 512 pix.
= 368.64 Å		0.72 Å/pix.
x 512 pix.
= 368.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.43511197 - 0.71511155
Average (Standard dev.)0.0010454459 (±0.016122995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 368.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55115_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55115_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_55115_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : oligomeric assembly of human CBS enzyme

EntireName: oligomeric assembly of human CBS enzyme
Components
  • Complex: oligomeric assembly of human CBS enzyme
    • Protein or peptide: Cystathionine beta-synthase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: oligomeric assembly of human CBS enzyme

SupramoleculeName: oligomeric assembly of human CBS enzyme / 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: 56.290477 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LWIRPDAPSR CTWQLGRPAS ESPHHHTAPA KSPKILPDIL KKIGDTPMVR INKIGKKFGL KCELLAKCEF FNAGGSV (LLP)D RISLRMIEDA ERDGTLKPGD TIIEPTSGNT GIGLALAAAV RGYRCIIVMP EKMSSEKVDV LRALGAEIVR TPTN ARFDS PESHVGVAWR ...String:
LWIRPDAPSR CTWQLGRPAS ESPHHHTAPA KSPKILPDIL KKIGDTPMVR INKIGKKFGL KCELLAKCEF FNAGGSV (LLP)D RISLRMIEDA ERDGTLKPGD TIIEPTSGNT GIGLALAAAV RGYRCIIVMP EKMSSEKVDV LRALGAEIVR TPTN ARFDS PESHVGVAWR LKNEIPNSHI LDQYRNASNP LAHYDTTADE ILQQCDGKLD MLVASVGTGG TITGIARKLK EKCPG CRII GVDPEGSILA EPEELNQTEQ TTYEVEGIGY DFIPTVLDRT VVDKWFKSND EEAFTFARML IAQEGLLCGG SAGSTV AVA VKAAQELQEG QRCVVILPDS VRNYMTKFLS DRWMLQKGFL KEEDLTEKKP WWWHLRVQEL GLSAPLTVLP TITCGHT IE ILREKGFDQA PVVDEAGVIL GMVTLGNMLS SLLAGKVQPS DQVGKVIYKQ FKQIRLTDTL GRLSHILEMD HFALVVHE Q IQYHSTGKSS QRQMVFGVVT AIDLLNFVAA QER

UniProtKB: Cystathionine beta-synthase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 10 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 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: 49.97 Å
Applied symmetry - Helical parameters - Δ&Phi: -116.06 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 335525
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

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9sqq:
Structure of trans-basal conformer of wild-type human CBS enzyme in absence of substrate and allosteric activators- by Helical approach

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