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- EMDB-54905: Structure of trans-basal conformer of human CBS trapped in PLP-se... -

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Basic information

Entry
Database: EMDB / ID: EMD-54905
TitleStructure of trans-basal conformer of human CBS trapped in PLP-serine external aldemine intermediate (CBS-PLP-Ser)- by single particle approach
Map data
Sample
  • Complex: human CBS protein complex
    • Protein or peptide: Cystathionine beta-synthase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine
Keywordstranssulfuration pathway / L-serine hydro-lyase / heme-binding protein / CBS domain / CYTOSOLIC PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsInayathulla M / Tomas M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_177195 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
DepositionAug 27, 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_54905.png

Downloads & links

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Map

FileDownload / File: emd_54905.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 336 pix.
= 303.744 Å		0.9 Å/pix.
x 336 pix.
= 303.744 Å		0.9 Å/pix.
x 336 pix.
= 303.744 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.904 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.0860428 - 2.6272066
Average (Standard dev.)0.0007003447 (±0.031501457)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 303.744 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54905_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: unsharpened map

Fileemd_54905_additional_1.map
Annotationunsharpened map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_54905_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54905_half_map_2.map
Projections & Slices
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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
    • Protein or peptide: Cystathionine beta-synthase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine

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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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Macromolecule #1: Cystathionine beta-synthase

MacromoleculeName: Cystathionine beta-synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cystathionine beta-synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.402684 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPMV RINKIGKKFG LKCELLAKCE FFNAGGSVKD RISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLALAAA VRGYRCIIVM PEKMSSEKVD VLRALGAEIV RTPTNARFDS P ESHVGVAW ...String:
PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPMV RINKIGKKFG LKCELLAKCE FFNAGGSVKD RISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLALAAA VRGYRCIIVM PEKMSSEKVD VLRALGAEIV RTPTNARFDS P ESHVGVAW RLKNEIPNSH ILDQYRNASN PLAHYDTTAD EILQQCDGKL DMLVASVGTG GTITGIARKL KEKCPGCRII GV DPEGSIL AEPEELNQTE QTTYEVEGIG YDFIPTVLDR TVVDKWFKSN DEEAFTFARM LIAQEGLLCG GSAGSTVAVA VKA AQELQE GQRCVVILPD SVRNYMTKFL SDRWMLQKGF LKEEDLTEKK PWWWHLRVQE LGLSAPLTVL PTITCGHTIE ILRE KGFDQ APVVDEAGVI LGMVTLGNML SSLLAGKVQP SDQVGKVIYK QFKQIRLTDT LGRLSHILEM DHFALVVHEQ IQYHS TGKS SQRQMVFGVV TAIDLLNFVA AQERDQ

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: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}m...

MacromoleculeName: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine
type: ligand / ID: 3 / Number of copies: 2 / Formula: KOU
Molecular weightTheoretical: 334.219 Da
Chemical component information

ChemComp-KOU:
(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine

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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: 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: 2.5 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 reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: D1 symmetry imposed / Number images used: 135813
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
Output model

PDB-9shn:
Structure of trans-basal conformer of human CBS trapped in PLP-serine external aldemine intermediate (CBS-PLP-Ser)- by single particle approach

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