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- EMDB-55099: Structure of cis-basal conformer of human CBS induced by non-acti... -

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Basic information

Entry
Database: EMDB / ID: EMD-55099
TitleStructure of cis-basal conformer of human CBS induced by non-activating allosteric SAO ligand - by single particle approach.
Map data
Sample
  • Complex: human CBS protein complex
    • Protein or peptide: Cystathionine beta-synthase
  • Protein or peptide: Cystathionine beta-synthase
  • Ligand: SINEFUNGIN
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
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: 4.11 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
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_55099.png

Downloads & links

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Map

FileDownload / File: emd_55099.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: 0.06
Minimum - Maximum-0.33872378 - 0.7105725
Average (Standard dev.)0.0005593959 (±0.013039743)
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_55099_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_55099_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55099_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55099_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 CBS protein complex

EntireName: human CBS protein complex
Components
  • Complex: human CBS protein complex
    • Protein or peptide: Cystathionine beta-synthase
  • Protein or peptide: Cystathionine beta-synthase
  • Ligand: SINEFUNGIN
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: human CBS protein complex

SupramoleculeName: human CBS protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
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: 1 / 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: Cystathionine beta-synthase

MacromoleculeName: Cystathionine beta-synthase / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO / EC number: cystathionine beta-synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.8935 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPM VRINKIGKKF GLKCELLAKC EFFNAGGSV(LLP) DRISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLAL AA AVRGYRCIIV ...String:
MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA SESPHHHTAP AKSPKILPDI LKKIGDTPM VRINKIGKKF GLKCELLAKC EFFNAGGSV(LLP) DRISLRMIED AERDGTLKPG DTIIEPTSGN TGIGLAL AA AVRGYRCIIV MPEKMSSEKV DVLRALGAEI VRTPTNARFD SPESHVGVAW RLKNEIPNSH ILDQYRNASN PLAHYDTT A DEILQQCDGK LDMLVASVGT GGTITGIARK LKEKCPGCRI IGVDPEGSIL AEPEELNQTE QTTYEVEGIG YDFIPTVLD RTVVDKWFKS NDEEAFTFAR MLIAQEGLLC GGSAGSTVAV AVKAAQELQE GQRCVVILPD SVRNYMTKFL SDRWMLQKGF LKEEDLTEK KPWWWHLRVQ ELGLSAPLTV LPTITCGHTI EILREKGFDQ APVVDEAGVI LGMVTLGNML SSLLAGKVQP S DQVGKVIY KQFKQIRLTD TLGRLSHILE MDHFALVVHE QIQYHSTGKS SQRQMVFGVV TAIDLLNFVA AQERDQK

UniProtKB: Cystathionine beta-synthase

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Macromolecule #3: SINEFUNGIN

MacromoleculeName: SINEFUNGIN / type: ligand / ID: 3 / Number of copies: 6 / Formula: SFG
Molecular weightTheoretical: 381.387 Da
Chemical component information

ChemComp-SFG:
SINEFUNGIN

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Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 4 / Number of copies: 2 / 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
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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 106308
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: FLEXIBLE FIT
Output model

PDB-9spw:
Structure of cis-basal conformer of human CBS induced by non-activating allosteric SAO ligand - by single particle approach.

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