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- EMDB-38392: MAT2A in complex with SAM and allosteric inhibitor SCR-7952 -

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Basic information

Entry
Database: EMDB / ID: EMD-38392
TitleMAT2A in complex with SAM and allosteric inhibitor SCR-7952
Map data
Sample
  • Complex: Complex of MAT2A with SAM and allosteric inhibitor SCR-7952
    • Protein or peptide: S-adenosylmethionine synthase isoform type-2
  • Ligand: 7-chloranyl-5-(2-cyclopropylpyridin-3-yl)-1-methyl-imidazo[4,5-c]quinolin-4-one
  • Ligand: S-ADENOSYLMETHIONINE
Keywordsmethionine adenosyltransferase / cancer / SAM / ANTITUMOR PROTEIN
Function / homology
Function and homology information


methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding / one-carbon metabolic process / positive regulation of TORC1 signaling / cellular response to leukemia inhibitory factor / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2.
Similarity search - Domain/homology
S-adenosylmethionine synthase isoform type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsZhou F
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: MAT2A in complex with SAM and allosteric inhibitor SCR-7952
Authors: Zhou F
History
DepositionDec 20, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38392.png

Downloads & links

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Map

FileDownload / File: emd_38392.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 211. Å		1.06 Å/pix.
x 200 pix.
= 211. Å		1.06 Å/pix.
x 200 pix.
= 211. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.378
Minimum - Maximum-2.5412505 - 4.110828
Average (Standard dev.)0.006217533 (±0.16034065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 210.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38392_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_38392_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 : Complex of MAT2A with SAM and allosteric inhibitor SCR-7952

EntireName: Complex of MAT2A with SAM and allosteric inhibitor SCR-7952
Components
  • Complex: Complex of MAT2A with SAM and allosteric inhibitor SCR-7952
    • Protein or peptide: S-adenosylmethionine synthase isoform type-2
  • Ligand: 7-chloranyl-5-(2-cyclopropylpyridin-3-yl)-1-methyl-imidazo[4,5-c]quinolin-4-one
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: Complex of MAT2A with SAM and allosteric inhibitor SCR-7952

SupramoleculeName: Complex of MAT2A with SAM and allosteric inhibitor SCR-7952
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: S-adenosylmethionine synthase isoform type-2

MacromoleculeName: S-adenosylmethionine synthase isoform type-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: methionine adenosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.720625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNGQLNGFHE AFIEEGTFLF TSESVGEGHP DKICDQISDA VLDAHLQQDP DAKVACETVA KTGMILLAGE ITSRAAVDYQ KVVREAVKH IGYDDSSKGF DYKTCNVLVA LEQQSPDIAQ GVHLDRNEED IGAGDQGLMF GYATDETEEC MPLTIVLAHK L NAKLAELR ...String:
MNGQLNGFHE AFIEEGTFLF TSESVGEGHP DKICDQISDA VLDAHLQQDP DAKVACETVA KTGMILLAGE ITSRAAVDYQ KVVREAVKH IGYDDSSKGF DYKTCNVLVA LEQQSPDIAQ GVHLDRNEED IGAGDQGLMF GYATDETEEC MPLTIVLAHK L NAKLAELR RNGTLPWLRP DSKTQVTVQY MQDRGAVLPI RVHTIVISVQ HDEEVCLDEM RDALKEKVIK AVVPAKYLDE DT IYHLQPS GRFVIGGPQG DAGLTGRKII VDTYGGWGAH GGGAFSGKDY TKVDRSAAYA ARWVAKSLVK GGLCRRVLVQ VSY AIGVSH PLSISIFHYG TSQKSERELL EIVKKNFDLR PGVIVRDLDL KKPIYQRTAA YGHFGRDSFP WEVPKKLKY

UniProtKB: S-adenosylmethionine synthase isoform type-2

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Macromolecule #2: 7-chloranyl-5-(2-cyclopropylpyridin-3-yl)-1-methyl-imidazo[4,5-c]...

MacromoleculeName: 7-chloranyl-5-(2-cyclopropylpyridin-3-yl)-1-methyl-imidazo[4,5-c]quinolin-4-one
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1LVL
Molecular weightTheoretical: 350.802 Da

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Macromolecule #3: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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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

Concentration1.0 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Alphafold2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 679996
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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