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- EMDB-53277: CryoEM structure of human MATa2 in complex with MAT2B isoform v1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53277
TitleCryoEM structure of human MATa2 in complex with MAT2B isoform v1 at 2.6 A resolution
Map data
Sample
  • Complex: human MATA2 in complex with MATB isoform v1
    • Protein or peptide: Methionine adenosyltransferase 2 subunit beta
  • Protein or peptide: S-adenosylmethionine synthase isoform type-2
  • Ligand: water
KeywordsMethylation / Adomet / SAMe / protein-protein complexes / TRANSFERASE
Function / homology
Function and homology information


methionine adenosyltransferase regulator activity / methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding ...methionine adenosyltransferase regulator activity / methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / protein heterooligomerization / Methylation / cellular response to methionine / protein hexamerization / small molecule binding / enzyme regulator activity / one-carbon metabolic process / positive regulation of TORC1 signaling / cellular response to leukemia inhibitory factor / Ub-specific processing proteases / enzyme binding / extracellular exosome / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate binding domain / 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 ...dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate binding domain / 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. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
S-adenosylmethionine synthase isoform type-2 / Methionine adenosyltransferase 2 subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsKhaja F / Antonyuk SV / Muench SP / Hasnain SS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: High resolution cryoEM structures reveal allosteric regulation of the catalytic activity of the multi-protein human MAT enzyme complexes
Authors: Khaja F / Vara R / Aspinall LP / Merriman C / Maerivoet A / White JBR / Muench SP / Hasnain SS / Antonyuk SV
History
DepositionMar 27, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53277.png

Downloads & links

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Map

FileDownload / File: emd_53277.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 380 pix.
= 281.2 Å		0.74 Å/pix.
x 380 pix.
= 281.2 Å		0.74 Å/pix.
x 380 pix.
= 281.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0647
Minimum - Maximum-0.50312614 - 1.22154
Average (Standard dev.)0.0003190375 (±0.03331969)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 281.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map from the final map as obtained from cryosparc

Fileemd_53277_additional_1.map
AnnotationSharpened map from the final map as obtained from cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer generated sharpened map

Fileemd_53277_additional_2.map
AnnotationDeepEMhancer generated sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local resolution map for MATBV1 subunit

Fileemd_53277_additional_3.map
AnnotationLocal resolution map for MATBV1 subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53277_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_53277_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human MATA2 in complex with MATB isoform v1

EntireName: human MATA2 in complex with MATB isoform v1
Components
  • Complex: human MATA2 in complex with MATB isoform v1
    • Protein or peptide: Methionine adenosyltransferase 2 subunit beta
  • Protein or peptide: S-adenosylmethionine synthase isoform type-2
  • Ligand: water

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Supramolecule #1: human MATA2 in complex with MATB isoform v1

SupramoleculeName: human MATA2 in complex with MATB isoform v1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2 / Details: 4MATA2 plus 2MATB
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 249.75 KDa

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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: Escherichia coli (E. coli)
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: Methionine adenosyltransferase 2 subunit beta

MacromoleculeName: Methionine adenosyltransferase 2 subunit beta / type: protein_or_peptide / ID: 2
Details: The residues at position 20,21 and 23 in Chain F and Chain G i.e. 'VFH', are actually the C-terminal residues 332, 333 and 334 of the same chain.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.603781 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MVGREKELSI HFVPGSCRLV EEEVNIPNRR VLVTGATGLL GRAVHKEFQQ NNWHAVGCGF RRARPKFEQV NLLDSNAVHH IIHDFQPHV IVHCAAERRP DVVENQPDAA SQLNVDASGN LAKEAAAVGA FLIYISSDYV FDGTNPPYRE EDIPAPLNLY G KTKLDGEK ...String:
MVGREKELSI HFVPGSCRLV EEEVNIPNRR VLVTGATGLL GRAVHKEFQQ NNWHAVGCGF RRARPKFEQV NLLDSNAVHH IIHDFQPHV IVHCAAERRP DVVENQPDAA SQLNVDASGN LAKEAAAVGA FLIYISSDYV FDGTNPPYRE EDIPAPLNLY G KTKLDGEK AVLENNLGAA VLRIPILYGE VEKLEESAVT VMFDKVQFSN KSANMDHWQQ RFPTHVKDVA TVCRQLAEKR ML DPSIKGT FHWSGNEQMT KYEMACAIAD AFNLPSSHLR PITDSPVLGA QRPRNAQLDC SKLETLGIGQ RTPFRIGIKE SLW PFLIDK RWRQTVFH

UniProtKB: Methionine adenosyltransferase 2 subunit beta

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 173 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.125 mg/mL
BufferpH: 7.5 / Component - Concentration: 0.05 Molar / Component - Name: Hepes / Details: 50mM HEPES pH 7.5, 150mM NaCl and 1mM DTT
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
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: PDB ENTRY
PDB model - PDB ID:

4ndn

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 122584
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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