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- PDB-30gd: CryoEM structure of human MATa2 in complex with MAT2B isoform v1 ... -

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Basic information

Entry
Database: PDB / ID: 30gd
TitleCryoEM structure of human MATa2 in complex with MAT2B isoform v1 at 2.6 A resolution
Components
  • Isoform 1 of Methionine adenosyltransferase 2 subunit beta
  • S-adenosylmethionine synthase isoform type-2
KeywordsTRANSFERASE / Methylation / Adomet / SAMe / protein-protein complexes
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKhaja, F. / Antonyuk, S.V. / Muench, S.P. / Hasnain, S.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: IUCrJ / Year: 2026
Title: CryoEM structures reveal allosteric regulation of the catalytic activity of the multi-protein human MAT enzyme complexes.
Authors: Faisal T Khaja / Reedhi Vara / Louie P Aspinall / Ciara Merriman / Alana Maerivoet / Joshua B R White / Stephen P Muench / S Samar Hasnain / S V Antonyuk /
Abstract: S-Adenosyl methionine (SAMe), the biological methyl donor essential for sustaining the life of most complex organisms, is the second most widely used cofactor, after ATP, in biochemical reactions and ...S-Adenosyl methionine (SAMe), the biological methyl donor essential for sustaining the life of most complex organisms, is the second most widely used cofactor, after ATP, in biochemical reactions and is synthesized by the enzyme methionine adenosyl transferase (MAT) from ATP and methionine. MAT, also known as S-adenosylmethionine synthetase, is found in almost every organism. SAMe is employed universally by different methyltransferases that catalyze the methylation of biomolecules such as nucleic acids, proteins and lipids. In plant cells SAMe produced by MAT enzymes controls the level of critical metabolites such as ethylene, polyamines and biotin, and regulates essential cellular processes such as cell division and synthesis of cell wall, chlorophyll and membrane. MAT enzyme complex MATα2β, comprising the catalytic unit MATα2 and the regulatory protein MATβ, is found in nearly all human tissues and is essential for providing the necessary SAMe flux for methylation of DNA and various proteins including histones. The enzymatic activity of MATα2 is enhanced by several fold upon complexation with both variants of MATβ (βV1 and βV2). Using cryogenic electron microscopy, we determined the high-resolution resting-state structures of the MATα2βV1 and MATα2βV2 complexes, providing insights into the allosteric regulation of MAT catalytic activity, revealing how MATβV association could facilitate substrate binding, stabilize the transition state and promote product release to drive the catalytic cycle, and opening new possibilities for inhibitor binding.
History
DepositionApr 23, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Isoform 1 of Methionine adenosyltransferase 2 subunit beta
F: Isoform 1 of Methionine adenosyltransferase 2 subunit beta
B: S-adenosylmethionine synthase isoform type-2
A: S-adenosylmethionine synthase isoform type-2
C: S-adenosylmethionine synthase isoform type-2
D: S-adenosylmethionine synthase isoform type-2


Theoretical massNumber of molelcules
Total (without water)250,0906
Polymers250,0906
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Isoform 1 of Methionine adenosyltransferase 2 subunit beta / Methionine adenosyltransferase II beta / MAT II beta / Putative dTDP-4-keto-6-deoxy-D-glucose 4-reductase


Mass: 37603.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2B, TGR, MSTP045, Nbla02999, UNQ2435/PRO4995 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZL9
#2: Protein
S-adenosylmethionine synthase isoform type-2 / AdoMet synthase 2 / Methionine adenosyltransferase 2 / MAT 2 / Methionine adenosyltransferase II / MAT-II


Mass: 43720.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P31153, methionine adenosyltransferase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human MATA2 in complex with MATB isoform v1 / Type: COMPLEX / Details: 4MATA2 plus 2MATB / Entity ID: #2 / Source: RECOMBINANT
Molecular weightValue: 0.24975 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 50mM HEPES pH 7.5, 150mM NaCl and 1mM DTT
Buffer componentConc.: .05 Molar / Name: Hepes
SpecimenConc.: 0.125 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95318 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00517276
ELECTRON MICROSCOPYf_angle_d0.69423391
ELECTRON MICROSCOPYf_dihedral_angle_d4.8522351
ELECTRON MICROSCOPYf_chiral_restr0.0472585
ELECTRON MICROSCOPYf_plane_restr0.0053054

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