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- PDB-9qpp: CryoEM structure of human MATa2 in complex with MAT2B isoform v1 ... -

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Basic information

Entry
Database: PDB / ID: 9qpp
TitleCryoEM structure of human MATa2 in complex with MAT2B isoform v1 at 2.6 A resolution
Components
  • 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: 2.6 Å
AuthorsKhaja, F. / Antonyuk, S.V. / Muench, S.P. / Hasnain, S.S.
Funding support1items
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, L.P. / Merriman, C. / Maerivoet, A. / White, J.B.R. / Muench, S.P. / Hasnain, S.S. / Antonyuk, S.V.
History
DepositionMar 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)287,6947
Polymers287,6947
Non-polymers00
Water3,117173
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
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
#2: Protein 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.: 3 / Mutation: NONE
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2B, TGR, MSTP045, Nbla02999, UNQ2435/PRO4995 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9NZL9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122584 / Symmetry type: POINT
RefinementHighest resolution: 2.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314521
ELECTRON MICROSCOPYf_angle_d0.53219653
ELECTRON MICROSCOPYf_dihedral_angle_d5.0581995
ELECTRON MICROSCOPYf_chiral_restr0.0452180
ELECTRON MICROSCOPYf_plane_restr0.0042554

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