[English] 日本語
Yorodumi
- EMDB-57756: CryoEM structure of human MATa2 in complex with MAT2B isoform v1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-57756
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: S-adenosylmethionine synthase isoform type-2
  • Protein or peptide: Isoform 1 of Methionine adenosyltransferase 2 subunit beta
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: 3.1 Å
AuthorsKhaja F / Antonyuk SV / Muench SP / Hasnain SS
Funding support1 items
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, 2026-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_57756.png

Downloads & links

-
Map

FileDownload / File: emd_57756.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: 0.0932
Minimum - Maximum-0.61339164 - 1.0422328
Average (Standard dev.)-0.000019013283 (±0.030234033)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_57756_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_57756_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: S-adenosylmethionine synthase isoform type-2
  • Protein or peptide: Isoform 1 of Methionine adenosyltransferase 2 subunit beta

-
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: #1 / Details: 4MATA2 plus 2MATB
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 249.75 KDa

-
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

-
Macromolecule #2: Isoform 1 of Methionine adenosyltransferase 2 subunit beta

MacromoleculeName: Isoform 1 of Methionine adenosyltransferase 2 subunit beta
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.603781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4ndn

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 51299
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more