[English] 日本語
Yorodumi
- EMDB-18300: MTHFR + SAM inhibited state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18300
TitleMTHFR + SAM inhibited state
Map dataMain Sharpened
Sample
  • Complex: Human 5,10-methylenetetrahydrofolate reductase in complex with S-Adenosyl-L-Methionine
    • Protein or peptide: Methylenetetrahydrofolate reductase (NADPH)
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordsInhibited / allosteric / folate / S-Adenosylmethionin / FLAVOPROTEIN
Function / homology
Function and homology information


methylenetetrahydrofolate reductase (NADPH) / response to vitamin B2 / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / modified amino acid binding / methionine metabolic process / homocysteine metabolic process / heterochromatin organization / Metabolism of folate and pterines / methionine biosynthetic process ...methylenetetrahydrofolate reductase (NADPH) / response to vitamin B2 / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / modified amino acid binding / methionine metabolic process / homocysteine metabolic process / heterochromatin organization / Metabolism of folate and pterines / methionine biosynthetic process / S-adenosylmethionine metabolic process / response to folic acid / tetrahydrofolate interconversion / response to amino acid / response to interleukin-1 / FAD binding / neural tube closure / flavin adenine dinucleotide binding / NADP binding / response to hypoxia / response to xenobiotic stimulus / protein-containing complex binding / cytosol
Similarity search - Function
Eukaryotic-type methylenetetrahydrofolate reductase / : / MTHFR, SAM-binding regulatory domain / Methylenetetrahydrofolate reductase-like / Methylenetetrahydrofolate reductase / FAD-linked oxidoreductase-like
Similarity search - Domain/homology
Methylenetetrahydrofolate reductase (NADPH)
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsBlomgren LKM / Yue WW / Froese DS / McCorvie TJ
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_192505 Switzerland
CitationJournal: Nat Commun / Year: 2024
Title: Dynamic inter-domain transformations mediate the allosteric regulation of human 5, 10-methylenetetrahydrofolate reductase.
Authors: Linnea K M Blomgren / Melanie Huber / Sabrina R Mackinnon / Céline Bürer / Arnaud Baslé / Wyatt W Yue / D Sean Froese / Thomas J McCorvie /
Abstract: 5,10-methylenetetrahydrofolate reductase (MTHFR) commits folate-derived one-carbon units to generate the methyl-donor S-adenosyl-L-methionine (SAM). Eukaryotic MTHFR appends to the well-conserved ...5,10-methylenetetrahydrofolate reductase (MTHFR) commits folate-derived one-carbon units to generate the methyl-donor S-adenosyl-L-methionine (SAM). Eukaryotic MTHFR appends to the well-conserved catalytic domain (CD) a unique regulatory domain (RD) that confers feedback inhibition by SAM. Here we determine the cryo-electron microscopy structures of human MTHFR bound to SAM and its demethylated product S-adenosyl-L-homocysteine (SAH). In the active state, with the RD bound to a single SAH, the CD is flexible and exposes its active site for catalysis. However, in the inhibited state the RD pocket is remodelled, exposing a second SAM-binding site that was previously occluded. Dual-SAM bound MTHFR demonstrates a substantially rearranged inter-domain linker that reorients the CD, inserts a loop into the active site, positions Tyr404 to bind the cofactor FAD, and blocks substrate access. Our data therefore explain the long-distance regulatory mechanism of MTHFR inhibition, underpinned by the transition between dual-SAM and single-SAH binding in response to cellular methylation status.
History
DepositionAug 22, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18300.png

Downloads & links

-
Map

FileDownload / File: emd_18300.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 400 pix.
= 229.6 Å		0.57 Å/pix.
x 400 pix.
= 229.6 Å		0.57 Å/pix.
x 400 pix.
= 229.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.574 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.1348393 - 1.9430718
Average (Standard dev.)-0.00014706767 (±0.046766635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 229.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18300_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Non-sharpened

Fileemd_18300_additional_1.map
AnnotationNon-sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18300_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18300_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human 5,10-methylenetetrahydrofolate reductase in complex with S-...

EntireName: Human 5,10-methylenetetrahydrofolate reductase in complex with S-Adenosyl-L-Methionine
Components
  • Complex: Human 5,10-methylenetetrahydrofolate reductase in complex with S-Adenosyl-L-Methionine
    • Protein or peptide: Methylenetetrahydrofolate reductase (NADPH)
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

-
Supramolecule #1: Human 5,10-methylenetetrahydrofolate reductase in complex with S-...

SupramoleculeName: Human 5,10-methylenetetrahydrofolate reductase in complex with S-Adenosyl-L-Methionine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

-
Macromolecule #1: Methylenetetrahydrofolate reductase (NADPH)

MacromoleculeName: Methylenetetrahydrofolate reductase (NADPH) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.461195 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVNEARGNSS LNPCLEGSAS SGSESSKDSS RCSTPGLDPE RHERLREKMR RRLESGDKWF SLEFFPPRTA EGAVNLISRF DRMAAGGPL YIDVTWHPAG DPGSDKETSS MMIASTAVNY CGLETILHMT CCRQRLEEIT GHLHKAKQLG LKNIMALRGD P IGDQWEEE ...String:
MVNEARGNSS LNPCLEGSAS SGSESSKDSS RCSTPGLDPE RHERLREKMR RRLESGDKWF SLEFFPPRTA EGAVNLISRF DRMAAGGPL YIDVTWHPAG DPGSDKETSS MMIASTAVNY CGLETILHMT CCRQRLEEIT GHLHKAKQLG LKNIMALRGD P IGDQWEEE EGGFNYAVDL VKHIRSEFGD YFDICVAGYP KGHPEAGSFE ADLKHLKEKV SAGADFIITQ LFFEADTFFR FV KACTDMG ITCPIVPGIF PIQGYHSLRQ LVKLSKLEVP QEIKDVIEPI KDNDAAIRNY GIELAVSLCQ ELLASGLVPG LHF YTLNRE MATTEVLKRL GMWTEDPRRP LPWALSAHPK RREEDVRPIF WASRPKSYIY RTQEWDEFPN GRWGNSSSPA FGEL KDYYL FYLKSKSPKE ELLKMWGEEL TSEASVFEVF VLYLSGEPNR NGHKVTCLPW NDEPLAAETS LLKEELLRVN RQGIL TINS QPNINGKPSS DPIVGWGPSG GYVFQKAYLE FFTSRETAEA LLQVLKKYEL RVNYHLVNVK GENITNAPEL QPNAVT WGI FPGREIIQPT VVDPVSFMFW KDEAFALWIE QWGKLYEEES PSRTIIQYIH DNYFLVNLVD NDFPLDNCLW QVVEDTL EL LNRPTQNARE TEAPAENLYF Q

UniProtKB: Methylenetetrahydrofolate reductase (NADPH)

-
Macromolecule #2: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

-
Macromolecule #3: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES, pH 7.5, 150 mM NaCl, 5 mM S-Adenosyl-L-Methionine, filter sterilised
GridModel: Au-flat 1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 3 / Number real images: 2394 / Average exposure time: 6.17 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 240000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 882000
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 135192
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChainDetails

6151

source_name: AlphaFold, initial_model_type: in silico model
source_name: SwissModel, initial_model_type: in silico modelHomology modeling of human MTHFR using the AlphaFold models as a template
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 105.2 / Target criteria: Cross-correlation coeficient
Output model

PDB-8qa6:
MTHFR + SAM inhibited state

+
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