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Open data
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Basic information
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Title | MTHFR + SAH symmetric dis-inhibited state | |||||||||
![]() | Main Sharpened | |||||||||
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![]() | Dis-inhibited / allosteric / folate / S-adenosylhomocysteine / FLAVOPROTEIN | |||||||||
Function / homology | ![]() methylenetetrahydrofolate reductase (NADPH) / response to vitamin B2 / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine metabolic process / modified amino acid binding / homocysteine metabolic process / heterochromatin organization / S-adenosylmethionine metabolic process / Metabolism of folate and pterines ...methylenetetrahydrofolate reductase (NADPH) / response to vitamin B2 / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine metabolic process / modified amino acid binding / homocysteine metabolic process / heterochromatin organization / S-adenosylmethionine metabolic process / Metabolism of folate and pterines / methionine biosynthetic process / response to folic acid / tetrahydrofolate interconversion / response to amino acid / response to interleukin-1 / FAD binding / neural tube closure / NADP binding / flavin adenine dinucleotide binding / response to hypoxia / response to xenobiotic stimulus / protein-containing complex binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Blomgren LKM / Yue WW / Froese DS / McCorvie TJ | |||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 229.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.7 KB 20.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 35.3 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() ![]() | 120.9 MB 226.2 MB 226.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qa4MC ![]() 8qa5C ![]() 8qa6C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Main Sharpened | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.574 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Non-sharpened
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Annotation | Non-sharpened | ||||||||||||
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-Half map: #2
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-Half map: #1
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Sample components
-Entire : Human 5,10-methylenetetrahydrofolate reductase in complex with S-...
Entire | Name: Human 5,10-methylenetetrahydrofolate reductase in complex with S-Adenosyl-L-homocysteine, regulatory domains |
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Components |
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-Supramolecule #1: Human 5,10-methylenetetrahydrofolate reductase in complex with S-...
Supramolecule | Name: Human 5,10-methylenetetrahydrofolate reductase in complex with S-Adenosyl-L-homocysteine, regulatory domains type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Methylenetetrahydrofolate reductase (NADPH)
Macromolecule | Name: Methylenetetrahydrofolate reductase (NADPH) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 75.461195 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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-ADENOSYL-L-HOMOCYSTEINE
Macromolecule | Name: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: SAH |
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Molecular weight | Theoretical: 384.411 Da |
Chemical component information | ![]() ChemComp-SAH: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 28 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.0 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM HEPES, pH 7.5, 150 mM NaCl, 0.0025% Tween20, 1 mM S-Adenosyl-L-homocysteine, filter sterilised |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 5606 / Average exposure time: 5.18 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 90.1 / Target criteria: Cross-correlation coeficient |
Output model | ![]() PDB-8qa4: |