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Open data
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Basic information
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Title | Cryo-EM structure of the Human SHMT1-RNA complex | |||||||||
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![]() | Riboregulation / Metabolism / 1 carbon metablism / Moonlighting protein / RNA BINDING PROTEIN / TRANSFERASE | |||||||||
Function / homology | ![]() cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / Metabolism of folate and pterines ...cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / serine binding / Metabolism of folate and pterines / L-serine catabolic process / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / dTMP biosynthetic process / cobalt ion binding / folic acid metabolic process / small molecule binding / mRNA regulatory element binding translation repressor activity / cellular response to leukemia inhibitory factor / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / negative regulation of translation / protein homodimerization activity / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | |||||||||
![]() | Spizzichino S / Marabelli C / Bharadwaj A / Jakobi AJ / Chaves-Sanjuan A / Giardina G / Bolognesi M / Cutruzzola F | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the Human SHMT1-RNA complex Authors: Spizzichino S / Marabelli C / Bharadwaj A / Jakobi AJ / Chaves-Sanjuan A / Giardina G / Bolognesi M / Cutruzzola F | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 144.4 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 194.7 MB 194.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 673.3 KB | Display | ![]() |
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Full document | ![]() | 672.9 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8a11MC 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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Voxel size | X=Y=Z: 0.889 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_15065_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15065_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50)
Entire | Name: human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50) |
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Components |
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-Supramolecule #1: human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50)
Supramolecule | Name: human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: SHMT1= homotetramer of 53kDa subunits |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 53 kDa/nm |
-Macromolecule #1: Serine hydroxymethyltransferase, cytosolic
Macromolecule | Name: Serine hydroxymethyltransferase, cytosolic / type: protein_or_peptide / ID: 1 Details: first 3 N-ter residues come from removal of His-tag. Sequence numbering starts from first M residue. K257 is covalently bound to PLP forming an internal aldimine (LLP) Number of copies: 4 / Enantiomer: LEVO / EC number: glycine hydroxymethyltransferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 53.434797 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMTMPVNG AHKDADLWSS HDKMLAQPLK DSDVEVYNII KKESNRQRVG LELIASENFA SRAVLEALGS CLNNKYSEGY PGQRYYGGT EFIDELETLC QKRALQAYKL DPQCWGVNVQ PYSGSPANFA VYTALVEPHG RIMGLDLPDG GHLTHGFMTD K KKISATSI ...String: GSHMTMPVNG AHKDADLWSS HDKMLAQPLK DSDVEVYNII KKESNRQRVG LELIASENFA SRAVLEALGS CLNNKYSEGY PGQRYYGGT EFIDELETLC QKRALQAYKL DPQCWGVNVQ PYSGSPANFA VYTALVEPHG RIMGLDLPDG GHLTHGFMTD K KKISATSI FFESMPYKVN PDTGYINYDQ LEENARLFHP KLIIAGTSCY SRNLEYARLR KIADENGAYL MADMAHISGL VA AGVVPSP FEHCHVVTTT THKTLRGCRA GMIFYRKGVK SVDPKTGKEI LYNLESLINS AVFPGLQGGP HNHAIAGVAV ALK QAMTLE FKVYQHQVVA NCRALSEALT ELGYKIVTGG SDNHLILVDL RSKGTDGGRA EKVLEACSIA CNKNTCPGDR SALR PSGLR LGTPALTSRG LLEKDFQKVA HFIHRGIELT LQIQSDTGVR ATLKEFKERL AGDKYQAAVQ ALREEVESFA SLFPL PGLP DF UniProtKB: Serine hydroxymethyltransferase, cytosolic |
-Macromolecule #2: PYRIDOXAL-5'-PHOSPHATE
Macromolecule | Name: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 3 / Formula: PLP |
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Molecular weight | Theoretical: 247.142 Da |
Chemical component information | ![]() ChemComp-PLP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | |||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blotted for 4 seconds before plunging. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5450 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |