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- EMDB-15065: Cryo-EM structure of the Human SHMT1-RNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-15065
TitleCryo-EM structure of the Human SHMT1-RNA complex
Map data
Sample
  • Complex: human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50)
    • Protein or peptide: Serine hydroxymethyltransferase, cytosolic
    • RNA: SHMT2 5'UTR 1-50 (5'-R(P*CP*UP*AP*CP*AP*A)-3')
KeywordsRiboregulation / Metabolism / 1 carbon metablism / Moonlighting protein / RNA BINDING PROTEIN / TRANSFERASE
Function / homology
Function and homology information


cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine ...cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / serine binding / L-serine catabolic process / L-serine metabolic process / glycine metabolic process / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / dTMP biosynthetic process / folic acid metabolic process / small molecule binding / cellular response to leukemia inhibitory factor / mRNA regulatory element binding translation repressor activity / mRNA 5'-UTR binding / pyridoxal phosphate binding / protein homotetramerization / negative regulation of translation / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsSpizzichino S / Marabelli C / Bharadwaj A / Jakobi AJ / Chaves-Sanjuan A / Giardina G / Bolognesi M / Cutruzzola F
Funding support Italy, 2 items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchAIRC IG-23125 Italy
Other private
CitationJournal: To Be Published
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
DepositionMay 30, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15065.png

Downloads & links

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Map

FileDownload / File: emd_15065.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.5
Minimum - Maximum-12.296768 - 34.365400000000001
Average (Standard dev.)0.050466806 (±0.66861546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 355.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_15065_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15065_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50)

EntireName: human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50)
Components
  • Complex: human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50)
    • Protein or peptide: Serine hydroxymethyltransferase, cytosolic
    • RNA: SHMT2 5'UTR 1-50 (5'-R(P*CP*UP*AP*CP*AP*A)-3')

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Supramolecule #1: human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50)

SupramoleculeName: human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: SHMT1= homotetramer of 53kDa subunits
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine hydroxymethyltransferase, cytosolic

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.662914 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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 TH(LLP)TLRGCRA GMIFYRKGVK SVDPKTGKEI LYNLESLINS AVFPGLQGGP HNHAIAGVA VALKQAMTLE FKVYQHQVVA NCRALSEALT ELGYKIVTGG SDNHLILVDL RSKGTDGGRA EKVLEACSIA CNKNTCPGDR SALRPSGLR LGTPALTSRG LLEKDFQKVA HFIHRGIELT LQIQSDTGVR ATLKEFKERL AGDKYQAAVQ ALREEVESFA S LFPLPGLP DF

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Macromolecule #2: SHMT2 5'UTR 1-50 (5'-R(P*CP*UP*AP*CP*AP*A)-3')

MacromoleculeName: SHMT2 5'UTR 1-50 (5'-R(P*CP*UP*AP*CP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.228851 KDa
SequenceString:
AUAAAGAAAA AAGCGGUGAG UGGGCGAACU ACAAUUCCCA AAAGGCCACA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chlorideSodium Chloride
20.0 mMC8H18N2O4SHepes
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen 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

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4900000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6fl5

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 94430
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1bj4


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 132
Output model

PDB-8a11:
Cryo-EM structure of the Human SHMT1-RNA complex

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