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

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Basic information

Entry
Database: PDB / ID: 8a11
TitleCryo-EM structure of the Human SHMT1-RNA complex
ComponentsSerine hydroxymethyltransferase, cytosolic
KeywordsTRANSFERASE / Riboregulation / Metabolism / 1 carbon metablism / Moonlighting protein / RNA BINDING PROTEIN
Function / homology
Function and homology information


cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process ...cellular response to tetrahydrofolate / Carnitine synthesis / purine nucleobase biosynthetic process / L-serine metabolic process / glycine metabolic process / serine binding / glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / L-serine catabolic process / Metabolism of folate and pterines / 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 / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / 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
PYRIDOXAL-5'-PHOSPHATE / Serine hydroxymethyltransferase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsSpizzichino, S. / Marabelli, C. / Bharadwaj, A. / Jakobi, A.J. / Chaves-Sanjuan, A. / Giardina, G. / Bolognesi, M. / Cutruzzola, F.
Funding support Italy, 2items
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, A.J. / Chaves-Sanjuan, A. / Giardina, G. / Bolognesi, M. / Cutruzzola, F.
History
DepositionMay 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_entity_assembly / em_entity_assembly_molwt / entity / entity_poly / entity_poly_seq / ndb_struct_na_base_pair / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.chain_id / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_entity_assembly.entity_id_list / _em_entity_assembly_molwt.units / _em_entity_assembly_molwt.value / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_mutation / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model completeness
Details: As requested from the reviewers we removed the previously modelled RNA and the PLP molecule from the active site when it's not visible.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase, cytosolic
B: Serine hydroxymethyltransferase, cytosolic
C: Serine hydroxymethyltransferase, cytosolic
D: Serine hydroxymethyltransferase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,4817
Polymers213,7394
Non-polymers7413
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, native gel electrophoresis, gel filtration, only for the protein tetramer
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Serine hydroxymethyltransferase, cytosolic / SHMT / Glycine hydroxymethyltransferase / Serine methylase


Mass: 53434.797 Da / Num. of mol.: 4 / Mutation: Chain B has not PLP bond to the active site
Source method: isolated from a genetically manipulated source
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)
Source: (gene. exp.) Homo sapiens (human) / Gene: SHMT1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34896, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human SHMT1 in complex with RNA (SHMT2 5' UTR 1-50) / Type: COMPLEX / Details: SHMT1= homotetramer of 53kDa subunits / Entity ID: #1 / Source: RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.21 MDaNO
2153 kDa/nmNO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
220 mMHepesC8H18N2O4S1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blotted for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5450

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPU2.8image acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
8Coot0.9.6model fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
20PHENIX1-17-1-3660model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4900000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94430 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 132 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 1BJ4

1bj4


Pdb chain-ID: A / Accession code: 1BJ4 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 133.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001514943
ELECTRON MICROSCOPYf_angle_d0.410420257
ELECTRON MICROSCOPYf_chiral_restr0.03532247
ELECTRON MICROSCOPYf_plane_restr0.0034488
ELECTRON MICROSCOPYf_dihedral_angle_d9.03662147

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