8A11

Cryo-EM structure of the Human SHMT1-RNA complex

• PDB DOI: https://doi.org/10.2210/pdb8A11/pdb
• EM Map EMD-15065: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-05-30 Released: 2023-06-14 
• Deposition Author(s): Spizzichino, S., Marabelli, C., Bharadwaj, A., Jakobi, A.J., Chaves-Sanjuan, A., Giardina, G., Bolognesi, M., Cutruzzola, F.
• Funding Organization(s): Italian Association for Cancer Research, Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the Human SHMT1-RNA complex

Spizzichino, S., Marabelli, C., Bharadwaj, A., Jakobi, A.J., Chaves-Sanjuan, A., Giardina, G., Bolognesi, M., Cutruzzola, F.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, native gel electrophoresis, gel filtration

Macromolecule Content

• Total Structure Weight: 214.48 kDa 
• Atom Count: 14,450 
• Modelled Residue Count: 1,870 
• Deposited Residue Count: 1,944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, cytosolic	A, B, C, D	486	Homo sapiens	Mutation(s): 0  Gene Names: SHMT1 EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34896 (Homo sapiens) Explore P34896  Go to UniProtKB:  P34896
PHAROS:  P34896 GTEx:  ENSG00000176974

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	E [auth A], F [auth C], G [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1-17-1-3660

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Spizzichino, S., Marabelli, C., Bharadwaj, A., Jakobi, A.J., Chaves-Sanjuan, A., Giardina, G., Bolognesi, M., Cutruzzola, F.

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Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	AIRC IG-23125
Other private		--

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 2.0: 2024-05-08
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary