8RCH

CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, overall refinement

• PDB DOI: https://doi.org/10.2210/pdb8RCH/pdb
• EM Map EMD-19052: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-12-06 Released: 2024-09-11 
• Deposition Author(s): Anandapadamanaban, M., Hay, I.M., Perisic, O., Williams, R.L.
• Funding Organization(s): Cancer Research UK, Medical Research Council (MRC, United Kingdom), European Molecular Biology Organization (EMBO)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

cryoEM structure of mTORC1 with the cancer-associated 1455-EWED-1458 duplication variant, overall refinement

Anandapadamanaban, M., Hay, I., Perisic, O., Williams, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B2C2D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A2B2C1D1E1F1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 975.03 kDa 
• Atom Count: 49,608 
• Modelled Residue Count: 6,194 
• Deposited Residue Count: 8,656 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase mTOR	A, E [auth B]	2,549	Homo sapiens	Mutation(s): 0  Gene Names: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens) Explore P42345  Go to UniProtKB:  P42345
PHAROS:  P42345 GTEx:  ENSG00000198793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Target of rapamycin complex subunit LST8	B [auth D], F [auth E]	326	Homo sapiens	Mutation(s): 0  Gene Names: MLST8, GBL, LST8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVC4 (Homo sapiens) Explore Q9BVC4  Go to UniProtKB:  Q9BVC4
PHAROS:  Q9BVC4 GTEx:  ENSG00000167965

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory-associated protein of mTOR	C [auth W], G [auth Y]	1,335	Homo sapiens	Mutation(s): 0  Gene Names: RPTOR, KIAA1303, RAPTOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N122 (Homo sapiens) Explore Q8N122  Go to UniProtKB:  Q8N122
PHAROS:  Q8N122 GTEx:  ENSG00000141564

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 4E-binding protein 1	D [auth Z], H [auth X]	118	Homo sapiens	Mutation(s): 0  Gene Names: EIF4EBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13541 (Homo sapiens) Explore Q13541  Go to UniProtKB:  Q13541
PHAROS:  Q13541 GTEx:  ENSG00000187840

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	I [auth A], L [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	J [auth A], K [auth A], M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Anandapadamanaban, M., Hay, I.M., Perisic, O., Williams, R.L.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	DRCPGM 100014
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_U105184308
European Molecular Biology Organization (EMBO)	European Union	EMBO ALTF 603-2019

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release