Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.49 kDa 
• Atom Count: 1630 
• Modelled Residue Count: 201 
• Deposited Residue Count: 201 
• Unique protein chains: 2

2RSE

NMR structure of FKBP12-mTOR FRB domain-rapamycin complex structure determined based on PCS

• PDB DOI: 10.2210/pdb2RSE/pdb
• BMRB: 11471

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


• Deposited: 2012-01-25 Released: 2012-05-30 
• Deposition Author(s): Kobashigawa, Y., Ushio, M., Saio, T., Inagaki, F.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based protein-protein complex structure determination.

Kobashigawa, Y., Saio, T., Ushio, M., Sekiguchi, M., Yokochi, M., Ogura, K., Inagaki, F.

(2012) J Biomol NMR 53: 53-63

• PubMed: 22487935 
• DOI: 10.1007/s10858-012-9623-8
• Primary Citation of Related Structures:  
  2RSE


• PubMed Abstract: 
  

Pseudo contact shifts (PCSs) induced by paramagnetic lanthanide ions fixed in a protein frame provide long-range distance and angular information, and are valuable for the structure determination of protein-protein and protein-ligand complexes. We have been developing a lanthanide-binding peptide tag (hereafter LBT) anchored at two points via a peptide bond and a disulfide bond to the target proteins. However, the magnetic susceptibility tensor displays symmetry, which can cause multiple degenerated solutions in a structure calculation based solely on PCSs. Here we show a convenient method for resolving this degeneracy by changing the spacer length between the LBT and target protein. We applied this approach to PCS-based rigid body docking between the FKBP12-rapamycin complex and the mTOR FRB domain, and demonstrated that degeneracy could be resolved using the PCS restraints obtained from two-point anchored LBT with two different spacer lengths. The present strategy will markedly increase the usefulness of two-point anchored LBT for protein complex structure determination.

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Organizational Affiliation: 

Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Sapporo 001-0021, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	A	107	Homo sapiens	Mutation(s): 0  Gene Names: FKBP1A, FKBP1, FKBP12 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens) Explore P62942  Go to UniProtKB:  P62942
PHAROS:  P62942 GTEx:  ENSG00000088832

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase mTOR	B	94	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TB	C [auth A], D [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2RSE Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-25 
• Released Date: 2012-05-30 
Deposition Author(s): Kobashigawa, Y., Ushio, M., Saio, T., Inagaki, F.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release