5ZCS

4.9 Angstrom Cryo-EM structure of human mTOR complex 2

  • Classification: GENE REGULATION
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens

  • Deposited: 2018-02-20 Released: 2018-03-21 
  • Deposition Author(s): Chen, X., Liu, M., Tian, Y., Wang, H., Wang, J., Xu, Y.
  • Funding Organization(s): Ministry of Science and Technology (China); National Natural Science Foundation of China; Strategic Priority Research Program of the Chinese Academy of Sciences; National Program for support of Top-Notch Young Professionals 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structure of human mTOR complex 2.

Chen, X.Liu, M.Tian, Y.Li, J.Qi, Y.Zhao, D.Wu, Z.Huang, M.Wong, C.C.L.Wang, H.W.Wang, J.Yang, H.Xu, Y.

(2018) Cell Res. 28: 518-528

  • DOI: 10.1038/s41422-018-0029-3

  • PubMed Abstract: 
  • Mechanistic target of rapamycin (mTOR) complex 2 (mTORC2) plays an essential role in regulating cell proliferation through phosphorylating AGC protein kinase family members, including AKT, PKC and SGK1. The functional core complex consists of mTOR, m ...

    Mechanistic target of rapamycin (mTOR) complex 2 (mTORC2) plays an essential role in regulating cell proliferation through phosphorylating AGC protein kinase family members, including AKT, PKC and SGK1. The functional core complex consists of mTOR, mLST8, and two mTORC2-specific components, Rictor and mSin1. Here we investigated the intermolecular interactions within mTORC2 complex and determined its cryo-electron microscopy structure at 4.9 Å resolution. The structure reveals a hollow rhombohedral fold with a 2-fold symmetry. The dimerized mTOR serves as a scaffold for the complex assembly. The N-terminal half of Rictor is composed of helical repeat clusters and binds to mTOR through multiple contacts. mSin1 is located close to the FRB domain and catalytic cavity of mTOR. Rictor and mSin1 together generate steric hindrance to inhibit binding of FKBP12-rapamycin to mTOR, revealing the mechanism for rapamycin insensitivity of mTORC2. The mTOR dimer in mTORC2 shows more compact conformation than that of mTORC1 (rapamycin sensitive), which might result from the interaction between mTOR and Rictor-mSin1. Structural comparison shows that binding of Rictor and Raptor (mTORC1-specific component) to mTOR is mutually exclusive. Our study provides a basis for understanding the assembly of mTORC2 and a framework to further characterize the regulatory mechanism of mTORC2 pathway.


    Organizational Affiliation

    National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201210, China.,Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. xuyh@fudan.edu.cn.,Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. xuyh@fudan.edu.cn.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. yanghr@fudan.edu.cn.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Science, Peking University, Beijing, 100871, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China. xuyh@fudan.edu.cn.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. yanghr@fudan.edu.cn.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China. yanghr@fudan.edu.cn.,Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. xuyh@fudan.edu.cn.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.,Center for Precision Medicine Multi-Omics Research (CPMMOR), Peking University Health Science Center, Beijing, 100871, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase mTOR
A, B
2549Homo sapiensMutation(s): 0 
Gene Names: MTOR (FRAP, FRAP1, FRAP2, RAFT1, RAPT1)
EC: 2.7.11.1
Find proteins for P42345 (Homo sapiens)
Go to Gene View: MTOR
Go to UniProtKB:  P42345
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Target of rapamycin complex subunit LST8
C, D
326Homo sapiensMutation(s): 0 
Gene Names: MLST8 (GBL, LST8)
Find proteins for Q9BVC4 (Homo sapiens)
Go to Gene View: MLST8
Go to UniProtKB:  Q9BVC4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Rapamycin-insensitive companion of mTOR
E, F
1708Homo sapiensMutation(s): 0 
Gene Names: RICTOR (KIAA1999)
Find proteins for Q6R327 (Homo sapiens)
Go to Gene View: RICTOR
Go to UniProtKB:  Q6R327
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Target of rapamycin complex 2 subunit MAPKAP1
G, H
522Homo sapiensMutation(s): 0 
Gene Names: MAPKAP1 (MIP1, SIN1)
Find proteins for Q9BPZ7 (Homo sapiens)
Go to Gene View: MAPKAP1
Go to UniProtKB:  Q9BPZ7
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
E, F, G, H
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0500700,2016YFA0501100
National Natural Science Foundation of ChinaChina31770781,U1432242,31425008,91419301
Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08000000
National Program for support of Top-Notch Young ProfessionalsChina--

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references
  • Version 1.2: 2018-05-30
    Type: Data collection, Database references