7FJF | pdb_00007fjf

Cryo-EM structure of a membrane protein(CS)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7FJF

This is version 1.1 of the entry. See complete history

Literature

Cholesterol inhibits TCR signaling by directly restricting TCR-CD3 core tunnel motility.

Chen, Y.Zhu, Y.Li, X.Gao, W.Zhen, Z.Huang, B.Ma, Z.Zhang, A.Song, X.Ma, Y.Guo, C.Zhang, F.Huang, Z.

(2022) Mol Cell 82: 1278-1287.e5

  • DOI: https://doi.org/10.1016/j.molcel.2022.02.017
  • Primary Citation Related Structures: 
    7FJD, 7FJE, 7FJF

  • PubMed Abstract: 

    Cholesterol molecules specifically bind to the resting αβTCR to inhibit cytoplasmic CD3ζ ITAM phosphorylation through sequestering the TCR-CD3 complex in an inactive conformation. The mechanisms of cholesterol-mediated inhibition of TCR-CD3 and its activation remain unclear. Here, we present cryoelectron microscopy structures of cholesterol- and cholesterol sulfate (CS)-inhibited TCR-CD3 complexes and an auto-active TCR-CD3 variant. The structures reveal that cholesterol molecules act like a latch to lock CD3ζ into an inactive conformation in the membrane. Mutations impairing binding of cholesterol molecules to the tunnel result in the movement of the proximal C terminus of the CD3ζ transmembrane helix, thereby activating the TCR-CD3 complex in human cells. Together, our data reveal the structural basis of TCR inhibition by cholesterol, illustrate how the cholesterol-binding tunnel is allosterically coupled to TCR triggering, and lay a foundation for the development of immunotherapies through directly targeting the TCR-CD3 complex.


  • Organizational Affiliation
    • HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China.

Macromolecule Content 

  • Total Structure Weight: 189.72 kDa 
  • Atom Count: 8,377 
  • Modeled Residue Count: 1,058 
  • Deposited Residue Count: 1,681 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 zeta chainA [auth b],
H [auth a]
165Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P20963 (Homo sapiens)
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PHAROS:  P20963
GTEx:  ENSG00000198821 
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UniProt GroupP20963
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainB [auth d]171Homo sapiensMutation(s): 0 
Gene Names: CD3DT3D
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P04234 (Homo sapiens)
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PHAROS:  P04234
GTEx:  ENSG00000167286 
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UniProt GroupP04234
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 epsilon chainC [auth e],
D [auth f]
207Homo sapiensMutation(s): 0 
Gene Names: CD3ET3E
Membrane Entity: Yes 
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Find proteins for P07766 (Homo sapiens)
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PHAROS:  P07766
GTEx:  ENSG00000198851 
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UniProt GroupP07766
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chainE [auth g]182Homo sapiensMutation(s): 0 
Gene Names: CD3GT3G
Membrane Entity: Yes 
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Find proteins for P09693 (Homo sapiens)
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PHAROS:  P09693
GTEx:  ENSG00000160654 
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UniProt GroupP09693
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constantF [auth m]272Homo sapiensMutation(s): 0 
Gene Names: TRAV12-3Tcr-alphaTRACTCRA
Membrane Entity: Yes 
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Find proteins for A0A0B4J271 (Homo sapiens)
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PHAROS:  A0A0B4J271
GTEx:  ENSG00000211794 
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Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupsA0A0B4J271P01848A0N4Z6
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2G [auth n]312Homo sapiensMutation(s): 0 
Gene Names: TRBV6-5TRBTRBC2
Membrane Entity: Yes 
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Find proteins for A0A0K0K1A5 (Homo sapiens)
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PHAROS:  A0A0K0K1A5
GTEx:  ENSG00000211721 
Find proteins for P0DSE2 (Homo sapiens)
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UniProt GroupsP0DSE2A0A0K0K1A5
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31825008

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Structure summary