9BBC

TCR GDN detergent micelle

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-04-05 Released: 2024-10-02 
  • Deposition Author(s): Notti, R.Q., Walz, T.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS), Other private, Shapiro-Silverberg Fund for the Advancement of Translational Research, The Mark Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The resting and ligand-bound states of the membrane-embedded human T-cell receptor-CD3 complex.

Notti, R.Q.Yi, F.Heissel, S.Bush, M.W.Molvi, Z.Das, P.Molina, H.Klebanoff, C.A.Walz, T.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2023.08.22.554360
  • Primary Citation of Related Structures:  
    8TW4, 8TW6, 9BBC, 9C3E

  • PubMed Abstract: 

    The T-cell receptor (TCR) initiates T-lymphocyte activation, but mechanistic questions remain( 1-4 ). Here, we present cryogenic electron microscopy structures for the unliganded and human leukocyte antigen (HLA)-bound human TCR-CD3 complex in nanodiscs that provide a native-like lipid environment. Distinct from the "open and extended" conformation seen in detergent( 5-8 ), the unliganded TCR-CD3 in nanodiscs adopts two related "closed and compacted" conformations that represent its physiologic resting state in vivo . By contrast, the HLA-bound complex adopts the open and extended conformation, and conformation-locking disulfide mutants show that ectodomain opening is necessary for maximal ligand-dependent T-cell activation. Together, these results reveal allosteric conformational change during TCR activation and highlight the importance of native-like lipid environments for membrane protein structure determination.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TCRa273Homo sapiensMutation(s): 0 
Entity Groups  
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Glycosylation
Glycosylation Sites: 5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TCRb305Homo sapiensMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainC [auth D]171Homo sapiensMutation(s): 0 
Gene Names: CD3DT3D
UniProt & NIH Common Fund Data Resources
Find proteins for P04234 (Homo sapiens)
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Go to UniProtKB:  P04234
PHAROS:  P04234
GTEx:  ENSG00000167286 
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UniProt GroupP04234
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P04234-1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 epsilon chainD [auth E],
E [auth F]
207Homo sapiensMutation(s): 0 
Gene Names: CD3ET3E
UniProt & NIH Common Fund Data Resources
Find proteins for P07766 (Homo sapiens)
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PHAROS:  P07766
GTEx:  ENSG00000198851 
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UniProt GroupP07766
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chainF [auth G]137Homo sapiensMutation(s): 0 
Gene Names: CD3GT3G
UniProt & NIH Common Fund Data Resources
Find proteins for P09693 (Homo sapiens)
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Go to UniProtKB:  P09693
PHAROS:  P09693
GTEx:  ENSG00000160654 
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UniProt GroupP09693
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P09693-1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 zeta chainG [auth X],
H [auth Y]
164Homo sapiensMutation(s): 0 
Gene Names: CD247CD3ZT3ZTCRZ
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Find proteins for P20963 (Homo sapiens)
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PHAROS:  P20963
GTEx:  ENSG00000198821 
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UniProt GroupP20963
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Oligosaccharides

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Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI,
K [auth R]
2N-Glycosylation
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth O],
L [auth C],
M [auth H]
3N-Glycosylation
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesT32CA9207
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesKL2TR001865
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesUL1TR001866
Other privateUnited StatesBlack Family Metastasis Center
Shapiro-Silverberg Fund for the Advancement of Translational ResearchUnited States--
The Mark FoundationUnited StatesWalz-Notti Aspire

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release