8TW6

TCR in nanodisc ND-II


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 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
T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFPA [auth Y],
H [auth X]
412Homo sapienshuman respiratory syncytial virus
This entity is chimeric
Mutation(s): 0 
Gene Names: CD247
UniProt & NIH Common Fund Data Resources
Find proteins for A0A5P9VSM6 (Human respiratory syncytial virus)
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Go to UniProtKB:  A0A5P9VSM6
Find proteins for P20963 (Homo sapiens)
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Go to UniProtKB:  P20963
PHAROS:  P20963
GTEx:  ENSG00000198821 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP20963A0A5P9VSM6
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TCR alphaB [auth A]274Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRYC [auth B]556Homo sapiensEscherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Gene Names: TRBV6-5TRBmCherry
UniProt & NIH Common Fund Data Resources
Find proteins for A0A4D6FVK6 (Escherichia coli str. K-12 substr. MG1655)
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Go to UniProtKB:  A0A4D6FVK6
Find proteins for P0DTU4 (Homo sapiens)
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Go to UniProtKB:  P0DTU4
Find proteins for A0A0K0K1A5 (Homo sapiens)
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PHAROS:  A0A0K0K1A5
GTEx:  ENSG00000211721 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0DTU4A0A4D6FVK6A0A0K0K1A5
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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
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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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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainF [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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PHAROS:  P04234
GTEx:  ENSG00000167286 
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UniProt GroupP04234
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chain190Homo 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
Sequence Annotations
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Oligosaccharides

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Entity ID: 7
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-glucopyranoseI [auth C]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary