9C3E

TCR - CD3 complex bound to HLA

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 
  • Membrane Protein: Yes  PDBTM

  • Deposited: 2024-05-31 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: 3.50 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
TCRa272Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TCRb (EGFP fusion)557Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 delta chainC [auth D]125Homo sapiensMutation(s): 0 
Gene Names: CD3DT3D
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P04234 (Homo sapiens)
Explore P04234 
Go to UniProtKB:  P04234
PHAROS:  P04234
GTEx:  ENSG00000167286 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04234
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P04234-1
Sequence Annotations
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  • Reference Sequence
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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: CD3E
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07766 (Homo sapiens)
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Go to UniProtKB:  P07766
PHAROS:  P07766
GTEx:  ENSG00000198851 
Entity Groups  
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UniProt GroupP07766
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell surface glycoprotein CD3 gamma chainF [auth G]194Homo sapiensMutation(s): 0 
Gene Names: CD3GT3G
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P09693 (Homo sapiens)
Explore P09693 
Go to UniProtKB:  P09693
PHAROS:  P09693
GTEx:  ENSG00000160654 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09693
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P09693-1
Sequence Annotations
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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
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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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cancer/testis antigen 1,Beta-2-microglobulin,MHC class I antigenI [auth H]593Homo sapiensMutation(s): 1 
Gene Names: 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P78358 (Homo sapiens)
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Go to UniProtKB:  P78358
PHAROS:  P78358
Find proteins for H9BNV4 (Homo sapiens)
Explore H9BNV4 
Go to UniProtKB:  H9BNV4
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsH9BNV4P78358P61769
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Oligosaccharides

Help

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 N]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
S [auth G],
T [auth Y]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth B],
Q [auth D],
R [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 privateBlack 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: 2024-10-16
    Changes: Data collection, Structure summary