1xiw

Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody fragment

Method: X-RAY DIFFRACTION D_max: 118.4 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

T-cell surface glycoprotein CD3 epsilon chain

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 23–126	Fragment：ectodomain	T-cell surface glycoprotein CD3 delta chain × 1 （P04234） immunoglobulin light chain variable region × 1 immunoglobulin heavy chain variable region × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 3350, sodium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 1.90 Å R-free 0.241
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 23–126	Fragment：ectodomain	T-cell surface glycoprotein CD3 delta chain × 1 （P04234） immunoglobulin light chain variable region × 1 immunoglobulin heavy chain variable region × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 3350, sodium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 1.90 Å R-free 0.241

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1XIW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A81 CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM Deposited 1998-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 186–203（18 aa） Chain J 186–203（18 aa） Chain L 186–203（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5	Resolution 3.00 Å R-free 0.317
1A81 CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM Deposited 1998-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 186–203（18 aa） Chain D 186–203（18 aa） Chain F 186–203（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5	Resolution 3.00 Å R-free 0.317
1A81 CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM Deposited 1998-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 186–203（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5	Resolution 3.00 Å R-free 0.317
1A81 CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM Deposited 1998-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 186–203（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5	Resolution 3.00 Å R-free 0.317
1A81 CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM Deposited 1998-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 186–203（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5	Resolution 3.00 Å R-free 0.317
1A81 CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM Deposited 1998-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 186–203（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5	Resolution 3.00 Å R-free 0.317
1A81 CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM Deposited 1998-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 186–203（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5	Resolution 3.00 Å R-free 0.317
1A81 CRYSTAL STRUCTURE OF THE TANDEM SH2 DOMAIN OF THE SYK KINASE BOUND TO A DUALLY TYROSINE-PHOSPHORYLATED ITAM Deposited 1998-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 186–203（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；10% (W/V) PEG800, 10% (V/V) PEG 200, 0.1M TRIS HCL PH 8.5	Resolution 3.00 Å R-free 0.317
1SY6 Crystal Structure of CD3gammaepsilon Heterodimer in Complex with OKT3 Fab Fragment Deposited 2004-03-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 23–118（96 aa） Fragment：CD3 epsilon/gamma ecto domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；PEG3350, potassium formate, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 323K, temperature 294K	Resolution 2.10 Å R-free 0.255
2JXB Structure of CD3epsilon-Nck2 first SH3 domain complex Deposited 2007-11-09	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 177–188（12 aa） Fragment：;Fusion protein of T-cell surface glycoprotein CD3 epsilon chain cytoplasmic domain residues 177-188 and Cytoplasmic protein NCK2 first SH3 domain ;	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 2 mM [U-13C; U-15N] entity, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2ROL Structural Basis of PxxDY motif recognition in SH3 binding Deposited 2008-04-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 181–192（12 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Pressure AMBIENT NMR sample composition 0.8mM [U-98% 13C; U-98% 15N] Eps8L1SH3; 2.4mM CD3e peptide; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6JXR Structure of human T cell receptor-CD3 complex Deposited 2019-04-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.70 Å
7FJD Cryo-EM structure of a membrane protein(WT) Deposited 2021-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.20 Å
7FJE Cryo-EM structure of a membrane protein(LL) Deposited 2021-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
7FJF Cryo-EM structure of a membrane protein(CS) Deposited 2021-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	C3S CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.10 Å
7PHR Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I Deposited 2021-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: undecameric	Chain E 23–158（136 aa） Chain e 23–158（136 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
8ES7 CryoEM structure of PN45545 TCR-CD3 complex Deposited 2022-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain E 2–207（206 aa） Chain F 2–207（206 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
8ES8 CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239) Deposited 2022-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric	Chain E 2–207（206 aa） Chain F 2–207（206 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.65 Å
8ES9 CryoEM structure of PN45428 TCR-CD3 in complex with HLA-A2 MAGEA4 Deposited 2022-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric	Chain E 2–207（206 aa） Chain F 2–207（206 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8F0L Crystal Structure of the Human T cell Receptor CD3(EPSILON) N-Terminal Peptide Complexed with ADI-26906 FAB Deposited 2022-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain P 22–34（13 aa） Chain Q 22–34（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Crystals of the ADI-26906 Fab complexed to CD3 epsilon N13 peptide were obtained by the sitting drop vapor diffusion method. The ADI-26906 Fab buffered in PBS, was first buffer-exchanged into 20 mM Bis-Tris pH 6.0 and 150 mM NaCl. The Fab (0.31 mM) was mixed with the N13 peptide (7.8 mM) at a Fab:peptide ratio of 1:25 and incubated on ice for 1.5 h. A BCS screen (Molecular Dimensions Ltd.) was set up using a mosquito crystallization robot (STP Labtech), with each drop consisting of 100 nL protein and 100 nL of reservoir solution, and left to equilibrate against a 40 uL reservoir solution at 293 K. After a few days, crystals were obtained in condition A6 (0.1 M MES pH 6.5, 25% w/v PEG Smear Broad).	Resolution 1.81 Å R-free 0.195
8JC0 V gamma9 V delta2 TCR and CD3 complex in LMNG Deposited 2023-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8JCB Vgamma5 Vdelta1 T cell receptor complex Deposited 2023-05-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain E 1–207（207 aa） Chain F 1–207（207 aa） Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.50 Å
8TW4 TCR in nanodisc ND-I Deposited 2023-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–207（207 aa） Chain F 1–207（207 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8TW6 TCR in nanodisc ND-II Deposited 2023-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–207（207 aa） Chain F 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8WXE Vgamma5Vdelta1 EH TCR-CD3 complex Deposited 2023-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8WY0 T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A Deposited 2023-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8WYI T cell receptor delta 2 gamma 9 with TCRD TM domain chimera of TRAC Deposited 2023-10-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8YC0 T cell receptor V delta2 V gamma9 in GDN Deposited 2024-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.12 Å
8ZA6 Cryo-EM structure of the gdTCR-CD3 complex Deposited 2024-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.43 Å
9BBC TCR GDN detergent micelle Deposited 2024-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–207（207 aa） Chain F 1–207（207 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9C3E TCR - CD3 complex bound to HLA Deposited 2024-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain E 1–207（207 aa） Chain F 1–207（207 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9CI8 T cell receptor complex Deposited 2024-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain e 33–156（124 aa） Chain f 33–156（124 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；Hepes buffer saline cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9CIA T cell receptor complex Deposited 2024-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain e 33–155（123 aa） Chain f 33–155（123 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；HEPES buffer saline cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9CQ4 G115 gamma delta TCR/CD3 complex bound by OKT3 Fab Deposited 2024-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain E 1–207（207 aa） Chain F 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
9IP8 Poly-alanine model for HL-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (closed conformation) Deposited 2024-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 23–118（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.91 Å
9IP9 Poly-alanine model for HL-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (middle conformation) Deposited 2024-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 23–118（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.64 Å
9IPA Poly-alanine model for HL-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (open conformation) Deposited 2024-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 23–118（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.85 Å
9IPC Poly-alanine model for LH-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (closed conformation) Deposited 2024-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 23–118（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9IPD Poly-alanine model for LH-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (middle conformation) Deposited 2024-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 23–118（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
9IPE Poly-alanine model for LH-type bispecific diabody Ex3 composed of 528 and OKT3 Fvs in ternary complex with sEGFR and CD3gamma-epsilon (open conformation) Deposited 2024-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 23–118（96 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
9IRS Cryo-EM structure of the TCR-OKT3 complex Deposited 2024-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.18 Å
9IRU Cryo-em structure of TCR-4B1 complex Deposited 2024-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.14 Å
9JXZ V gamma9 V delta2 TCR and CD3 complex Deposited 2024-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 2 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
9JY0 Fab-CD3-gamma epsilon-TCR complex Deposited 2024-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: decameric	Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å
9JY1 delta epsilon/delta epsilon Fab-TCR tetramer Deposited 2024-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: eicosameric	Chain E 1–207（207 aa） Chain F 1–207（207 aa） Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
9JY2 Fab-CD3-delta epsilon-TCR complex Deposited 2024-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain e 33–154（122 aa） Chain f 33–154（122 aa）	Not recorded	CLR CHOLESTEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
9JY3 delta epsilon/gamma epsilon Fab-TCR tetramer Deposited 2024-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain E 33–154（122 aa） Chain F 33–154（122 aa） Chain e 33–154（122 aa） Chain f 33–154（122 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
9JY4 gamma epsilon/gamma epsilon Fab-TCR tetramer Deposited 2024-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: eicosameric	Chain E 1–207（207 aa） Chain F 1–207（207 aa） Chain e 1–207（207 aa） Chain f 1–207（207 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
9T46 Crystal structure of the Fab 40G5c in complex with a CD3 epsilon peptide Deposited 2025-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 22–30（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 ACT ACETATE ION × 9 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；294 K；0.1 M sodium acetate, pH 4.6, 2 M (NH4)2SO4	Resolution 1.65 Å R-free 0.225

42 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD3E_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–105； UniProt 23–126 Author chain E； PDBConstruct 2–105； UniProt 23–126

T-cell surface glycoprotein CD3 delta chain

Homo sapiens

UniProt P04234

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 23–100	Fragment：ectodomain	T-cell surface glycoprotein CD3 epsilon chain × 1 （P07766） immunoglobulin light chain variable region × 1 immunoglobulin heavy chain variable region × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 3350, sodium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 1.90 Å R-free 0.241
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 23–100	Fragment：ectodomain	T-cell surface glycoprotein CD3 epsilon chain × 1 （P07766） immunoglobulin light chain variable region × 1 immunoglobulin heavy chain variable region × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 3350, sodium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 1.90 Å R-free 0.241

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1XIW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6JXR Structure of human T cell receptor-CD3 complex Deposited 2019-04-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.70 Å
7FJD Cryo-EM structure of a membrane protein(WT) Deposited 2021-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.20 Å
7FJE Cryo-EM structure of a membrane protein(LL) Deposited 2021-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
7FJF Cryo-EM structure of a membrane protein(CS) Deposited 2021-08-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	C3S CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.10 Å
7PHR Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I Deposited 2021-08-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: undecameric	Chain D 22–132（111 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
8ES7 CryoEM structure of PN45545 TCR-CD3 complex Deposited 2022-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–171（171 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
8ES8 CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239) Deposited 2022-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric	Chain D 1–171（171 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.65 Å
8ES9 CryoEM structure of PN45428 TCR-CD3 in complex with HLA-A2 MAGEA4 Deposited 2022-10-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric	Chain D 1–171（171 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 Y01 CHOLESTEROL HEMISUCCINATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8JC0 V gamma9 V delta2 TCR and CD3 complex in LMNG Deposited 2023-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8JCB Vgamma5 Vdelta1 T cell receptor complex Deposited 2023-05-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain D 1–171（171 aa） Chain d 1–171（171 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.50 Å
8TW4 TCR in nanodisc ND-I Deposited 2023-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–171（171 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8TW6 TCR in nanodisc ND-II Deposited 2023-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8WXE Vgamma5Vdelta1 EH TCR-CD3 complex Deposited 2023-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8WY0 T cell receptor delta 2 gamma 9 with F283A, F290A, and F291A Deposited 2023-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8WYI T cell receptor delta 2 gamma 9 with TCRD TM domain chimera of TRAC Deposited 2023-10-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8YC0 T cell receptor V delta2 V gamma9 in GDN Deposited 2024-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.12 Å
8ZA6 Cryo-EM structure of the gdTCR-CD3 complex Deposited 2024-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.43 Å
9BBC TCR GDN detergent micelle Deposited 2024-04-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–171（171 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9C3E TCR - CD3 complex bound to HLA Deposited 2024-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain D 1–125（125 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9CI8 T cell receptor complex Deposited 2024-07-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain d 22–126（105 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；Hepes buffer saline cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9CIA T cell receptor complex Deposited 2024-07-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain d 22–127（106 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；HEPES buffer saline cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9CQ4 G115 gamma delta TCR/CD3 complex bound by OKT3 Fab Deposited 2024-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain K 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
9IRS Cryo-EM structure of the TCR-OKT3 complex Deposited 2024-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.18 Å
9IRU Cryo-em structure of TCR-4B1 complex Deposited 2024-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.14 Å
9JXZ V gamma9 V delta2 TCR and CD3 complex Deposited 2024-10-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 2 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
9JY0 Fab-CD3-gamma epsilon-TCR complex Deposited 2024-10-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: decameric	Chain d 1–171（171 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å
9JY1 delta epsilon/delta epsilon Fab-TCR tetramer Deposited 2024-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: eicosameric	Chain D 1–171（171 aa） Chain d 1–171（171 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
9JY2 Fab-CD3-delta epsilon-TCR complex Deposited 2024-10-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain d 22–126（105 aa）	Not recorded	CLR CHOLESTEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
9JY3 delta epsilon/gamma epsilon Fab-TCR tetramer Deposited 2024-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain D 22–126（105 aa） Chain d 22–126（105 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
9JY4 gamma epsilon/gamma epsilon Fab-TCR tetramer Deposited 2024-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: eicosameric	Chain D 1–171（171 aa） Chain d 1–171（171 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD3D_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–79； UniProt 23–100 Author chain F； PDBConstruct 2–79； UniProt 23–100

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1xiw
Deposition date deposition_date	2004-09-22
Structure title title	Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody fragment
Keywords keywords	CD3-epsilon, CD3-delta, UCHT1-scFv, immunoglobulin fold, antibody-antigen complex, membrane protein-Immune System COMPLEX; membrane protein/Immune System
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.33 Å
Radius of gyration Rg (electron density) rg_electron	32.29 Å
Forward intensity I(0) i0	120165000.00
Molecular weight molecular_weight	86020.0 kDa
Excluded volume excluded_volume	106850 Å³
Envelope volume envelope_volume	135120 Å³
Hydration-shell volume shell_volume	36537 Å³
Envelope diameter envelope_diameter	128.7 Å
Shell Rg shell_rg	37.65 Å
Envelope Rg envelope_rg	31.94 Å
Shape Rg shape_rg	32.23 Å
Total Rg total_rg	32.87 Å
Total atoms total_atoms	6044
Residues n_residues	765
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	118.4 Å
Rg (real space) rg_real	32.55 Å
Rg uncertainty (real space) rg_real_error	1.42 Å
I(0) (real space) i0_real	1.2020e+08
I(0) uncertainty (real space) i0_real_error	2.0840e+06
Rg (reciprocal space) rg_reciprocal	32.45 Å
I(0) (reciprocal space) i0_reciprocal	120200000.0000
Solution quality estimate total_estimate	0.8314
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	116.0 Å
Skewness Skewness skewness	0.524
Kurtosis Kurtosis kurtosis	-0.156
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15560000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.667; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.844; Smooth: 0.960

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	T-cell surface glycoprotein CD3 epsilon chain
Molecular weight formula_weight	11893.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	6363

MDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCENCMEMD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	T-cell surface glycoprotein CD3 delta chain
Molecular weight formula_weight	9106.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDLGKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	immunoglobulin light chain variable region
Molecular weight formula_weight	11994.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

MDIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSKFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKLEIK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	immunoglobulin heavy chain variable region
Molecular weight formula_weight	13650.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H

EVQLQQSGPELVKPGASMKISCKASGYSFTGYTMNWVKQSHGKNLEWMGLINPYKGVSTYNQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCARSGYYGDSDWYFDVWGQGTTLTVFS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	319

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1xiwa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d1xiwb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d1xiwc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1xiwd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1xiwe_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d1xiwf_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

Domain ID domain_id	d1xiwg_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1xiwh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (8 domains)

Domain ID domain_id	1xiwA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1xiwB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1xiwC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1xiwD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1xiwE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1xiwF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1xiwG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1xiwH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	64.874 Å
Unit-cell length b length_b	79.326 Å
Unit-cell length c length_c	150.747 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	49.170 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2410

fit	/app/data/saxs_computation/xi/1xiw/1xiw.fit
pddf	/app/data/pr_computation/xi/1xiw/1xiw.pr.out
profile	/app/data/saxs_computation/xi/1xiw/1xiw.dat

Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody fragment

1. Protein Identity and Related Structures Protein Identity & Related Structures

T-cell surface glycoprotein CD3 epsilon chain

State in the Current Structure

Other States of the Same Protein in the Database

T-cell surface glycoprotein CD3 delta chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)