1XIW: Human CD3-e/d dimer

Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody fragment. Determined by X-ray diffraction at 1.9 Å resolution. Released 16 Nov 2004.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 8
Atoms: 6,363
Mol. weight: 93.29 kDa
Released: 16 Nov 2004

Explore 1XIW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1XIW contains 25 α-helices and 78 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-15	2
β-strand	16-20	5	1
β-strand	23-27	5	1
β-strand	36-40	5	2
β-strand	43-45	3	2
β-strand	54-57	4	1
β-strand	60-63	4	1
α-helix	68-71	4
β-strand	73-79	7	2
β-strand	80	1	3
β-strand	82	1	3
α-helix	84-86	3
β-strand	89-95	7	2

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-8	4	4
β-strand	11-15	5	4
β-strand	20-25	6	2
β-strand	29-31	3	4
α-helix	32-34	3
β-strand	36-41	6	4
α-helix	42-44	3
β-strand	47-52	6	2
β-strand	63-70	8	2

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-6	2	5
β-strand	11-13	3	6
β-strand	20-26	7	5
β-strand	34-39	6	6
β-strand	45-50	6	6
β-strand	54-55	2	6
α-helix	56	1
β-strand	63-68	6	5
β-strand	71-76	6	5
α-helix	81-83	3
β-strand	85-91	7	6
α-helix	97	1
β-strand	98-99	2	6
β-strand	103-106	4	6

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	6
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	32-40	9	6
β-strand	44-52	9	6
β-strand	57-60	4	6
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-100	9	6
β-strand	111-112	2	6
β-strand	116-120	5	6

Chain E: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
β-strand	16-20	5	8
β-strand	23-27	5	8
β-strand	36-40	5	9
β-strand	43-45	3	9
β-strand	54-57	4	8
β-strand	60-63	4	8
α-helix	68-71	4
β-strand	73-79	7	9
β-strand	80	1	10
β-strand	82	1	10
α-helix	84-86	3
β-strand	89-95	7	9

Chain F: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-4	2
β-strand	5-8	4	11
β-strand	11-15	5	11
β-strand	20-25	6	9
β-strand	29-31	3	11
α-helix	32-34	3
β-strand	36-41	6	11
α-helix	42-44	3
β-strand	47-52	6	9
β-strand	63-70	8	9

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	12
β-strand	11-13	3	13
β-strand	20-26	7	12
β-strand	34-39	6	13
β-strand	45-50	6	13
β-strand	54-55	2	13
α-helix	56	1
β-strand	63-68	6	12
β-strand	71-76	6	12
α-helix	81-83	3
β-strand	85-91	7	13
α-helix	97	1
β-strand	98-99	2	13
β-strand	103-106	4	13

Chain H: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
β-strand	10-12	3	13
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	32-39	8	13
β-strand	46-52	7	13
β-strand	57-60	4	13
α-helix	62-64	3
β-strand	68-73	6	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-100	9	13
β-strand	109-112	4	13
β-strand	116-120	5	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD3 epsilon chain	A, E	protein	105	Homo sapiens	P07766 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain	B, F	protein	79	Homo sapiens	P04234 (AlphaFold model)
immunoglobulin light chain variable region	C, G	protein	108	Mus musculus
immunoglobulin heavy chain variable region	D, H	protein	122	Mus musculus

Sequence of entity 1 (A, E), FASTA

>1XIW_1 T-cell surface glycoprotein CD3 epsilon chain (chains A, E)
MDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDH
LSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCENCMEMD

Sequence of entity 2 (B, F), FASTA

>1XIW_2 T-cell surface glycoprotein CD3 delta chain (chains B, F)
MKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDLGKRILDPRGIYRCNGTDIYKD
KESTVQVHYRMCQSCVELD

Sequence of entity 3 (C, G), FASTA

>1XIW_3 immunoglobulin light chain variable region (chains C, G)
MDIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVP
SKFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKLEIK

Sequence of entity 4 (D, H), FASTA

>1XIW_4 immunoglobulin heavy chain variable region (chains D, H)
EVQLQQSGPELVKPGASMKISCKASGYSFTGYTMNWVKQSHGKNLEWMGLINPYKGVSTY
NQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCARSGYYGDSDWYFDVWGQGTTLTV
FS

Primary citation

Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment. Arnett, K.L., Harrison, S.C., Wiley, D.C. Proc Natl Acad Sci U S A (2004) 101:16268-16273. DOI 10.1073/pnas.0407359101 · PubMed

Other PDB entries of the same protein (UniProt P07766 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5QU2 1.04 Å, Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY
9T46 1.65 Å, Crystal structure of the Fab 40G5c in complex with a CD3 epsilon peptide
8VY4 1.7 Å, Engineering a Tumor-Selective Prodrug T Cell Engager Bispecific Antibody for Safer…
8F0L 1.81 Å, Crystal Structure of the Human T cell Receptor CD3(EPSILON) N-Terminal Peptide Complexed…
1SY6 2.1 Å, Crystal Structure of CD3gammaepsilon Heterodimer in Complex with OKT3 Fab Fragment
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
1A81 3.0 Å, Crystal structure of the tandem SH2 domain of the syk kinase bound to a dually…
7FJE 3.0 Å, Cryo-EM structure of a membrane protein(LL)
9CI8 3.01 Å, T cell receptor complex
8ES7 3.04 Å, CryoEM structure of PN45545 TCR-CD3 complex
7PHR 3.08 Å, Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
9JY1 3.08 Å, delta epsilon/delta epsilon Fab-TCR tetramer

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