4P5T: 14.C6 TCR

14.C6 TCR complexed with MHC class II I-Ab/3K peptide. Determined by X-ray diffraction at 3.26 Å resolution. Released 28 May 2014.

Method: X-ray diffraction
Resolution: 3.26 Å
Organisms: Homo sapiens, Mus musculus
Chains: 8
Atoms: 12,366
Mol. weight: 191.5 kDa
Released: 28 May 2014

Explore 4P5T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P5T contains 50 α-helices and 149 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: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	9-13	5	2
α-helix	17	1
β-strand	18-24	7	1
β-strand	31-37	7	2
β-strand	44-50	7	2
β-strand	56-59	4	1
β-strand	62-67	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	87-90	4	2
β-strand	91-92	2	3
β-strand	93	1	2
α-helix	100	1
β-strand	101-102	2	3
β-strand	106-111	6	2
α-helix	112-114	3
β-strand	120-125	6	4
β-strand	126	1	5
β-strand	133-138	6	4
β-strand	154-156	3	4
α-helix	157-159	3
β-strand	160-164	5	4
β-strand	169-178	10	4
β-strand	199	1	4

Chain B: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	6
β-strand	8-11	4	7
β-strand	17-23	7	6
β-strand	29-36	8	7
β-strand	40-49	10	7
β-strand	52-55	4	7
β-strand	63-65	3	6
β-strand	71-76	6	6
α-helix	81-83	3
β-strand	85-92	8	7
β-strand	100-101	2	7
β-strand	105-109	5	7
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	5
α-helix	125-127	3
α-helix	128-133	6
β-strand	136-146	11	5
β-strand	147	1	8
β-strand	151-157	7	9
β-strand	160-162	3	9
β-strand	166-168	3	5
α-helix	172	1
β-strand	173-174	2	5
β-strand	184-193	10	5
α-helix	194-198	5
β-strand	203-210	8	9
β-strand	213	1	10
α-helix	224-225	2
β-strand	227	1	10
β-strand	229-236	8	9

Chain C: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	11
β-strand	19-26	8	11
β-strand	29-35	7	11
β-strand	40-43	4	11
α-helix	46-49	4
β-strand	53	1	12
α-helix	56-76	21
α-helix	80-84	5
β-strand	88	1	13
β-strand	91-93	3	14
β-strand	103-112	10	14
β-strand	118-123	6	15
β-strand	126-127	2	15
β-strand	132-134	3	14
β-strand	138-139	2	14
β-strand	145-153	9	14
β-strand	161-166	6	15
β-strand	174-177	4	15

Chain D: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-24	1	12
α-helix	-18--14	5
β-strand	7-18	12	11
β-strand	23-32	10	11
β-strand	35-41	7	11
β-strand	46-49	4	11
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-84	4
α-helix	86-89	4
β-strand	96	1	16
α-helix	97-98	2
β-strand	99-104	6	17
α-helix	107-108	2
β-strand	115-123	9	17
β-strand	124	1	16
β-strand	129-134	6	18
β-strand	137-139	3	18
β-strand	143-145	3	17
α-helix	146-148	3
β-strand	149-150	2	17
β-strand	156-163	8	17
β-strand	171-177	7	18
β-strand	185-190	6	18

Chain E: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
β-strand	9-13	5	20
α-helix	17	1
β-strand	18-24	7	19
β-strand	31-37	7	20
β-strand	44-50	7	20
β-strand	56-59	4	19
β-strand	62-67	6	19
β-strand	72-77	6	19
α-helix	82-84	3
β-strand	87-90	4	20
β-strand	91-92	2	21
β-strand	93	1	20
β-strand	101-102	2	21
β-strand	106-111	6	20
β-strand	120-126	7	22
β-strand	133-138	6	22
β-strand	154-156	3	22
α-helix	157-159	3
β-strand	160-164	5	22
β-strand	169-178	10	22
β-strand	199	1	22

Chain F: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	23
β-strand	8-12	5	24
β-strand	17-23	7	23
β-strand	29-36	8	24
β-strand	40-47	8	24
β-strand	54-55	2	24
β-strand	63-65	3	23
β-strand	71-76	6	23
α-helix	81-83	3
β-strand	85-92	8	24
β-strand	100-101	2	24
β-strand	105-110	6	24
β-strand	117	1	25
α-helix	118-119	2
β-strand	120-125	6	22
α-helix	126-127	2
α-helix	128-133	6
β-strand	136-146	11	22
β-strand	147	1	25
β-strand	151-157	7	26
β-strand	160-162	3	26
β-strand	166-168	3	22
α-helix	172	1
β-strand	173-174	2	22
β-strand	184-193	10	22
α-helix	194-198	5
β-strand	203-210	8	26
β-strand	213	1	27
β-strand	227	1	27
β-strand	229-236	8	26

Chain G: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	28
β-strand	19-26	8	28
β-strand	29-35	7	28
β-strand	40-43	4	28
α-helix	46-49	4
β-strand	53	1	29
α-helix	56-76	21
α-helix	81-84	4
β-strand	88	1	30
β-strand	91-93	3	31
β-strand	103-112	10	31
β-strand	118-123	6	32
β-strand	126-127	2	32
α-helix	128	1
β-strand	132-134	3	31
α-helix	137	1
β-strand	138-139	2	31
β-strand	145-153	9	31
β-strand	161-166	6	32
β-strand	174-177	4	32

Chain H: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	-24	1	29
α-helix	-18--14	5
β-strand	7-18	12	28
β-strand	23-32	10	28
β-strand	36-41	6	28
β-strand	46-49	4	28
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-82	2
α-helix	83-87	5
β-strand	96	1	33
α-helix	97-98	2
β-strand	99-104	6	34
β-strand	115-123	9	34
β-strand	124	1	33
β-strand	129-134	6	35
β-strand	138	1	35
β-strand	143-145	3	34
α-helix	146-148	3
β-strand	149-150	2	34
β-strand	156-163	8	34
β-strand	171-177	7	35
β-strand	185-190	6	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TRA protein	A, E	protein	206	Homo sapiens
Human nkt tcr beta chain	B, F	protein	241	Homo sapiens
H-2 class II histocompatibility antigen, A-B alpha chain	C, G	protein	182	Mus musculus	P14434 (AlphaFold model)
protein of 3K peptide (FEAQKAKANKAVD),Linker region - GGGGSLVPRGSGGGG,H-2 class II…	D, H	protein	217	Mus musculus	P14483 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>4P5T_1 TRA protein (chains A, E)
MQQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLIAIRSVSDKKEDG
RFTIFFNKREKKLSLHITDSQPGDSATYFCAASRDSGQKLVFGQGTILKVYLHIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B, F), FASTA

>4P5T_2 Human nkt tcr beta chain (chains B, F)
MAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIP
DGYKASRPSQENFSLILELATPSQTSVYFCASGDFWGDTLYFGAGTRLSVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Sequence of entity 3 (C, G), FASTA

>4P5T_3 H-2 class II histocompatibility antigen, A-B alpha chain (chains C, G)
IEADHVGTYGISVYQSPGDIGQYTFEFDGDELFYVDLDKKETVWMLPEFGQLASFDPQGG
LQNIAVVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINI
TWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWE
PE

Sequence of entity 4 (D, H), FASTA

>4P5T_4 protein of 3K peptide (FEAQKAKANKAVD),Linker region - GGGGSLVPRGSGGGG,H-2 class II histocompatibility antigen, A beta chain,H-2 class II histocompatibility antigen, A beta chain (chains D, H)
FEAQKAKANKAVDGGGGSLVPRGSGGGGSERHFVYQFMGECYFTNGTQRIRYVTRYIYNR
EEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSLRR
LEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDW
TFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA

Primary citation

Effect of CDR3 Sequences and Distal V Gene Residues in Regulating TCR-MHC Contacts and Ligand Specificity. Stadinski, B.D., Trenh, P., Duke, B. et al. J Immunol (2014) 192:6071-6082. DOI 10.4049/jimmunol.1303209 · PubMed

Other PDB entries of the same protein (UniProt P14434 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VQ8 2.01 Å, Immune receptor complex
8RAL 2.1 Å, CL3E peptide bound to the I-Ab murine MHC class II receptor
1MUJ 2.15 Å, Crystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide
4P23 2.25 Å, J809.B5 TCR bound to IAb/3K
1LNU 2.5 Å, Crystal structure of class II MHC molecule iab bound to EALPHA3K peptide
3C5Z 2.55 Å, Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506
6MNG 2.66 Å, 4738 TCR bound to IAb Padi4
3RDT 2.7 Å, Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide
6MNN 2.83 Å, 6236 TCR bound to I-Ab Padi4
4P46 2.85 Å, J809.B5 Y31A TCR bound to IAb3K
6MNO 2.9 Å, 6235 TCR bound to I-Ab Padi4
9AUD 2.9 Å, Immune receptor complex

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