3PQY: 6218 TCR

Crystal Structure of 6218 TCR in complex with the H2Db-PA224. Determined by X-ray diffraction at 3.19 Å resolution. Released 18 May 2011.

Method: X-ray diffraction
Resolution: 3.19 Å
Organisms: Mus musculus, synthetic construct, Homo sapiens
Chains: 20
Atoms: 25,956
Mol. weight: 376.43 kDa
Released: 18 May 2011

Explore 3PQY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PQY contains 70 α-helices and 297 β-strands across 16 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: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
β-strand	21-28	8	1
β-strand	32-37	6	1
β-strand	46-47	2	1
α-helix	57-85	29
α-helix	87-88	2
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	140-149	10
α-helix	152-157	6
α-helix	158-164	7
α-helix	165-175	11
β-strand	183	1	2
β-strand	188-193	6	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	213-219	7	4
β-strand	222-224	3	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-263	7	4
β-strand	270-272	3	4

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	91-94	4	7

Chain D: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	10-14	5	9
α-helix	17	1
β-strand	18-25	8	8
β-strand	32-44	8	9
β-strand	51-56	6	9
β-strand	68	1	8
β-strand	80-83	4	8
α-helix	84	1
β-strand	85-93	9	8
α-helix	96-98	3
β-strand	100-108	9	9
β-strand	120-125	6	9
β-strand	135-138	4	10
β-strand	139	1	11
β-strand	146-151	6	10
β-strand	168-169	2	10
α-helix	170-172	3
β-strand	173-174	2	10
β-strand	185-190	6	10

Chain E: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	24	1	12
β-strand	31-44	7	13
β-strand	50-58	9	13
β-strand	61-67	3	13
β-strand	77-79	3	14
β-strand	86	1	12
β-strand	88-91	4	14
α-helix	96-98	3
β-strand	101-107	7	13
β-strand	113-114	2	13
β-strand	118-123	6	13
α-helix	126-128	3
β-strand	130	1	15
α-helix	131-132	2
β-strand	133-137	5	11
α-helix	138-140	3
α-helix	143-146	4
β-strand	149-159	11	11
β-strand	160	1	15
β-strand	164-170	7	16
β-strand	173-174	2	16
β-strand	179-181	3	11
α-helix	185	1
β-strand	186-187	2	11
α-helix	195-196	2
β-strand	197-206	10	11
α-helix	207-210	4
β-strand	216-223	8	16
β-strand	226	1	17
β-strand	240	1	17
β-strand	242-249	8	16

Chain F: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	18
α-helix	20	1
β-strand	21-28	8	18
β-strand	32-37	6	18
β-strand	46-47	2	18
α-helix	50-52	3
α-helix	59-84	26
β-strand	93-98	6	18
β-strand	101-103	3	18
β-strand	109-112	4	18
β-strand	115-119	5	18
β-strand	121-126	6	18
β-strand	133-135	3	18
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-173	9
α-helix	175-177	3
β-strand	188-195	8	19
β-strand	198-204	7	19
β-strand	208	1	20
β-strand	214-217	4	21
β-strand	229-230	2	19
α-helix	231-233	3
β-strand	234-235	2	20
β-strand	241-242	2	20
β-strand	245-250	6	19
β-strand	259-262	4	21
β-strand	270-272	3	21

Chain G: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	22
β-strand	6-11	6	23
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	36-41	6	24
β-strand	45	1	24
β-strand	50-51	2	23
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-83	6	24
α-helix	90	1
β-strand	91-94	4	24

Chain I: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	25
β-strand	10-14	5	26
α-helix	18	1
β-strand	19-25	7	25
β-strand	32-44	8	26
β-strand	51-56	6	26
β-strand	66-68	3	25
β-strand	80-83	4	25
β-strand	85-91	7	25
α-helix	96-98	3
β-strand	100-108	9	26
β-strand	120-125	6	26
β-strand	133-137	5	27
β-strand	139	1	28
β-strand	147-151	5	27
β-strand	168-169	2	27
α-helix	170-172	3
β-strand	173	1	29
β-strand	186	1	29
β-strand	188-190	3	27

Chain J: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	30
β-strand	10-14	5	31
β-strand	19-21	3	32
β-strand	24	1	30
β-strand	31-44	7	31
β-strand	50-56	7	31
β-strand	66-67	2	31
β-strand	77-79	3	32
β-strand	86	1	30
β-strand	88-91	4	32
α-helix	96-98	3
β-strand	100-107	8	31
β-strand	113-114	2	31
β-strand	118-123	6	31
α-helix	126-128	3
β-strand	130	1	33
α-helix	131-132	2
β-strand	133-137	5	28
α-helix	138-140	3
α-helix	143-145	3
β-strand	149-159	11	28
β-strand	160	1	33
β-strand	166-170	5	34
β-strand	173-175	3	34
β-strand	179-181	3	28
β-strand	186-187	2	28
α-helix	195-196	2
β-strand	197-206	10	28
α-helix	207-210	4
β-strand	216-223	8	34
β-strand	242-249	8	34

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-B alpha chain	A, F, K, P	protein	275	Mus musculus	P01899 (AlphaFold model)
Beta-2-microglobulin	B, G, L, Q	protein	99	Mus musculus	P01887 (AlphaFold model)
10-mer peptide from RNA-directed RNA polymerase	C, H, M, R	protein	10	synthetic construct	P13175
T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain	D, I, N, S	protein	195	Mus musculus, Homo sapiens	A0A075B6C4 (AlphaFold model), K7N5N2
T cell receptor beta, variable 29,Human nkt tcr beta chain	E, J, O, T	protein	240	Mus musculus, Homo sapiens	A0A0G2LB96, K7N5M4

Sequence of entity 1 (A, F, K, P), FASTA

>3PQY_1 H-2 class I histocompatibility antigen, D-B alpha chain (chains A, F, K, P)
PHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWE
RETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGR
DYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLR
TDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTF
QKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP

Sequence of entity 2 (B, G, L, Q), FASTA

>3PQY_2 Beta-2-microglobulin (chains B, G, L, Q)
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Sequence of entity 3 (C, H, M, R), FASTA

>3PQY_3 10-mer peptide from RNA-directed RNA polymerase (chains C, H, M, R)
SSLENFRAYV

Sequence of entity 4 (D, I, N, S), FASTA

>3PQY_4 T cell receptor alpha variable 21-DV12,T-cell receptor, sp3.4 alpha chain (chains D, I, N, S)
KTTQPDSMESTEGETVHLPCSHATISGNEYIYWYRQVPLQGPEYVTHGLQQNTTNSMAFL
AIASDRKSSTLILPHVSLRDAAVYHCILSGGSNYKLTFGKGTLLTVTPIQNPDPAVYQLR
DSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFAC
ANAFNNSIIPEDTFF

Sequence of entity 5 (E, J, O, T), FASTA

>3PQY_5 T cell receptor beta, variable 29,Human nkt tcr beta chain (chains E, J, O, T)
DMKVTQMPRYLIKRMGENVLLECGQDMSHETMYWYRQDPGLGLQLIYISYDVDSNSEGDI
PKGYRVSRKKREHFSLILDSAKTNQTSVYFCASSFGREQYFGPGTRLTVLEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Primary citation

Structural basis for enabling T-cell receptor diversity within biased virus-specific CD8+ T-cell responses. Day, E.B., Guillonneau, C., Gras, S. et al. Proc Natl Acad Sci U S A (2011) 108:9536-9541. DOI 10.1073/pnas.1106851108 · PubMed

Other PDB entries of the same protein (UniProt P01899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WZY 1.5 Å, Structure of DbNA(10) peptides bound to H-2Db MHC-I
6X00 1.55 Å, Structure of DbNA(11) peptides bound to H-2Db MHC-I
7N9J 1.74 Å, Crystal structure of H2DB in complex with HSF2 melanoma neoantigen
5M02 1.75 Å, Crystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
7N5Q 1.76 Å, Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation
7N4K 1.85 Å, 6218 TCR in complex with H2-Db PA 224
7N5C 1.87 Å, 6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond
6G9Q 1.89 Å, Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen…
1WBX 1.9 Å, Crystal structures of murine MHC class I H-2 db and kb molecules in complex with ctl…
4L8D 1.9 Å, Crystal structure of the H2Db in complex with the NP-N5D peptide
3CC5 1.91 Å, H-2Db complex with human gp100
5M00 1.95 Å, Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide…

Browse structure collections

About this viewer

MolViewer shows 3PQY directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.