2AK4: SB27 TCR

Crystal Structure of SB27 TCR in complex with HLA-B*3508-13mer peptide. Determined by X-ray diffraction at 2.5 Å resolution. Released 11 Oct 2005.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 20
Atoms: 26,609
Mol. weight: 390.03 kDa
Released: 11 Oct 2005

Explore 2AK4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2AK4 contains 119 α-helices and 310 β-strands across 20 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
α-helix	19-20	2
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	1
α-helix	104	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
α-helix	225-227	3
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chains B, G, L and R: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
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	78-83	6	7
α-helix	90	1
β-strand	91-94	4	7

Chains C and H: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	6	1	8
α-helix	9-12	4

Chain D: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	9
β-strand	9-13	5	10
β-strand	18-20	3	9
β-strand	23-25	3	9
β-strand	31-37	7	10
β-strand	44-50	7	10
β-strand	55-57A	4	9
β-strand	62-67	6	9
β-strand	72-77	6	9
α-helix	82-84	3
β-strand	86-93	8	10
β-strand	96	1	8
β-strand	105-106	2	10
β-strand	110-115	6	10
β-strand	124-128	5	11
β-strand	129	1	12
β-strand	137-142	6	11
α-helix	150-153	4
β-strand	159-160	2	11
α-helix	161-163	3
β-strand	164-168	5	11
α-helix	169-171	3
β-strand	173-182	10	11
β-strand	203	1	11

Chains E and J: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-21	3	15
β-strand	22-25	4	13
β-strand	32-38	7	14
β-strand	42-51	10	14
β-strand	54-57	4	14
β-strand	66-68	3	15
β-strand	74	1	13
β-strand	76-79	4	15
α-helix	84-86	3
β-strand	88-93	6	14
β-strand	108	1	14
β-strand	112-117	6	14
α-helix	120-122	3
β-strand	124	1	16
α-helix	125-126	2
β-strand	127-131	5	17
β-strand	132	1	12
α-helix	133-134	2
α-helix	135-141	7
β-strand	143-153	11	17
β-strand	154	1	16
β-strand	158-164	7	18
β-strand	167-169	3	18
β-strand	173-175	3	17
α-helix	179	1
β-strand	180-181	2	17
β-strand	191-200	10	17
α-helix	201-204	4
β-strand	210-217	8	18
β-strand	220	1	19
α-helix	231-232	2
β-strand	234	1	19
β-strand	236-243	8	18

Chain F: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	20
α-helix	19-20	2
β-strand	21-28	8	20
β-strand	31-37	7	20
β-strand	46-47	2	20
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	20
β-strand	109-118	10	20
β-strand	121-126	6	20
β-strand	133-135	3	20
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	21
α-helix	184-185	2
β-strand	186-193	8	22
β-strand	198-208	11	22
β-strand	209	1	21
β-strand	214-219	6	23
β-strand	222-223	2	23
α-helix	225-227	3
β-strand	229-230	2	22
α-helix	231-233	3
β-strand	234-235	2	22
β-strand	241-250	10	22
α-helix	254-256	3
β-strand	257-262	6	23
β-strand	270-272	3	23

Chain I: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	28
β-strand	9-13	5	29
β-strand	18-20	3	28
β-strand	23-25	3	28
β-strand	31-37	7	29
β-strand	44-50	7	29
β-strand	55-57A	4	28
β-strand	62-67	6	28
β-strand	72-77	6	28
α-helix	82-84	3
β-strand	86-93	8	29
β-strand	96	1	27
β-strand	105-106	2	29
β-strand	110-115	6	29
β-strand	124-128	5	30
β-strand	129	1	31
α-helix	130-131	2
β-strand	138-142	5	30
α-helix	150-153	4
β-strand	159-160	2	30
α-helix	161-163	3
β-strand	164-168	5	30
α-helix	169-171	3
β-strand	173-181	9	30
β-strand	203	1	30

Chain K: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	39
α-helix	19-20	2
β-strand	21-28	8	39
β-strand	31-37	7	39
β-strand	46-47	2	39
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	39
β-strand	109-118	10	39
β-strand	121-126	6	39
β-strand	133-135	3	39
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	40
α-helix	184-185	2
β-strand	186-195	10	41
β-strand	198-208	11	41
β-strand	209	1	40
β-strand	214-219	6	42
β-strand	222-223	2	42
α-helix	225-227	3
β-strand	229-230	2	41
α-helix	231-233	3
β-strand	234-235	2	41
β-strand	241-250	10	41
α-helix	254-256	3
β-strand	257-262	6	42
β-strand	270-272	3	42

6 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
HLA-B35 variant	A, F, K, Q	protein	276	Homo sapiens	P01889 (AlphaFold model)
Beta-2-microglobulin	B, G, L, R	protein	99	Homo sapiens	P61769 (AlphaFold model)
EBV peptide LPEPLPQGQLTAY	C, H, M, S	protein	13		P03206 (AlphaFold model)
SB27 T cell receptor alpha chain	D, I, N, T	protein	211	Homo sapiens	P01848 (AlphaFold model)
SB27 T cell receptor beta chain	E, J, P, U	protein	245	Homo sapiens	P01850

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

>2AK4_1 HLA-B35 variant (chains A, F, K, Q)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQRRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

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

>2AK4_2 Beta-2-microglobulin (chains B, G, L, R)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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

>2AK4_3 EBV peptide LPEPLPQGQLTAY (chains C, H, M, S)
LPEPLPQGQLTAY

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

>2AK4_4 SB27 T cell receptor alpha chain (chains D, I, N, T)
HMAQKVTQAQTEISVVEKEDVTLDCVYETRDTTYYLFWYKQPPSGELVFLIRRNSFDEQN
EISGRYSWNFQKSTSSFNFTITASQVVDSAVYFCALSGFYNTDKLIFGTGTRLQVFPNIQ
NPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAV
AWSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E, J, P, U), FASTA

>2AK4_5 SB27 T cell receptor beta chain (chains E, J, P, U)
HMNAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKG
EVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASPGLAGEYEQYFGPGTRLTVTEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Primary citation

T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide. Tynan, F.E., Burrows, S.R., Buckle, A.M. et al. Nat Immunol (2005) 6:1114-1122. DOI 10.1038/ni1257 · PubMed

Other PDB entries of the same protein (UniProt P01889 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6MT3 1.21 Å, Crystal Structure of HLA-B*18:01 in complex with NP338 influenza peptide
3LN4 1.3 Å, Crystal structure of HLA-B*4103 in complex with a 16mer self-peptide derived from…
3BWA 1.3 Å, Crystal Structure of HLA B*3508 in complex with a HCMV 8-mer peptide from the pp65 protein
3SPV 1.3 Å, Crystal structure of a peptide-HLA complex
6MT6 1.31 Å, Crystal Structure of HLA-B*37:01 in complex with NP338 influenza peptide
2BVP 1.35 Å, Structures of Three HIV-1 HLA-B5703-Peptide Complexes and Identification of Related HLAs…
6MTL 1.35 Å, Crystal Structure of HLA-B*44:05 in complex with NP338 influenza peptide
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
6PYW 1.38 Å, Crystal Structure of HLA-B*2705-W60A in complex with LRN, a self-peptide

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