4JRX: CA5 TCR-HLA B*3505-LPEP complex

Crystal Structure of CA5 TCR-HLA B*3505-LPEP complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 10 Apr 2013.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, Human herpesvirus 4
Chains: 5
Atoms: 6,865
Mol. weight: 96.35 kDa
Released: 10 Apr 2013

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

Secondary structure: helices and β-sheets

4JRX contains 30 α-helices and 76 β-strands across 5 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: 13 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
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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
α-helix	181-182	2
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

Chain B: 3 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
β-strand	91-94	4	7

Chain C: 1 helix, 1 β-strand

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

Chain D: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
β-strand	10-14	5	10
β-strand	19-21	3	9
β-strand	24-26	3	9
β-strand	38-44	7	10
β-strand	51-57	7	10
β-strand	67-68	2	9
β-strand	76-81	6	9
β-strand	87-92	6	9
α-helix	97-99	3
β-strand	101-108	8	10
β-strand	111	1	8
β-strand	120-121	2	10
β-strand	125-130	6	10
β-strand	139-142	4	11
α-helix	143	1
β-strand	144	1	12
α-helix	145-146	2
β-strand	152-157	6	11
α-helix	163-165	3
β-strand	173-175	3	11
α-helix	176-178	3
β-strand	179-183	5	11
β-strand	188-197	10	11
α-helix	204-207	4
β-strand	218	1	11

Chain E: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	39-45	7	14
β-strand	49-56	8	14
β-strand	67-68	2	14
β-strand	76-81	6	13
β-strand	86-91	6	13
α-helix	96-98	3
β-strand	100-105	6	14
β-strand	114	1	14
β-strand	118-123	6	14
α-helix	126-128	3
β-strand	130	1	15
α-helix	131-132	2
β-strand	133-137	5	16
β-strand	138	1	12
α-helix	139-140	2
α-helix	141-147	7
β-strand	149-159	11	16
β-strand	160	1	15
β-strand	164-170	7	17
β-strand	174-175	2	17
β-strand	179-181	3	16
β-strand	186-187	2	16
β-strand	197-206	10	16
α-helix	207-211	5
β-strand	216-223	8	17
β-strand	226	1	18
α-helix	237-238	2
β-strand	240	1	18
β-strand	242-249	8	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	C5MK56 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
Trans-activator protein BZLF1	C	protein	13	Human herpesvirus 4	Q3KSS8
CA5 TCR alpha chain	D	protein	204	Homo sapiens	P01848 (AlphaFold model)
CA5 TCR beta chain	E	protein	238	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>4JRX_1 MHC class I antigen (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQRRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>4JRX_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>4JRX_3 Trans-activator protein BZLF1 (chains C)
LPEPLPQGQLTAY

Sequence of entity 4 (D), FASTA

>4JRX_4 CA5 TCR alpha chain (chains D)
QKVTQAQTEISVVEKEDVTLDCVYETRDTTYYLFWYKQPPSGELVFLIRRNSFDEQNEIS
GRYSWNFQKSTSSFNFTITASQVVDSAVYFCALSGFYNTDKLIFGTGTRLQVFPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPQDTFFPS

Sequence of entity 5 (E), FASTA

>4JRX_5 CA5 TCR beta chain (chains E)
GVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPN
GYNVSRLNKREFSLRLESAAPSQTSVYFCASPGETEAFFGQGTRLTVTEDLKNVFPPEVA
VFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDS
RYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Primary citation

Highly divergent T-cell receptor binding modes underlie specific recognition of a bulged viral peptide bound to a human leukocyte antigen class I molecule. Liu, Y.C., Miles, J.J., Neller, M.A. et al. J Biol Chem (2013) 288:15442-15454. DOI 10.1074/jbc.M112.447185 · PubMed

Other PDB entries of the same protein (UniProt C5MK56 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VFN 1.5 Å, crystal structure of HLA B*3508LPEP151A, HLA mutant Ala151
4PRE 1.65 Å, Crystal structure of a HLA-B*35:08-HPVG-Q5
3VFO 1.7 Å, crystal structure of HLA B*3508 LPEP157A, HLA mutant Ala157
4PRB 1.75 Å, Crystal structure of a HLA-B*35:08-HPVG-A4
4PRD 1.75 Å, Crystal structure of a HLA-B*35:08-HPVG-D5
3VFP 1.85 Å, crystal structure of HLA B*3508 LPEP158G, HLA mutant Gly158
3VFR 1.85 Å, crystal structure of HLA B*3508LPEP-P4Ala, peptide mutant P4-ala
4PRA 1.85 Å, Crystal structure of a HLA-B*35:01-HPVG-Q5
3VFM 1.9 Å, crystal structure of HLA B*3508 LPEP155A, HLA mutant Ala155
4PRI 2.4 Å, Crystal structure of TK3 TCR-HLA-B*35:08-HPVG complex
4PRH 2.5 Å, Crystal structure of TK3 TCR-HLA-B*35:08-HPVG-D5 complex
4PRP 2.5 Å, Crystal structure of TK3 TCR-HLA-B*35:01-HPVG-Q5 complex

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