4PRH: TK3 TCR-HLA-B*35:08-HPVG-D5 complex

Crystal structure of TK3 TCR-HLA-B*35:08-HPVG-D5 complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 30 Apr 2014.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Human herpesvirus 4
Chains: 5
Atoms: 6,346
Mol. weight: 95.34 kDa
Released: 30 Apr 2014

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

Secondary structure: helices and β-sheets

4PRH contains 25 α-helices and 69 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: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
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	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-188	3	3
β-strand	204-208	5	3
β-strand	209	1	2
β-strand	214-215	2	4
β-strand	234-235	2	3
β-strand	241-243	3	3
β-strand	260-262	3	4
β-strand	270-271	2	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	5
β-strand	9-11	3	6
β-strand	23-25	3	6
β-strand	26-30	5	7
β-strand	36	1	8
α-helix	49	1
β-strand	50	1	9
α-helix	51	1
β-strand	55-56	2	7
β-strand	62-65	4	7
β-strand	67	1	9
β-strand	68	1	6
β-strand	83	1	8

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-14	5	11
β-strand	19-26	8	10
β-strand	30-44	9	11
β-strand	51-56	6	11
β-strand	66-69	4	10
β-strand	79-83	5	10
β-strand	86-91	6	10
α-helix	96-98	3
β-strand	100-108	9	11
β-strand	117-118	2	11
α-helix	119	1
β-strand	122-127	6	11
α-helix	128-129	2
β-strand	136-142	7	12
β-strand	149-154	6	12
α-helix	163-165	3
β-strand	170-172	3	12
α-helix	173-175	3
β-strand	176-179	4	12
α-helix	181-183	3
β-strand	186-194	9	12
α-helix	201-204	4
β-strand	215	1	12

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-14	5	14
β-strand	19-24	6	13
α-helix	25-26	2
β-strand	31-44	7	14
β-strand	50-57	8	14
β-strand	60-68	5	14
β-strand	76-80	5	13
β-strand	87-91	5	13
α-helix	96-98	3
β-strand	100-107	8	14
β-strand	113-115	3	14
β-strand	119-124	6	14
β-strand	131	1	15
α-helix	132-133	2
β-strand	134-139	6	12
α-helix	140-141	2
α-helix	142-148	7
β-strand	150-160	11	12
β-strand	161	1	15
β-strand	165-171	7	16
β-strand	174-176	3	16
β-strand	180-182	3	12
α-helix	186	1
β-strand	187-188	2	12
β-strand	198-207	10	12
α-helix	208-212	5
β-strand	217-224	8	16
β-strand	227	1	17
α-helix	238-239	2
β-strand	241	1	17
β-strand	243-250	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	272	Homo sapiens	C5MK56 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Epstein-Barr nuclear antigen 1	C	protein	11	Human herpesvirus 4	Q3KSS4
TK3 TCR alpha chain	D	protein	208	Homo sapiens	P01848 (AlphaFold model)
TK3 TCR beta chain	E	protein	243	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>4PRH_1 MHC class I antigen (chains A)
SHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYWD
RNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDGK
DYIALNEDLSSWTAADTAAQITQRKWEAARVAEQRRAYLEGLCVEWLRRYLENGKETLQR
ADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQDTELVETRPAGDRTFQK
WAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>4PRH_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERLEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>4PRH_3 Epstein-Barr nuclear antigen 1 (chains C)
HPVGDADYFEY

Sequence of entity 4 (D), FASTA

>4PRH_4 TK3 TCR alpha chain (chains D)
HMEDQVTQSPEALRLQEGESSSLNCSYTVSGLRGLFWYRQDPGKGPEFLFTLYSAGEEKE
KERLKATLTKKESFLHITAPKPEDSATYLCAVQDLGTSGSRLTFGEGTQLTVNPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>4PRH_5 TK3 TCR beta chain (chains E)
HMDSGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKG
NILERFSAQQFPDLHSELNLSSLELGDSALYFCASSARSGELFFGEGSRLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

A Molecular Basis for the Interplay between T Cells, Viral Mutants, and Human Leukocyte Antigen Micropolymorphism. Liu, Y.C., Chen, Z., Neller, M.A. et al. J Biol Chem (2014) 289:16688-16698. DOI 10.1074/jbc.M114.563502 · 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
4JRX 2.3 Å, Crystal Structure of CA5 TCR-HLA B*3505-LPEP complex
4PRI 2.4 Å, Crystal structure of TK3 TCR-HLA-B*35:08-HPVG complex
4PRP 2.5 Å, Crystal structure of TK3 TCR-HLA-B*35:01-HPVG-Q5 complex

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