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

Crystal structure of TK3 TCR-HLA-B*35:08-HPVG complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Human herpesvirus 4
Chains: 5
Atoms: 6,792
Mol. weight: 94.7 kDa
Released: 16 Apr 2014

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

Secondary structure: helices and β-sheets

4PRI contains 27 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	18-20	3
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
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	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
α-helix	182	1
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-192	7	3
β-strand	200-208	9	3
β-strand	209	1	2
β-strand	214-218	5	4
β-strand	223	1	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-248	8	3
β-strand	258-262	5	4
β-strand	270-272	3	4

Chain B: 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

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-14	5	9
β-strand	19-26	8	8
β-strand	30-44	9	9
β-strand	51-56	6	9
β-strand	66-69	4	8
β-strand	79-83	5	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-108	9	9
β-strand	117-118	2	9
β-strand	122-127	6	9
α-helix	128-129	2
β-strand	136-142	7	10
β-strand	149-154	6	10
α-helix	162-165	4
β-strand	170-172	3	10
α-helix	173-175	3
β-strand	176-180	5	10
α-helix	181-183	3
β-strand	185-194	10	10
β-strand	215	1	10

Chain E: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
α-helix	25-26	2
β-strand	31-45	8	12
β-strand	50-57	8	12
β-strand	60-68	5	12
β-strand	76-80	5	11
β-strand	87-91	5	11
α-helix	96-98	3
β-strand	100-107	8	12
β-strand	113-115	3	12
β-strand	119-124	6	12
β-strand	131	1	13
α-helix	132-133	2
β-strand	134-139	6	10
α-helix	140-141	2
α-helix	142-148	7
β-strand	150-160	11	10
β-strand	161	1	13
β-strand	165-171	7	14
β-strand	174-176	3	14
β-strand	180-182	3	10
β-strand	187-188	2	10
α-helix	191-193	3
β-strand	198-207	10	10
α-helix	208-212	5
β-strand	217-224	8	14
α-helix	238-239	2
β-strand	243-250	8	14

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)
Epstein-Barr nuclear antigen 1	C	protein	11	Human herpesvirus 4	P03211 (AlphaFold model)
TK3 TCR alpha chain	D	protein	202	Homo sapiens	P01848 (AlphaFold model)
TK3 TCR beta chain	E	protein	240	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>4PRI_1 MHC class I antigen (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQRRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>4PRI_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>4PRI_3 Epstein-Barr nuclear antigen 1 (chains C)
HPVGEADYFEY

Sequence of entity 4 (D), FASTA

>4PRI_4 TK3 TCR alpha chain (chains D)
EDQVTQSPEALRLQEGESSSLNCSYTVSGLRGLFWYRQDPGKGPEFLFTLYSAGEEKEKE
RLKATLTKKESFLHITAPKPEDSATYLCAVQDLGTSGSRLTFGEGTQLTVNPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPS

Sequence of entity 5 (E), FASTA

>4PRI_5 TK3 TCR beta chain (chains E)
SGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNIL
ERFSAQQFPDLHSELNLSSLELGDSALYFCASSARSGELFFGEGSRLTVLEDLKNVFPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

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
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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