4JRY: SB47 TCR-HLA B*3505-LPEP complex

Crystal Structure of SB47 TCR-HLA B*3505-LPEP complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 10 Apr 2013.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Human herpesvirus 4
Chains: 5
Atoms: 6,830
Mol. weight: 95.18 kDa
Ligands: MG
Released: 10 Apr 2013

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

Secondary structure: helices and β-sheets

4JRY contains 31 α-helices and 74 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	20	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
α-helix	105-107	3
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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
α-helix	182	1
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	214-218	5	4
β-strand	223	1	4
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	258-262	5	4
β-strand	270-272	3	4

Chain B: 2 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
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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	9-11	3

Chain D: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	38-44	7	9
β-strand	50-56	7	9
β-strand	65-68	4	8
β-strand	76-81	6	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	101-107	7	9
α-helix	113	1
β-strand	114-116	3	9
β-strand	120-125	6	9
β-strand	134-138	5	10
β-strand	139-140	2	11
β-strand	148-152	5	10
α-helix	158	1
β-strand	159	1	12
α-helix	160	1
β-strand	168-170	3	10
α-helix	171-173	3
β-strand	174-178	5	10
α-helix	179-181	3
β-strand	183-192	10	10
α-helix	199-202	4
β-strand	207	1	12
β-strand	213	1	10

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-13	4	14
β-strand	19-24	6	13
α-helix	25-26	2
β-strand	38-44	7	14
β-strand	51-57	7	14
β-strand	64-68	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	116-117	2	14
β-strand	121-125	5	14
α-helix	129-131	3
β-strand	133	1	15
β-strand	136-141	6	11
α-helix	142-143	2
α-helix	144-150	7
β-strand	152-162	11	11
β-strand	163	1	15
β-strand	167-173	7	16
β-strand	176-178	3	16
β-strand	182-184	3	11
α-helix	188	1
β-strand	189-190	2	11
β-strand	200-209	10	11
α-helix	210-214	5
β-strand	219-226	8	16
β-strand	229	1	17
β-strand	243	1	17
β-strand	245-252	8	16

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	100	Homo sapiens	P61769 (AlphaFold model)
Trans-activator protein BZLF1	C	protein	13	Human herpesvirus 4	Q3KSS8
SB47 TCR alpha chain	D	protein	201	Homo sapiens	P01848 (AlphaFold model)
SB47 TCR beta chain	E	protein	242	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>4JRY_1 MHC class I antigen (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQRRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>4JRY_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>4JRY_3 Trans-activator protein BZLF1 (chains C)
LPEPLPQGQLTAY

Sequence of entity 4 (D), FASTA

>4JRY_4 SB47 TCR alpha chain (chains D)
ELKVEQNPLFLSMQEGKNYTIYCNYSTTSDRLYWYRQDPGKSLESLFVLLSNGAVKQEGR
LMASLDTKARLSTLHITAAVHDLSATYFCAVGGGSNYQLIWGAGTKLIIKPNIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPS

Sequence of entity 5 (E), FASTA

>4JRY_5 SB47 TCR beta chain (chains E)
AGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFP
DRFSGHQFPNYSSELNVNALLLGDSALYLCASSRTGSTYEQYFGPGTRLTVTEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Water and common crystallization additives (NA) are not listed.

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
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
4PRH 2.5 Å, Crystal structure of TK3 TCR-HLA-B*35:08-HPVG-D5 complex

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