9D95: TCR - peptide - HLA complex

TCR - peptide - HLA complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 3 Sept 2025.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, human gammaherpesvirus 4
Chains: 20
Atoms: 25,533
Mol. weight: 394.1 kDa
Ligands: NAG
Released: 3 Sept 2025

Explore 9D95 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D95 contains 83 α-helices and 284 β-strands across 16 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.

Chains A and F: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	57-85	29
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	152-158	7
α-helix	159-164	6
α-helix	165-174	10
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	213-219	7	4
β-strand	222-223	2	4
β-strand	228-230	3	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	257-263	7	4
β-strand	270-272	3	4

Chains B, G, L and Q: 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

Chains D and I: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	8
β-strand	10-14	5	9
β-strand	19-24	6	8
β-strand	29-44	9	9
β-strand	51-56	6	9
β-strand	66-68	3	8
β-strand	76-80	5	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-108	9	9
α-helix	113	1
β-strand	114-116	3	9
β-strand	120-125	6	9
β-strand	134-140	7	10
β-strand	147-152	6	10
α-helix	160-163	4
β-strand	168-170	3	10
α-helix	171-173	3
β-strand	174-178	5	10
β-strand	183-192	10	10
β-strand	213	1	10

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-14	5	12
β-strand	19-25	7	11
β-strand	36-44	9	12
β-strand	50-57	8	12
β-strand	66-67	2	12
β-strand	76-83	7	11
β-strand	86-91	6	11
β-strand	100-108	9	12
β-strand	117-118	2	12
β-strand	122-127	6	12
β-strand	134	1	13
β-strand	137-142	6	10
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	10
β-strand	164	1	13
β-strand	168-174	7	14
β-strand	177-179	3	14
β-strand	183-185	3	10
α-helix	189	1
β-strand	190-191	2	10
β-strand	201-210	10	10
α-helix	211-214	4
β-strand	220-227	8	14
β-strand	230	1	15
β-strand	244	1	15
β-strand	246-253	8	14

Chain J: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	10-14	5	27
β-strand	19-25	7	26
β-strand	36-44	9	27
β-strand	50-57	8	27
β-strand	66-67	2	27
β-strand	76-83	7	26
β-strand	86-91	6	26
α-helix	96-98	3
β-strand	101-108	8	27
β-strand	117-118	2	27
β-strand	122-127	6	27
β-strand	134	1	28
β-strand	137-142	6	25
α-helix	143-144	2
α-helix	145-150	6
β-strand	153-163	11	25
β-strand	164	1	28
β-strand	168-174	7	29
β-strand	177-179	3	29
β-strand	183-185	3	25
α-helix	189	1
β-strand	190-191	2	25
β-strand	201-210	10	25
α-helix	211-214	4
β-strand	220-227	8	29
β-strand	230	1	30
β-strand	244	1	30
β-strand	246-253	8	29

Chain K: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	31
α-helix	20	1
β-strand	21-28	8	31
β-strand	31-37	7	31
β-strand	46-47	2	31
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	31
β-strand	109-118	10	31
β-strand	121-126	6	31
β-strand	133-135	3	31
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	32
β-strand	186-193	8	33
β-strand	198-208	11	33
β-strand	209	1	32
β-strand	213-219	7	34
β-strand	222-223	2	34
β-strand	229-230	2	33
α-helix	231-233	3
β-strand	234-235	2	33
β-strand	241-250	10	33
α-helix	254-256	3
β-strand	257-263	7	34
β-strand	270-272	3	34

Chain N: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	38
β-strand	10-14	5	39
β-strand	19-24	6	38
β-strand	29-44	9	39
β-strand	51-56	6	39
β-strand	66-68	3	38
β-strand	76-80	5	38
β-strand	86-91	6	38
α-helix	96-98	3
β-strand	100-108	9	39
α-helix	113	1
β-strand	114-116	3	39
β-strand	120-125	6	39
β-strand	134-138	5	40
β-strand	139-140	2	41
β-strand	148-152	5	40
α-helix	160-163	4
β-strand	168-170	3	40
α-helix	171-173	3
β-strand	174-178	5	40
β-strand	183-192	10	40
β-strand	213	1	40

Chain O: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	42
β-strand	10-14	5	43
β-strand	19-25	7	42
β-strand	36-44	9	43
β-strand	50-57	8	43
β-strand	66-67	2	43
β-strand	76-83	7	42
β-strand	86-91	6	42
α-helix	96-98	3
β-strand	101-108	8	43
β-strand	117-118	2	43
β-strand	122-127	6	43
β-strand	134	1	44
β-strand	137-142	6	41
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	41
β-strand	164	1	44
β-strand	168-174	7	45
β-strand	177-179	3	45
β-strand	183-185	3	41
α-helix	189	1
β-strand	190-191	2	41
β-strand	201-210	10	41
α-helix	211-214	4
β-strand	220-227	8	45
β-strand	230	1	46
β-strand	244	1	46
β-strand	246-253	8	45

3 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
MHC class I antigen	A, F, K, P	protein	276	Homo sapiens	E5FQ58 (AlphaFold model)
Beta-2-microglobulin	B, G, L, Q	protein	100	Homo sapiens	P61769 (AlphaFold model)
Epstein-Barr nuclear antigen 2	C, H, M, R	protein	10	human gammaherpesvirus 4	P12978 (AlphaFold model)
T cell receptor alpha chain	D, I, N, S	protein	214	Homo sapiens
T cell receptor beta chain	E, J, O, T	protein	256	Homo sapiens

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

>9D95_1 MHC class I antigen (chains A, F, K, P)
GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYW
DRNTQICKTNTQTYRENLRIALRYYNQSEAGSHTLQRMYGCDVGPDGRLLRGHNQFAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRTYLEGTCVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

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

>9D95_2 Beta-2-microglobulin (chains B, G, L, Q)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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

>9D95_3 Epstein-Barr nuclear antigen 2 (chains C, H, M, R)
YHLIVDTDSL

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

>9D95_4 T cell receptor alpha chain (chains D, I, N, S)
GQQLNQSPQSMFIQEGEDVSMNCTSSSIFNTWLWYKQDPGEGPVLLIALYKAGELTSNGR
LTAQFGITRKDSFLNISASIPSDVGIYFCAGRDEGTYKYIFGTGTRLKVLANIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESSGSGLEVLFQ

Sequence of entity 5 (E, J, O, T), FASTA

>9D95_5 T cell receptor beta chain (chains E, J, O, T)
GAVVSQHPSRVICKSGTSVKIECRSLDFQATTMFWYRQFPKKSLMLMATSNEGSKATYEQ
GVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSARDLQGVNYGYTFGSGTRLTVVEDL
NKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPL
KEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSA
EAWGRADGSGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	14

Water and common crystallization additives (P6G, SO4) are not listed.

Primary citation

T cell recognition of a viral antigen. Zhu, S., Petersen, J., Rossjohn, J. To be published.

Other PDB entries of the same protein (UniProt E5FQ58 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9D97 1.6 Å, KIR3DL - HLA complex
9D96 2.4 Å, KIR3DL - HLA complex

Browse structure collections

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