6D7G: 5F3 TCR

Structure of 5F3 TCR in complex with HLA-A2/MART-1. Determined by X-ray diffraction at 2.75 Å resolution. Released 23 Jan 2019.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,022
Mol. weight: 103.23 kDa
Ligands: NAG
Released: 23 Jan 2019

Explore 6D7G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D7G contains 28 α-helices and 71 β-strands across 3 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: 14 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	103	1	1
α-helix	104-105	2
β-strand	106-111	6	2
β-strand	121-130	10	2
β-strand	131	1	1
β-strand	136-141	6	3
β-strand	144-145	2	3
β-strand	150-151	2	2
α-helix	152-154	3
β-strand	155-156	2	2
β-strand	162-170	9	2
β-strand	178-183	6	3
α-helix	190	1
β-strand	191-194	4	3
β-strand	1002-1012	11	4
α-helix	1020	1
β-strand	1021-1028	8	4
β-strand	1031-1037	7	4
β-strand	1046-1047	2	4
α-helix	1050-1052	3
α-helix	1057-1084	28
β-strand	1094-1104	11	4
β-strand	1109-1118	10	4
β-strand	1121-1126	6	4
β-strand	1133-1135	3	4
α-helix	1139-1150	12
α-helix	1152-1158	7
α-helix	1159-1163	5
α-helix	1164-1174	11
α-helix	1176-1179	4
β-strand	1183	1	5
β-strand	1186-1193	8	6
β-strand	1198-1208	11	6
β-strand	1209	1	5
β-strand	1214-1219	6	7
β-strand	1222-1223	2	7
α-helix	1225-1227	3
β-strand	1229-1230	2	6
α-helix	1231-1233	3
β-strand	1234-1235	2	6
β-strand	1241-1250	10	6
α-helix	1254-1256	3
β-strand	1257-1262	6	7
β-strand	1270-1272	3	7

Chain D: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	8
β-strand	10-14	5	9
β-strand	19-21	3	8
β-strand	24-26	3	8
β-strand	33-39	7	9
β-strand	45-52	8	9
β-strand	59-60	2	8
β-strand	63-68	6	8
β-strand	73-78	6	8
α-helix	83-85	3
β-strand	87-93	7	9
β-strand	104-105	2	9
α-helix	106-107	2
β-strand	109-114	6	9
α-helix	115-117	3
β-strand	121	1	10
α-helix	122-123	2
β-strand	124-130	7	11
β-strand	133-141	9	11
β-strand	142	1	10
β-strand	147-150	4	12
β-strand	157-158	2	11
α-helix	160-161	2
β-strand	162-165	4	11
β-strand	171-178	8	11
α-helix	182-184	3
β-strand	187-191	5	12
β-strand	194-197	4	12
α-helix	198-200	3

Chain E: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2
β-strand	9-14	6	13
β-strand	19-23	5	14
β-strand	32-38	7	13
β-strand	45-51	7	13
β-strand	56-59	4	13
α-helix	60	1
β-strand	68-72	5	14
β-strand	78-82	5	14
α-helix	87-89	3
β-strand	91-98	8	13
β-strand	105-107	3	13
α-helix	108-110	3
β-strand	111-116	6	13
α-helix	117	1
β-strand	129-133	5	15
β-strand	134	1	11
α-helix	135-136	2
α-helix	137-143	7
β-strand	147-155	9	15
β-strand	161-165	5	16
β-strand	176-177	2	15
β-strand	181-183	3	15
β-strand	186-194	9	15
β-strand	205-209	5	16
β-strand	219-222	4	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MART1 peptide-beta-2-microglobulin-HLA-A*02 chimera	A	protein	427	Homo sapiens	P04439 (AlphaFold model), P61769 (AlphaFold model)
TRA@ protein	D	protein	229	Homo sapiens	Q6PJ56 (AlphaFold model)
T-cell receptor gamma variable 8,T-cell receptor gamma-2 chain C region	E	protein	258	Homo sapiens

Sequence of entity 1 (A), FASTA

>6D7G_1 MART1 PEPTIDE-BETA-2-MICROGLOBULIN-HLA-A*02 CHIMERA (chains A)
ELAGIGILTVGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDI
EVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKW
DRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQ
RMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQL
RAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLT
WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEH
HHHHHHH

Sequence of entity 2 (D), FASTA

>6D7G_2 TRA@ protein (chains D)
ADPAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQN
AKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGELGWDTDKLIFGKGTRVTVEPRS
QPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKLG
KYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETENTKQPSKSC

Sequence of entity 3 (E), FASTA

>6D7G_3 T-CELL RECEPTOR GAMMA VARIABLE 8,T-CELL RECEPTOR GAMMA-2 CHAIN C REGION (chains E)
ADLSSNLEGRTKSVTRPTGSSAVITCDLPVENAVYTHWYLHQEGKAPQRLLYYDSYNSRV
VLESGISREKYHTYASTGKSLKFILENLIERDSGVYYCATWASSDWIKTFAKGTRLIVTS
PDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDIIKIHWQEKKSNTILGSQE
GNTMKTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGIDQEIIFPPIKTDVTTVDPKY
NYSKDANDVITMDPKDNC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Generation and molecular recognition of melanoma-associated antigen-specific human gamma delta T cells. Benveniste, P.M., Roy, S., Nakatsugawa, M. et al. Sci Immunol (2018) 3. DOI 10.1126/sciimmunol.aav4036 · PubMed

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

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