7RE7: TCR mimic antibody

TCR mimic antibody (Fab fragment) in complex with AFP/HLA-A*02. Determined by X-ray diffraction at 2.55 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,099
Mol. weight: 190.97 kDa
Released: 27 Jul 2022

Explore 7RE7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RE7 contains 51 α-helices and 152 β-strands across 8 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	25
α-helix	20	1
β-strand	21-28	8	25
β-strand	31-37	7	25
β-strand	46-47	2	25
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	25
β-strand	109-118	10	25
β-strand	121-126	6	25
β-strand	133-135	3	25
α-helix	138-149	12
α-helix	152-157	6
α-helix	158-163	6
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	26
β-strand	186-193	8	27
β-strand	198-208	11	27
β-strand	209	1	26
β-strand	213-219	7	28
β-strand	222-223	2	28
β-strand	228-230	3	27
α-helix	231-233	3
β-strand	234-235	2	27
β-strand	241-250	10	27
α-helix	254-256	3
β-strand	257-263	7	28
α-helix	269	1
β-strand	270-272	3	28

Chains B and E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	29
α-helix	5-6	2
β-strand	7-12	6	30
β-strand	22-31	10	30
β-strand	32	1	29
β-strand	37-42	6	31
β-strand	45-46	2	31
α-helix	47	1
β-strand	51-52	2	30
β-strand	56-57	2	30
β-strand	63-71	9	30
β-strand	79-84	6	31
β-strand	92-95	4	31

Chain D: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	32
α-helix	20	1
β-strand	21-28	8	32
β-strand	31-37	7	32
β-strand	46-47	2	32
α-helix	52-54	3
α-helix	57-85	29
β-strand	94-103	10	32
β-strand	109-118	10	32
β-strand	121-126	6	32
β-strand	133-135	3	32
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	33
α-helix	184-185	2
β-strand	186-193	8	34
β-strand	198-208	11	34
β-strand	209	1	33
β-strand	213-219	7	35
β-strand	222-223	2	35
α-helix	225-227	3
β-strand	229-230	2	34
α-helix	231-233	3
β-strand	234-235	2	34
β-strand	241-250	10	34
α-helix	254-256	3
β-strand	257-263	7	35
β-strand	270-272	3	35

Chain H: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	14
β-strand	10-12	3	15
β-strand	18-24	7	14
β-strand	32-39	8	15
β-strand	45-51	7	15
β-strand	58-60	3	15
β-strand	68-73	6	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-100	9	15
β-strand	104-107	4	15
β-strand	111-115	5	15
α-helix	118-120	3
β-strand	121	1	16
α-helix	122-123	2
β-strand	124-128	5	17
α-helix	129-131	3
β-strand	140-149	10	17
β-strand	150	1	16
β-strand	155-158	4	18
β-strand	167-169	3	17
α-helix	170-172	3
β-strand	173-174	2	17
β-strand	180-188	9	17
α-helix	190-192	3
β-strand	199-204	6	18
α-helix	205-207	3
β-strand	209-214	6	18

Chain I: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-24	7	1
β-strand	32-39	8	2
β-strand	46-51	6	2
β-strand	58-60	3	2
β-strand	65	1	3
β-strand	68	1	3
β-strand	69-73	5	1
β-strand	78-83	6	1
β-strand	92-100	9	2
β-strand	104-107	4	2
β-strand	111-115	5	2
α-helix	118-120	3
β-strand	121	1	4
β-strand	124-128	5	5
α-helix	129-131	3
β-strand	139-149	11	5
β-strand	150	1	4
β-strand	155-158	4	6
α-helix	159-161	3
β-strand	167-169	3	5
α-helix	170-172	3
β-strand	173-174	2	5
β-strand	180-189	10	5
α-helix	190-192	3
β-strand	199-204	6	6
α-helix	205-207	3
β-strand	209-214	6	6

Chain J: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	7
β-strand	5	1	8
β-strand	9-12	4	9
β-strand	18-23	6	8
β-strand	35-40	6	9
β-strand	47-50	4	9
β-strand	51	1	10
β-strand	55	1	10
β-strand	64-69	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	87-94	8	9
β-strand	98-101	4	9
β-strand	102	1	7
β-strand	105-109	5	9
β-strand	115	1	11
β-strand	118-122	5	12
α-helix	123-125	3
α-helix	126-129	4
β-strand	134-143	10	12
β-strand	144	1	11
β-strand	149-154	6	13
β-strand	157-159	3	13
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-170	2	12
β-strand	176-184	9	12
α-helix	186-190	5
β-strand	195-201	7	13
β-strand	204-210	7	13

Chain L: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	19
β-strand	9-12	4	20
β-strand	18-23	6	19
β-strand	35-40	6	20
β-strand	47-50	4	20
β-strand	51	1	21
β-strand	55	1	21
β-strand	64-69	6	19
β-strand	72-77	6	19
α-helix	82-84	3
β-strand	87-94	8	20
β-strand	98-101	4	20
β-strand	105-109	5	20
β-strand	115	1	22
β-strand	118-122	5	23
α-helix	123-125	3
α-helix	126-129	4
β-strand	134-143	10	23
β-strand	144	1	22
β-strand	149-154	6	24
β-strand	157-158	2	24
β-strand	163-165	3	23
α-helix	166-168	3
β-strand	169-170	2	23
β-strand	176-184	9	23
α-helix	186-190	5
β-strand	195-201	7	24
β-strand	204-210	7	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab heavy chain	H, I	protein	224	Homo sapiens
Fab light chain	J, L	protein	216	Homo sapiens
MHC class I antigen	A, D	protein	295	Homo sapiens	A0A140T913 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Homo sapiens	P61769 (AlphaFold model)
Phe-met-asn-lys-phe-ile-tyr-glu-ile	C, F	protein	9	Homo sapiens	P02771 (AlphaFold model)

Sequence of entity 1 (H, I), FASTA

>7RE7_1 Fab heavy chain (chains H, I)
EVQLVQSGAEVKKPGESLTISCKASGYSFPNYWITWVRQMSGGGLEWMGRIDPGDSYTTY
NPSFQGHVTISIDKSTNTAYLHWNSLKASDTAMYYCARYYVSLVDIWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 2 (J, L), FASTA

>7RE7_2 Fab light chain (chains J, L)
QSVLTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVNNRPSEV
SNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTTGSRAVFGGGTKLTVLGQPKANPTVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (A, D), FASTA

>7RE7_3 MHC class I antigen (chains A, D)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPGSGGGLNDIFEAQKIGWHE

Sequence of entity 4 (B, E), FASTA

>7RE7_4 Beta-2-microglobulin (chains B, E)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (C, F), FASTA

>7RE7_5 PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILE (chains C, F)
FMNKFIYEI

Primary citation

Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma. Liu, C., Liu, H., Dasgupta, M. et al. Sci Rep (2022) 12:12068-12068. DOI 10.1038/s41598-022-15946-5 · PubMed

Other PDB entries of the same protein (UniProt A0A140T913 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O53 1.4 Å, Structure of HLA-A2:01 with peptide MM96
6O4Z 1.5 Å, Structure of HLA-A2:01 with peptide MM92
7QPJ 1.54 Å, Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10…
6O51 1.55 Å, Structure of HLA-A2:01 with peptide MM90
6O4Y 1.58 Å, Structure of HLA-A2:01 with peptide MM91
7MJ7 1.6 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7P3D 1.67 Å, MHC I A02 Allele presenting YLQPRTFLL
7MJ9 1.75 Å, HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide
7MJ8 1.79 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7SA2 1.85 Å, SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
2P5E 1.89 Å, Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native…
7MKB 1.9 Å, Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL

Browse structure collections

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