6VM9: T4H2 T cell receptor

T4H2 T cell receptor bound to HLA-A2 presenting gp100T2M peptide (IMDQVPFSV). Determined by X-ray diffraction at 2.9 Å resolution. Released 20 Jan 2021.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,642
Mol. weight: 94.97 kDa
Released: 20 Jan 2021

Explore 6VM9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VM9 contains 24 α-helices and 77 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	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	4
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	140-148	9
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	257-262	6	4
α-helix	269	1
β-strand	270-272	3	4

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7	1	6
α-helix	8	1
β-strand	10-12	3	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
α-helix	47	1
β-strand	51-52	2	6
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4

Chain D: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	8
α-helix	11	1
β-strand	12-15	4	9
β-strand	20-24	5	10
β-strand	25-26	2	8
β-strand	34-39	6	11
α-helix	44-45	2
β-strand	46-51	6	11
β-strand	55-59	5	10
β-strand	62-67	6	10
β-strand	72-77	6	10
α-helix	82-84	3
β-strand	87-94	8	11
β-strand	99-102	4	11
β-strand	106-107	2	11
β-strand	108-111	4	9
α-helix	112	1
β-strand	120-125	6	12
β-strand	126	1	13
β-strand	133-140	8	12
β-strand	154-156	3	12
β-strand	161-164	4	12
β-strand	169-178	10	12
β-strand	199	1	12

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	14
β-strand	9-13	5	15
β-strand	18-20	3	16
β-strand	21-23	3	14
β-strand	30-36	7	15
β-strand	42-48	7	15
β-strand	54-56	3	15
β-strand	63-65	3	16
β-strand	72	1	14
β-strand	75-77	3	16
β-strand	86-93	8	15
α-helix	99-100	2
β-strand	101-102	2	15
β-strand	106-111	6	15
α-helix	114-116	3
β-strand	118	1	17
β-strand	121-125	5	13
α-helix	126-128	3
α-helix	129-135	7
β-strand	137-147	11	13
β-strand	148	1	17
β-strand	152-158	7	18
β-strand	161-163	3	18
β-strand	167-169	3	13
α-helix	173	1
β-strand	174-175	2	13
β-strand	185-194	10	13
α-helix	195-198	4
β-strand	204-211	8	18
β-strand	214	1	19
α-helix	225-226	2
β-strand	228	1	19
β-strand	230-237	8	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen, A-2 alpha chain	A	protein	275	Homo sapiens	A0A140T913 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Melanocyte protein PMEL	C	protein	9	Homo sapiens	P40967 (AlphaFold model)
T4H2 T cell receptor alpha chain	D	protein	206	Homo sapiens
T4H2 T cell receptor beta chain	E	protein	241	Homo sapiens

Sequence of entity 1 (A), FASTA

>6VM9_1 MHC class I antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>6VM9_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6VM9_3 Melanocyte protein PMEL (chains C)
IMDQVPFSV

Sequence of entity 4 (D), FASTA

>6VM9_4 T4H2 T cell receptor alpha chain (chains D)
MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMSIYSNGDKEDG
RFTAQLNKASQYVSLLIRDSQPSDSATYLCAVNALLGNQFYFGTGTSLTVIPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>6VM9_5 T4H2 T cell receptor beta chain (chains E)
MGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIA
EGYSVSREKKESFPLTVTSAQKNPTAFYLCASSMGGTYEQYFGPGTRLTVTEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Primary citation

Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner. Smith, A.R., Alonso, J.A., Ayres, C.M. et al. Proc Natl Acad Sci U S A (2021) 118:e2018125118. DOI 10.1073/pnas.2018125118

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

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