6VM7: SILv44 T cell receptor

SILv44 T cell receptor bound to HLA-A2 presenting gp100 peptide (ITDQVPFSV). Determined by X-ray diffraction at 2.41 Å resolution. Released 20 Jan 2021.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,777
Mol. weight: 95.99 kDa
Released: 20 Jan 2021

Explore 6VM7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VM7 contains 20 α-helices and 75 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	11
α-helix	20	1
β-strand	21-28	8	11
β-strand	31-37	7	11
β-strand	46-47	2	11
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	11
β-strand	109-118	10	11
β-strand	121-126	6	11
β-strand	133-135	3	11
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
β-strand	183	1	12
β-strand	186-193	8	13
β-strand	198-208	11	13
β-strand	209	1	12
β-strand	213-218	6	14
β-strand	223-224	2	14
β-strand	228-230	3	13
α-helix	231-233	3
β-strand	234-235	2	13
β-strand	241-250	10	13
β-strand	258-263	6	14
β-strand	270-273	4	14

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	15
α-helix	5-6	2
β-strand	7-12	6	16
β-strand	22-31	10	16
β-strand	32	1	15
β-strand	36-42	7	17
β-strand	45-46	2	17
α-helix	47	1
β-strand	51-52	2	16
α-helix	53-55	3
β-strand	56-57	2	16
β-strand	63-71	9	16
β-strand	79-85	7	17
β-strand	92-95	4	17

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4

Chain D: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	11-15	5	2
β-strand	20-22	3	1
β-strand	25-26	2	1
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	57-59	3	1
α-helix	61-63	3
β-strand	65-69	5	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	103-104	2	2
β-strand	108-113	6	2
β-strand	122-127	6	3
β-strand	128	1	4
β-strand	135-140	6	3
α-helix	149-151	3
β-strand	156-158	3	3
α-helix	159-161	3
β-strand	162-166	5	3
β-strand	171-180	10	3
β-strand	201	1	3

Chain E: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	5
β-strand	9-12	4	6
β-strand	18-20	3	7
β-strand	22-24	3	5
β-strand	30-37	8	6
β-strand	41-50	10	6
β-strand	53-56	4	6
β-strand	63-65	3	7
β-strand	72	1	5
β-strand	75-77	3	7
β-strand	85-93	9	6
β-strand	103-104	2	6
β-strand	108-112	5	6
α-helix	116-118	3
β-strand	120	1	8
β-strand	123-127	5	4
α-helix	128-130	3
α-helix	131-137	7
β-strand	139-149	11	4
β-strand	150	1	8
β-strand	154-160	7	9
β-strand	163-165	3	9
β-strand	169-171	3	4
β-strand	176-177	2	4
β-strand	187-196	10	4
α-helix	197-200	4
β-strand	206-213	8	9
β-strand	216	1	10
β-strand	230	1	10
β-strand	232-239	8	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SILv44 T cell receptor alpha chain	D	protein	208	Homo sapiens
SILv44 T cell receptor beta chain	E	protein	243	Homo sapiens
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)

Sequence of entity 1 (D), FASTA

>6VM7_1 SILv44 T cell receptor alpha chain (chains D)
MAQSVSQHNHHVILSEAASLELGCNYSYGGTVNLFWYVQYPGQHLQLLLKYFSGDPLVKG
IKGFEAEFIKSKFSFNLRKPSVQWSDTAEYFCAVNARRNTPLVFGKGTRLSVIANIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (E), FASTA

>6VM7_2 SILv44 T cell receptor beta chain (chains E)
MGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIA
EGYSVSREKKESFPLTVTSAQKNPTAFYLCASSITLSSYNEQFFGPGTRLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 3 (A), FASTA

>6VM7_3 MHC class I antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 4 (B), FASTA

>6VM7_4 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (C), FASTA

>6VM7_5 Melanocyte protein PMEL (chains C)
ITDQVPFSV

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

Browse structure collections

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