6VM8: SILv44 T cell receptor
SILv44 T cell receptor bound to HLA-A2 presenting gp100T2M peptide (IMDQVPFSV). Determined by X-ray diffraction at 2.41 Å resolution. Released 25 Nov 2020.
- Method
- X-ray diffraction
- Resolution
- 2.41 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 6,747
- Mol. weight
- 95.94 kDa
- Ligands
- FLC
- Released
- 25 Nov 2020
Explore 6VM8 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6VM8 contains 26 α-helices and 74 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: 10 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 | 50-54 | 5 | |
| 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 | 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 | 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 | 222-224 | 3 | 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 | 257-262 | 6 | 4 |
| β-strand | 270-273 | 4 | 4 |
Chain B: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 14 |
| α-helix | 5-6 | 2 | |
| β-strand | 7-12 | 6 | 15 |
| β-strand | 22-31 | 10 | 15 |
| β-strand | 32 | 1 | 14 |
| β-strand | 36-42 | 7 | 16 |
| β-strand | 45-46 | 2 | 16 |
| α-helix | 47 | 1 | |
| β-strand | 51-52 | 2 | 15 |
| α-helix | 53-55 | 3 | |
| β-strand | 56-57 | 2 | 15 |
| β-strand | 63-71 | 9 | 15 |
| β-strand | 79-85 | 7 | 16 |
| β-strand | 92-95 | 4 | 16 |
Chain C: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-8 | 4 | |
Chain D: 5 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-6 | 2 | 12 |
| β-strand | 11-15 | 5 | 13 |
| β-strand | 20-22 | 3 | 12 |
| β-strand | 25-26 | 2 | 12 |
| β-strand | 33-39 | 7 | 13 |
| β-strand | 46-51 | 6 | 13 |
| β-strand | 57-59 | 3 | 12 |
| α-helix | 61-63 | 3 | |
| β-strand | 65-69 | 5 | 12 |
| β-strand | 74-79 | 6 | 12 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-95 | 8 | 13 |
| β-strand | 103-104 | 2 | 13 |
| β-strand | 108-113 | 6 | 13 |
| β-strand | 122-128 | 7 | 9 |
| β-strand | 135-140 | 6 | 9 |
| α-helix | 149-151 | 3 | |
| β-strand | 156-158 | 3 | 9 |
| α-helix | 159-161 | 3 | |
| β-strand | 162-166 | 5 | 9 |
| β-strand | 171-180 | 10 | 9 |
| α-helix | 187-189 | 3 | |
| β-strand | 201 | 1 | 9 |
Chain E: 7 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 |
| α-helix | 101-102 | 2 | |
| β-strand | 103-104 | 2 | 6 |
| β-strand | 108-112 | 5 | 6 |
| β-strand | 120 | 1 | 8 |
| α-helix | 121-122 | 2 | |
| β-strand | 123-128 | 6 | 9 |
| α-helix | 129-130 | 2 | |
| α-helix | 131-137 | 7 | |
| β-strand | 139-149 | 11 | 9 |
| β-strand | 150 | 1 | 8 |
| β-strand | 154-160 | 7 | 10 |
| β-strand | 163-165 | 3 | 10 |
| β-strand | 169-171 | 3 | 9 |
| α-helix | 175 | 1 | |
| β-strand | 176-177 | 2 | 9 |
| β-strand | 187-196 | 10 | 9 |
| α-helix | 197-200 | 4 | |
| β-strand | 206-213 | 8 | 10 |
| β-strand | 216 | 1 | 11 |
| α-helix | 227-228 | 2 | |
| β-strand | 230 | 1 | 11 |
| β-strand | 232-239 | 8 | 10 |
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) |
| SILv44 T cell receptor beta chain | E | protein | 243 | Homo sapiens | |
| SILv44 T cell receptor alpha chain | D | protein | 208 | Homo sapiens | |
| 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 (A), FASTA
>6VM8_1 MHC class I antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE
Sequence of entity 2 (E), FASTA
>6VM8_2 SILv44 T cell receptor beta chain (chains E)
MGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDIA
EGYSVSREKKESFPLTVTSAQKNPTAFYLCASSITLSSYNEQFFGPGTRLTVLEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD
Sequence of entity 3 (D), FASTA
>6VM8_3 SILv44 T cell receptor alpha chain (chains D)
MAQSVSQHNHHVILSEAASLELGCNYSYGGTVNLFWYVQYPGQHLQLLLKYFSGDPLVKG
IKGFEAEFIKSKFSFNLRKPSVQWSDTAEYFCAVNARRNTPLVFGKGTRLSVIANIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS
Sequence of entity 4 (B), FASTA
>6VM8_4 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
Sequence of entity 5 (C), FASTA
>6VM8_5 Melanocyte protein PMEL (chains C)
IMDQVPFSV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| FLC | Citrate anion | C6 H5 O7 | 1 |
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. DOI 10.1073/pnas.2018125118 · 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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