33CI: MAGE-A4 (230-239)-bound HLA-A*02:01
Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-58. Determined by electron microscopy at 2.2 Å resolution. Released 26 Aug 2026.
- Method
- Electron microscopy
- Resolution
- 2.2 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 7
- Atoms
- 6,642
- Mol. weight
- 146.79 kDa
- Released
- 26 Aug 2026
Explore 33CI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
33CI contains 27 α-helices and 78 β-strands across 6 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 | 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 | 50-52 | 3 | |
| 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 |
| α-helix | 184-185 | 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 |
| α-helix | 231-233 | 3 | |
| β-strand | 234-235 | 2 | 3 |
| β-strand | 241-250 | 10 | 3 |
| α-helix | 253-256 | 4 | |
| 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 | 3 | 1 | 5 |
| α-helix | 4-5 | 2 | |
| β-strand | 6-11 | 6 | 6 |
| β-strand | 21-30 | 10 | 6 |
| β-strand | 31 | 1 | 5 |
| β-strand | 36-41 | 6 | 7 |
| β-strand | 44-45 | 2 | 7 |
| α-helix | 46 | 1 | |
| β-strand | 50-51 | 2 | 6 |
| α-helix | 52-54 | 3 | |
| β-strand | 55-56 | 2 | 6 |
| β-strand | 62-70 | 9 | 6 |
| β-strand | 78-83 | 6 | 7 |
| β-strand | 91-94 | 4 | 7 |
Chain D: 3 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 12 |
| β-strand | 9-12 | 4 | 13 |
| β-strand | 18-23 | 6 | 12 |
| α-helix | 25-28 | 4 | |
| α-helix | 31-32 | 2 | |
| β-strand | 33-37 | 5 | 13 |
| β-strand | 44-47 | 4 | 13 |
| β-strand | 48 | 1 | 14 |
| β-strand | 52 | 1 | 14 |
| β-strand | 61-66 | 6 | 12 |
| β-strand | 69-74 | 6 | 12 |
| α-helix | 79-81 | 3 | |
| β-strand | 83-89 | 7 | 13 |
| β-strand | 99-100 | 2 | 13 |
| β-strand | 104-108 | 5 | 13 |
Chain E: 2 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 15 |
| β-strand | 11-12 | 2 | 16 |
| β-strand | 18-25 | 8 | 15 |
| β-strand | 34-39 | 6 | 17 |
| β-strand | 45-51 | 7 | 17 |
| β-strand | 57-59 | 3 | 17 |
| β-strand | 64 | 1 | 15 |
| β-strand | 67-72 | 6 | 15 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-82 | 6 | 15 |
| α-helix | 87-89 | 3 | |
| β-strand | 91-98 | 8 | 17 |
| β-strand | 109-112 | 4 | 17 |
| β-strand | 116-118 | 3 | 17 |
| β-strand | 119-120 | 2 | 16 |
Chain F: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 8 |
| β-strand | 10-13 | 4 | 9 |
| β-strand | 19-25 | 7 | 8 |
| β-strand | 33-38 | 6 | 9 |
| β-strand | 44-49 | 6 | 9 |
| β-strand | 53-54 | 2 | 9 |
| α-helix | 55 | 1 | |
| β-strand | 62-67 | 6 | 8 |
| β-strand | 70-75 | 6 | 8 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-90 | 6 | 9 |
| α-helix | 97 | 1 | |
| β-strand | 98 | 1 | 9 |
| α-helix | 99 | 1 | |
| β-strand | 102-106 | 5 | 9 |
Chain G: 4 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 10 |
| α-helix | 7-9 | 3 | |
| β-strand | 10-12 | 3 | 11 |
| β-strand | 18-25 | 8 | 10 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 11 |
| β-strand | 45-52 | 8 | 11 |
| β-strand | 57-60 | 4 | 11 |
| α-helix | 62-64 | 3 | |
| β-strand | 65 | 1 | 10 |
| β-strand | 68-73 | 6 | 10 |
| β-strand | 78-83 | 6 | 10 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-100 | 9 | 11 |
| β-strand | 105-109 | 5 | 11 |
| β-strand | 113-117 | 5 | 11 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| MHC class I antigen | A | protein | 296 | Homo sapiens | F6IQS1 (AlphaFold model) |
| Beta-2-microglobulin | B | protein | 100 | Homo sapiens | P61769 (AlphaFold model) |
| Melanoma-associated antigen 4 | C | protein | 10 | Homo sapiens | P43358 (AlphaFold model) |
| Fab BBM.1 light chain | F | protein | 214 | Mus musculus | |
| Fab BBM.1 heavy chain | G | protein | 222 | Mus musculus | |
| Fab VR-6 light chain | D | protein | 215 | Homo sapiens | |
| Fab VR-6 heavy chain | E | protein | 277 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>33CI_1 MHC class I antigen (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGCYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMCAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPGSGSGLNDIFEAQKIEWHE
Sequence of entity 2 (B), FASTA
>33CI_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
Sequence of entity 3 (C), FASTA
>33CI_3 Melanoma-associated antigen 4 (chains C)
GVYDGREHTV
Sequence of entity 4 (F), FASTA
>33CI_4 Fab BBM.1 light chain (chains F)
DIQMTQSPASQSASLGESVTITCLASQTIGTWLAWYQQKPGKSPQLLIYAATSLADGVPS
RFSGSGSGTKFSLKIRTLQAEDFVSYYCQQLYSKPYTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Sequence of entity 5 (G), FASTA
>33CI_5 Fab BBM.1 heavy chain (chains G)
EVQLQQSGAELVKPGASVKLSCTPSGFNVKDTYIHWVKQRPKQGLEWIGRIDPSDGDIKY
DPKFQGKATITADTSSNTVSLQLSSLTSEDTAVYYCARWFGDYGAMNYWGQGTSVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC
Sequence of entity 6 (D), FASTA
>33CI_6 Fab VR-6 light chain (chains D)
SYELTQPPSVSVSPGQTASITCTADTLSRSYASWYQQKPGQSPVLVIYRDTSRPSGIPER
FSGSNSGNTATLTISGTQAMDEADYYCATRPSSGSNFQLFGGGTKLTVLGQPKAAPSVTL
FPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSY
LSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS
Sequence of entity 7 (E), FASTA
>33CI_7 Fab VR-6 heavy chain (chains E)
ESQVLESGGGSVQPGGSLRLSCTVSGFSLSNYAMSWVRQAPGKGLEYIGIVSSGGTTYYA
SWAKGRFTISKDTSKNTVYLQMNSLRAEDTASYYCAKDLYYGPTTYSAFNLWGQGTSVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCAAAEQKLISEEDLNE
MEQKLISEEDLNEMEQKLISEEDLNEMAAHHHHHHHH
Primary citation
Systematic De-Risking of TCR-Mimic Therapeutics Through Proteome-Wide Off-Target Landscaping and a Generalizable Design Rule Framework. Schuster, S., Hartl, F.A., Stehle, J. et al. To be published.
Other PDB entries of the same protein (UniProt F6IQS1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6TDP 1.4 Å, Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GL…
- 6TDQ 1.6 Å, Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM…
- 6TDO 1.65 Å, Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM…
- 6TDS 1.7 Å, Crystal structure of the disulfide engineered HLA-A0201 molecule without peptide bound…
- 6TDR 1.75 Å, Crystal structure of the disulfide engineered HLA-A0201 molecule devoid of peptide…
- 33CG 2.2 Å, Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6
- 33CH 2.4 Å, Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-4
Browse structure collections
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