6IY6: Human cytosolic aspartyl-tRNA synthetase
Crystal structure of human cytosolic aspartyl-tRNA synthetase (DRS) in complex with glutathion-S transferase (GST) domains from Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2) and glutamyl-prolyl-tRNA synthetase (EPRS). Determined by X-ray diffraction at 3.6 Å resolution. Released 11 Sept 2019.
- Method
- X-ray diffraction
- Resolution
- 3.6 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 24,539
- Mol. weight
- 401.39 kDa
- Ligands
- ZN, PO4
- Released
- 11 Sept 2019
Explore 6IY6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6IY6 contains 152 α-helices and 132 β-strands across 12 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.
Chains A and B: 20 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 29-31 | 3 | 1 |
| β-strand | 45 | 1 | 1 |
| α-helix | 48-50 | 3 | |
| α-helix | 53-55 | 3 | |
| β-strand | 59-72 | 14 | 1 |
| β-strand | 75-82 | 8 | 1 |
| β-strand | 85-92 | 8 | 1 |
| β-strand | 93 | 1 | 2 |
| β-strand | 97 | 1 | 2 |
| α-helix | 99-107 | 9 | |
| α-helix | 109 | 1 | |
| β-strand | 113-122 | 10 | 1 |
| β-strand | 135-146 | 12 | 1 |
| α-helix | 180-186 | 7 | |
| α-helix | 190-212 | 23 | |
| β-strand | 216-217 | 2 | 3 |
| α-helix | 251-258 | 8 | |
| β-strand | 264-272 | 9 | 3 |
| β-strand | 285-294 | 10 | 3 |
| α-helix | 300-320 | 21 | |
| α-helix | 322-329 | 8 | |
| α-helix | 335-337 | 3 | |
| β-strand | 340 | 1 | 4 |
| β-strand | 344-347 | 4 | 3 |
| α-helix | 348-357 | 10 | |
| α-helix | 370-383 | 14 | |
| β-strand | 388-392 | 5 | 3 |
| β-strand | 395 | 1 | 5 |
| α-helix | 396-398 | 3 | |
| β-strand | 403 | 1 | 3 |
| α-helix | 404 | 1 | |
| β-strand | 405 | 1 | 6 |
| α-helix | 406 | 1 | |
| β-strand | 412 | 1 | 5 |
| β-strand | 413 | 1 | 6 |
| β-strand | 415-420 | 6 | 3 |
| β-strand | 423-431 | 9 | 3 |
| α-helix | 435-444 | 10 | |
| α-helix | 449-452 | 4 | |
| α-helix | 453-457 | 5 | |
| β-strand | 466-472 | 7 | 3 |
| α-helix | 473-481 | 9 | |
| α-helix | 486-489 | 4 | |
Chains C, D, I and J: 10 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 121-126 | 6 | 13 |
| α-helix | 133-143 | 11 | |
| β-strand | 148-154 | 7 | 13 |
| β-strand | 155 | 1 | 4 |
| α-helix | 163-166 | 4 | |
| β-strand | 183-189 | 7 | 13 |
| β-strand | 196-198 | 3 | 13 |
| α-helix | 205-206 | 2 | |
| β-strand | 207-208 | 2 | 13 |
| α-helix | 210-218 | 9 | |
| α-helix | 227-238 | 12 | |
| α-helix | 239-244 | 6 | |
| α-helix | 249-265 | 17 | |
| α-helix | 276-285 | 10 | |
| α-helix | 297-308 | 12 | |
| α-helix | 310-317 | 8 | |
Chains E and F: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 15 |
| α-helix | 15-24 | 10 | |
| β-strand | 30-35 | 6 | 15 |
| β-strand | 39-41 | 3 | 15 |
| β-strand | 47-48 | 2 | 15 |
| α-helix | 51-61 | 11 | |
| α-helix | 72-84 | 13 | |
| α-helix | 85-89 | 5 | |
| α-helix | 95-105 | 11 | |
| α-helix | 119-130 | 12 | |
| α-helix | 132-139 | 8 | |
| α-helix | 145-157 | 13 | |
Chain G: 20 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 29-31 | 3 | 17 |
| β-strand | 45 | 1 | 17 |
| α-helix | 48-50 | 3 | |
| α-helix | 53-55 | 3 | |
| β-strand | 59-72 | 14 | 17 |
| β-strand | 75-82 | 8 | 17 |
| β-strand | 85-92 | 8 | 17 |
| β-strand | 93 | 1 | 18 |
| β-strand | 97 | 1 | 18 |
| α-helix | 99-107 | 9 | |
| α-helix | 109 | 1 | |
| β-strand | 113-122 | 10 | 17 |
| β-strand | 135-146 | 12 | 17 |
| α-helix | 180-186 | 7 | |
| α-helix | 190-212 | 23 | |
| β-strand | 216-217 | 2 | 19 |
| α-helix | 251-258 | 8 | |
| β-strand | 264-271 | 8 | 19 |
| β-strand | 286-294 | 9 | 19 |
| α-helix | 300-320 | 21 | |
| α-helix | 322-329 | 8 | |
| α-helix | 335-337 | 3 | |
| β-strand | 340 | 1 | 20 |
| β-strand | 344-347 | 4 | 19 |
| α-helix | 348-357 | 10 | |
| α-helix | 370-383 | 14 | |
| β-strand | 388-392 | 5 | 19 |
| β-strand | 395 | 1 | 21 |
| α-helix | 396-398 | 3 | |
| β-strand | 403 | 1 | 19 |
| α-helix | 404 | 1 | |
| β-strand | 405 | 1 | 22 |
| α-helix | 406 | 1 | |
| β-strand | 412 | 1 | 21 |
| β-strand | 413 | 1 | 22 |
| β-strand | 415-420 | 6 | 19 |
| β-strand | 423-431 | 9 | 19 |
| α-helix | 435-444 | 10 | |
| α-helix | 449-452 | 4 | |
| α-helix | 453-457 | 5 | |
| β-strand | 466-472 | 7 | 19 |
| α-helix | 473-481 | 9 | |
| α-helix | 486-489 | 4 | |
Chain H: 20 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 29-31 | 3 | 23 |
| β-strand | 45 | 1 | 23 |
| α-helix | 48-50 | 3 | |
| α-helix | 53-55 | 3 | |
| β-strand | 59-72 | 14 | 23 |
| β-strand | 75-82 | 8 | 23 |
| β-strand | 85-92 | 8 | 23 |
| β-strand | 93 | 1 | 24 |
| β-strand | 97 | 1 | 24 |
| α-helix | 99-107 | 9 | |
| α-helix | 109 | 1 | |
| β-strand | 113-122 | 10 | 23 |
| β-strand | 135-146 | 12 | 23 |
| α-helix | 181-186 | 6 | |
| α-helix | 190-212 | 23 | |
| β-strand | 216-217 | 2 | 25 |
| α-helix | 251-258 | 8 | |
| β-strand | 264-271 | 8 | 25 |
| β-strand | 286-294 | 9 | 25 |
| α-helix | 300-320 | 21 | |
| α-helix | 322-329 | 8 | |
| α-helix | 335-337 | 3 | |
| β-strand | 340 | 1 | 26 |
| β-strand | 344-347 | 4 | 25 |
| α-helix | 348-357 | 10 | |
| α-helix | 370-383 | 14 | |
| β-strand | 388-392 | 5 | 25 |
| β-strand | 395 | 1 | 27 |
| α-helix | 396-398 | 3 | |
| β-strand | 403 | 1 | 25 |
| α-helix | 404 | 1 | |
| β-strand | 405 | 1 | 28 |
| α-helix | 406 | 1 | |
| β-strand | 412 | 1 | 27 |
| β-strand | 413 | 1 | 28 |
| β-strand | 415-420 | 6 | 25 |
| β-strand | 423-431 | 9 | 25 |
| α-helix | 435-444 | 10 | |
| α-helix | 449-452 | 4 | |
| α-helix | 453-457 | 5 | |
| β-strand | 466-472 | 7 | 25 |
| α-helix | 473-481 | 9 | |
| α-helix | 486-489 | 4 | |
Chains K and L: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 31 |
| α-helix | 15-22 | 8 | |
| β-strand | 30-35 | 6 | 31 |
| β-strand | 39-41 | 3 | 31 |
| β-strand | 47-48 | 2 | 31 |
| α-helix | 51-61 | 11 | |
| α-helix | 72-84 | 13 | |
| α-helix | 85-89 | 5 | |
| α-helix | 95-105 | 11 | |
| α-helix | 119-130 | 12 | |
| α-helix | 132-139 | 8 | |
| α-helix | 145-157 | 13 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Aspartate--tRNA ligase, cytoplasmic | A, B, G, H | protein | 502 | Homo sapiens | P14868 (AlphaFold model) |
| Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 | C, D, I, J | protein | 215 | Homo sapiens | Q13155 (AlphaFold model) |
| Bifunctional glutamate/proline--tRNA ligase | E, F, K, L | protein | 165 | Homo sapiens | P07814 (AlphaFold model) |
Sequence of entity 1 (A, B, G, H), FASTA
>6IY6_1 Aspartate--tRNA ligase, cytoplasmic (chains A, B, G, H)
MGSSHHHHHHSSGLVPRGSHMAEDYAKERYGISSMIQSQEKPDRVLVRVRDLTIQKADEV
VWVRARVHTSRAKGKQCFLVLRQQQFNVQALVAVGDHASKQMVKFAANINKESIVDVEGV
VRKVNQKIGSCTQQDVELHVQKIYVISLAEPRLPLQLDDAVRPEAEGEEEGRATVNQDTR
LDNRVIDLRTSTSQAVFRLQSGICHLFRETLINKGFVEIQTPKIISAASEGGANVFTVSY
FKNNAYLAQSPQLYKQMCICADFEKVFSIGPVFRAEDSNTHRHLTEFVGLDIEMAFNYHY
HEVMEEIADTMVQIFKGLQERFQTEIQTVNKQFPCEPFKFLEPTLRLEYCEALAMLREAG
VEMGDEDDLSTPNEKLLGHLVKEKYDTDFYILDKYPLAVRPFYTMPDPRNPKQSNSYDMF
MRGEEILSGAQRIHDPQLLTERALHHGIDLEKIKAYIDSFRFGAPPHAGGGIGLERVTML
FLGLHNVRQTSMFPRDPKRLTP
Sequence of entity 2 (C, D, I, J), FASTA
>6IY6_2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (chains C, D, I, J)
MDYGALKDIVINANPASPPLSLLVLHRLLCEHFRVLSTVHTHSSVKSVPENLLKCFGEQN
KKQPRQDYQLGFTLIWKNVPKTQMKFSIQTMCPIEGEGNIARFLFSLFGQKHNAVNATLI
DSWVDIAIFQLKEGSSKEKAAVFRSMNSALGKSPWLAGNELTVADVVLWSVLQQIGGCSV
TVPANVQRWMRSCENLAPFNTALKLLKLEHHHHHH
Sequence of entity 3 (E, F, K, L), FASTA
>6IY6_3 Bifunctional glutamate/proline--tRNA ligase (chains E, F, K, L)
MATLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLAR
VATTAGLYGSNLMEHTEIDHWLEFSATKLSSCDSFTSTINELNHCLSLRTYLVGNSLSLA
DLCVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQLEHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
| PO4 | Phosphate ion | O4 P | 17 |
Primary citation
The DRS-AIMP2-EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex. Hahn, H., Park, S.H., Kim, H.J. et al. IUCrJ (2019) 6:958-967. DOI 10.1107/S2052252519010790 · PubMed
Other PDB entries of the same protein (UniProt P14868 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4J15 2.24 Å, Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA…
- 5Y6L 2.9 Å, A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and…
Browse structure collections
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