Crystal structure of E. coli glutaminyl-tRNA synthetase bound to ATP and native tRNA(Gln) containing the cmnm5s2U34 anticodon wobble base. Determined by X-ray diffraction at 2.5 Å resolution. Released 29 May 2013.
Explore 4JYZ in 3D Show helices and sheets RCSB PDB PDBe
4JYZ contains 24 α-helices and 37 β-strands across 1 chain. 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 10-21 | 12 | |
| β-strand | 28-31 | 4 | 1 |
| β-strand | 40 | 1 | 2 |
| α-helix | 41-56 | 16 | |
| β-strand | 60-63 | 4 | 1 |
| β-strand | 64-65 | 2 | 3 |
| α-helix | 70-72 | 3 | |
| α-helix | 75-87 | 13 | |
| β-strand | 97-98 | 2 | 3 |
| α-helix | 99-102 | 4 | |
| α-helix | 103-115 | 13 | |
| β-strand | 119-122 | 4 | 4 |
| α-helix | 126-133 | 8 | |
| α-helix | 150-162 | 13 | |
| β-strand | 171-174 | 4 | 4 |
| α-helix | 183-185 | 3 | |
| β-strand | 189-193 | 5 | 4 |
| β-strand | 198 | 1 | 5 |
| β-strand | 202 | 1 | 5 |
| β-strand | 207-209 | 3 | 4 |
| α-helix | 211-222 | 12 | |
| β-strand | 226-230 | 5 | 6 |
| α-helix | 231-233 | 3 | |
| α-helix | 234-246 | 13 | |
| β-strand | 254-258 | 5 | 6 |
| α-helix | 259-261 | 3 | |
| β-strand | 263 | 1 | 7 |
| α-helix | 270-278 | 9 | |
| β-strand | 292 | 1 | 2 |
| α-helix | 293-299 | 7 | |
| α-helix | 303-313 | 11 | |
| β-strand | 322 | 1 | 7 |
| α-helix | 324-336 | 13 | |
| α-helix | 340 | 1 | |
| β-strand | 341-342 | 2 | 8 |
| β-strand | 344-345 | 2 | 8 |
| β-strand | 348-350 | 3 | 9 |
| β-strand | 361-366 | 6 | 10 |
| α-helix | 372-374 | 3 | |
| β-strand | 376-381 | 6 | 10 |
| β-strand | 386-388 | 3 | 9 |
| α-helix | 389-391 | 3 | |
| β-strand | 392-393 | 2 | 11 |
| β-strand | 403-404 | 2 | 11 |
| β-strand | 410-411 | 2 | 12 |
| β-strand | 416 | 1 | 12 |
| β-strand | 417-424 | 8 | 9 |
| β-strand | 430-437 | 8 | 9 |
| α-helix | 451-453 | 3 | |
| β-strand | 455-456 | 2 | 12 |
| β-strand | 459 | 1 | 9 |
| β-strand | 465-472 | 8 | 8 |
| β-strand | 476 | 1 | 13 |
| α-helix | 481-483 | 3 | |
| α-helix | 487-490 | 4 | |
| β-strand | 491 | 1 | 13 |
| β-strand | 496-503 | 8 | 8 |
| α-helix | 505-509 | 5 | |
| β-strand | 516-518 | 3 | 8 |
| β-strand | 522-526 | 5 | 8 |
| β-strand | 537-543 | 7 | 8 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Glutamine--tRNA ligase | A | protein | 553 | Escherichia coli | P00962 (AlphaFold model) |
| RNA (72-mer) | B | RNA | 75 | Escherichia coli |
>4JYZ_1 Glutamine--tRNA ligase (chains A) SEAEARPTNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQ CNLRFDDTNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAY VDELTPEQIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMAS PFIVMRDPVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLY DWVLDNITIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRG YTAASIREFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYQGEG EMVTMPNHPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAE RVEKDAEGNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPN PGAADDFLSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPVFNR TVGLRDTWAKVGE
>4JYZ_2 RNA (72-MER) (chains B) UGGGGUAUCGCCAAGCGGUAAGGCACCGGUUUXUGAUACCGGCAUUCGCAGGUUCGAAUC CUGCUACCCCAGCCA
| ID | Name | Formula | Copies |
|---|---|---|---|
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
Water and common crystallization additives (SO4) are not listed.
Structural and Mechanistic Basis for Enhanced Translational Efficiency by 2-Thiouridine at the tRNA Anticodon Wobble Position. Rodriguez-Hernandez, A., Spears, J.L., Gaston, K.W. et al. J Mol Biol (2013) 425:3888-3906. DOI 10.1016/j.jmb.2013.05.018 · PubMed
Other PDB entries of the same protein (UniProt P00962 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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