4Y49: Yeast N-terminal acetyltransferase (ppGpp) NatE
Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate. Determined by X-ray diffraction at 3.95 Å resolution. Released 13 Jul 2016.
- Method
- X-ray diffraction
- Resolution
- 3.95 Å
- Organisms
- Saccharomyces cerevisiae, Homo sapiens
- Chains
- 12
- Atoms
- 20,122
- Mol. weight
- 449.31 kDa
- Ligands
- ACO, CMC, G4P
- Released
- 13 Jul 2016
Explore 4Y49 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4Y49 contains 195 α-helices and 65 β-strands across 9 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: 56 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 49-55 | 7 | |
| α-helix | 67-76 | 10 | |
| α-helix | 82-88 | 7 | |
| α-helix | 102-105 | 4 | |
| α-helix | 109-112 | 4 | |
| α-helix | 118-129 | 12 | |
| α-helix | 138-141 | 4 | |
| α-helix | 153-163 | 11 | |
| α-helix | 179-183 | 5 | |
| α-helix | 186-192 | 7 | |
| α-helix | 218-222 | 5 | |
| α-helix | 235-244 | 10 | |
| α-helix | 272-278 | 7 | |
| α-helix | 279-281 | 3 | |
| α-helix | 287-290 | 4 | |
| α-helix | 292-295 | 4 | |
| α-helix | 302-308 | 7 | |
| α-helix | 310-313 | 4 | |
| α-helix | 325-327 | 3 | |
| α-helix | 336-341 | 6 | |
| α-helix | 345-348 | 4 | |
| α-helix | 354-357 | 4 | |
| α-helix | 370-376 | 7 | |
| α-helix | 379-381 | 3 | |
| α-helix | 391-394 | 4 | |
| α-helix | 401-404 | 4 | |
| α-helix | 411-414 | 4 | |
| α-helix | 416-422 | 7 | |
| α-helix | 432-437 | 6 | |
| α-helix | 445-456 | 12 | |
| α-helix | 469-475 | 7 | |
| α-helix | 484-487 | 4 | |
| α-helix | 511-518 | 8 | |
| α-helix | 525-527 | 3 | |
| α-helix | 551-569 | 19 | |
| α-helix | 571-580 | 10 | |
| α-helix | 596-599 | 4 | |
| α-helix | 603-606 | 4 | |
| α-helix | 607-609 | 3 | |
| α-helix | 613-626 | 14 | |
| α-helix | 627-629 | 3 | |
| α-helix | 696-698 | 3 | |
| α-helix | 706-710 | 5 | |
| α-helix | 711-717 | 7 | |
| α-helix | 725-731 | 7 | |
| α-helix | 739-745 | 7 | |
| α-helix | 749-752 | 4 | |
| α-helix | 757-764 | 8 | |
| α-helix | 779-781 | 3 | |
| α-helix | 783-788 | 6 | |
| α-helix | 809-812 | 4 | |
| α-helix | 821-829 | 9 | |
| α-helix | 838-841 | 4 | |
| α-helix | 843-846 | 4 | |
| α-helix | 854-857 | 4 | |
Chain B: 3 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 1 |
| α-helix | 13-17 | 5 | |
| β-strand | 45-47 | 3 | 1 |
| β-strand | 94-96 | 3 | 1 |
| β-strand | 100 | 1 | 2 |
| β-strand | 112 | 1 | 3 |
| β-strand | 113 | 1 | 2 |
| β-strand | 118-120 | 3 | 1 |
| α-helix | 134-141 | 8 | |
| β-strand | 149 | 1 | 3 |
| β-strand | 153-154 | 2 | 4 |
| β-strand | 177 | 1 | 5 |
| β-strand | 187 | 1 | 5 |
| β-strand | 188-189 | 2 | 4 |
| β-strand | 193 | 1 | 3 |
| α-helix | 196-198 | 3 | |
Chain C: 7 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 35-39 | 5 | |
| β-strand | 59 | 1 | 6 |
| β-strand | 62 | 1 | 7 |
| β-strand | 65 | 1 | 8 |
| β-strand | 70 | 1 | 8 |
| β-strand | 74 | 1 | 7 |
| β-strand | 77 | 1 | 6 |
| β-strand | 79 | 1 | 9 |
| β-strand | 90 | 1 | 9 |
| β-strand | 91 | 1 | 10 |
| β-strand | 96 | 1 | 7 |
| α-helix | 103-105 | 3 | |
| α-helix | 110-113 | 4 | |
| α-helix | 117-121 | 5 | |
| β-strand | 127 | 1 | 10 |
| β-strand | 132 | 1 | 11 |
| α-helix | 136-139 | 4 | |
| α-helix | 142-145 | 4 | |
| β-strand | 158 | 1 | 12 |
| β-strand | 166 | 1 | 12 |
| β-strand | 168 | 1 | 11 |
Chain G: 56 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-29 | 5 | |
| α-helix | 50-56 | 7 | |
| α-helix | 67-73 | 7 | |
| α-helix | 75-77 | 3 | |
| α-helix | 82-88 | 7 | |
| α-helix | 91-93 | 3 | |
| α-helix | 102-104 | 3 | |
| α-helix | 106-112 | 7 | |
| α-helix | 118-129 | 12 | |
| α-helix | 138-141 | 4 | |
| α-helix | 143-146 | 4 | |
| α-helix | 153-160 | 8 | |
| α-helix | 176-183 | 8 | |
| α-helix | 186-193 | 8 | |
| α-helix | 206-208 | 3 | |
| α-helix | 211-214 | 4 | |
| α-helix | 216-222 | 7 | |
| α-helix | 235-242 | 8 | |
| α-helix | 251-254 | 4 | |
| α-helix | 275-279 | 5 | |
| α-helix | 287-295 | 9 | |
| α-helix | 302-305 | 4 | |
| α-helix | 307-311 | 5 | |
| α-helix | 320-324 | 5 | |
| α-helix | 325-327 | 3 | |
| α-helix | 336-350 | 15 | |
| α-helix | 370-379 | 10 | |
| α-helix | 391-394 | 4 | |
| α-helix | 411-413 | 3 | |
| α-helix | 415-421 | 7 | |
| α-helix | 430-440 | 11 | |
| α-helix | 445-448 | 4 | |
| α-helix | 450-456 | 7 | |
| α-helix | 466-472 | 7 | |
| α-helix | 484-487 | 4 | |
| α-helix | 515-518 | 4 | |
| α-helix | 551-554 | 4 | |
| α-helix | 557-581 | 25 | |
| α-helix | 599-601 | 3 | |
| α-helix | 603-606 | 4 | |
| α-helix | 607-609 | 3 | |
| α-helix | 613-615 | 3 | |
| α-helix | 620-626 | 7 | |
| α-helix | 627-630 | 4 | |
| α-helix | 706-709 | 4 | |
| α-helix | 711-717 | 7 | |
| α-helix | 738-745 | 8 | |
| α-helix | 746-748 | 3 | |
| α-helix | 749-752 | 4 | |
| α-helix | 758-764 | 7 | |
| α-helix | 778-786 | 9 | |
| α-helix | 808-814 | 7 | |
| α-helix | 821-827 | 7 | |
| α-helix | 838-841 | 4 | |
| α-helix | 843-846 | 4 | |
| α-helix | 854-857 | 4 | |
Chain H: 5 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-6 | 2 | 13 |
| α-helix | 13-16 | 4 | |
| α-helix | 18-22 | 5 | |
| β-strand | 45-47 | 3 | 13 |
| β-strand | 94-96 | 3 | 13 |
| β-strand | 100 | 1 | 14 |
| β-strand | 112 | 1 | 15 |
| β-strand | 113 | 1 | 14 |
| β-strand | 118-120 | 3 | 13 |
| α-helix | 131-141 | 11 | |
| β-strand | 149-150 | 2 | 15 |
| β-strand | 155 | 1 | 16 |
| α-helix | 160-162 | 3 | |
| β-strand | 176-177 | 2 | 16 |
| β-strand | 187-188 | 2 | 16 |
| β-strand | 192-193 | 2 | 15 |
| α-helix | 196-198 | 3 | |
Chain I: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9 | 1 | 17 |
| α-helix | 17-21 | 5 | |
| β-strand | 62 | 1 | 18 |
| β-strand | 63 | 1 | 17 |
| β-strand | 74 | 1 | 18 |
| α-helix | 110-120 | 11 | |
| α-helix | 136-139 | 4 | |
| α-helix | 143-146 | 4 | |
Chain M: 52 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 51-55 | 5 | |
| α-helix | 65-76 | 12 | |
| α-helix | 82-84 | 3 | |
| α-helix | 85-88 | 4 | |
| α-helix | 102-105 | 4 | |
| α-helix | 109-112 | 4 | |
| α-helix | 119-129 | 11 | |
| α-helix | 138-141 | 4 | |
| α-helix | 153-163 | 11 | |
| α-helix | 175-177 | 3 | |
| α-helix | 179-183 | 5 | |
| α-helix | 187-190 | 4 | |
| α-helix | 206-208 | 3 | |
| α-helix | 218-222 | 5 | |
| α-helix | 235-244 | 10 | |
| α-helix | 245-247 | 3 | |
| α-helix | 251-254 | 4 | |
| α-helix | 272-279 | 8 | |
| α-helix | 287-295 | 9 | |
| α-helix | 302-315 | 14 | |
| α-helix | 320-327 | 8 | |
| α-helix | 336-343 | 8 | |
| α-helix | 353-355 | 3 | |
| α-helix | 361-364 | 4 | |
| α-helix | 370-377 | 8 | |
| α-helix | 379-381 | 3 | |
| α-helix | 411-413 | 3 | |
| α-helix | 416-422 | 7 | |
| α-helix | 430-441 | 12 | |
| α-helix | 445-456 | 12 | |
| α-helix | 469-472 | 4 | |
| α-helix | 484-487 | 4 | |
| α-helix | 508-511 | 4 | |
| α-helix | 525-527 | 3 | |
| α-helix | 549-580 | 32 | |
| α-helix | 596-606 | 11 | |
| α-helix | 607-609 | 3 | |
| α-helix | 613-626 | 14 | |
| α-helix | 704-705 | 2 | |
| α-helix | 706-710 | 5 | |
| α-helix | 711-713 | 3 | |
| α-helix | 725-731 | 7 | |
| α-helix | 733-735 | 3 | |
| α-helix | 739-745 | 7 | |
| α-helix | 746-748 | 3 | |
| α-helix | 749-752 | 4 | |
| α-helix | 758-764 | 7 | |
| α-helix | 778-788 | 11 | |
| β-strand | 801 | 1 | 19 |
| β-strand | 803 | 1 | 19 |
| α-helix | 821-829 | 9 | |
| α-helix | 838-846 | 9 | |
| α-helix | 854-857 | 4 | |
Chain N: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-6 | 2 | 20 |
| α-helix | 13-22 | 10 | |
| α-helix | 36-39 | 4 | |
| α-helix | 41-43 | 3 | |
| β-strand | 45-47 | 3 | 20 |
| β-strand | 94-97 | 4 | 20 |
| β-strand | 100 | 1 | 21 |
| β-strand | 112 | 1 | 22 |
| β-strand | 113 | 1 | 21 |
| β-strand | 117-120 | 4 | 20 |
| α-helix | 131-133 | 3 | |
| α-helix | 134-137 | 4 | |
| β-strand | 149-155 | 7 | 22 |
| α-helix | 160-162 | 3 | |
| β-strand | 177 | 1 | 22 |
| β-strand | 187-193 | 7 | 22 |
| α-helix | 196-198 | 3 | |
1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| N-terminal acetyltransferase A complex subunit NAT1 | A, G, M | protein | 854 | Saccharomyces cerevisiae | P12945 (AlphaFold model) |
| N-terminal acetyltransferase A complex catalytic subunit ARD1 | B, H, N | protein | 238 | Saccharomyces cerevisiae | P07347 (AlphaFold model) |
| N-terminal acetyltransferase A complex subunit NAT5 | C, I, O | protein | 176 | Saccharomyces cerevisiae | Q08689 (AlphaFold model) |
| Ala-ala-ala-ala-ala-ala | E, K, Q | protein | 8 | Homo sapiens | P01189 (AlphaFold model) |
Sequence of entity 1 (A, G, M), FASTA
>4Y49_1 N-terminal acetyltransferase A complex subunit NAT1 (chains A, G, M)
MSRKRSTKPKPAAKIALKKYNDQFLEALKLYEGKQYKKSLKLLDAILKKDGSHVDSLALK
GLDLYSVGEKDDAASYVANAIRKIEGASASPICCHVLGIYMRNTKEYKESIKWFTAALNN
GSTNKQIYRDLATLQSQIGDFKNALVSRKKYWEAFLGYRANWTSLAVAQDVNGERQQAIN
TLSQFEKLAEGKISDSEKYEHSECLMYKNDIMYKAASDNQDKLQNVLKHLNDIEPCVFDK
FGLLERKATIYMKLGQLKDASIVYRTLIKRNPDNFKYYKLLEVSLGIQGDNKLKKALYGK
LEQFYPRCEPPKFIPLTFLQDKEELSKKLREYVLPQLERGVPATFSNVKPLYQRRKSKVS
PLLEKIVLDYLSGLDPTQDPIPFIWTNYYLSQHFLFLKDFPKAQEYIDAALDHTPTLVEF
YILKARILKHLGLMDTAAGILEEGRQLDLQDRFINCKTVKYFLRANNIDKAVEVASLFTK
NDDSVNGIKDLHLVEASWFIVEQAEAYYRLYLDRKKKLDDLASLKKEVESDKSEQIANDI
KENQWLVRKYKGLALKRFNAIPKFYKQFEDDQLDFHSYCMRKGTPRAYLEMLEWGKALYT
KPMYVRAMKEASKLYFQMHDDRLKRKSDSLDENSDEIQNNGQNSSSQKKKAKKEAAAMNK
RKETEAKSVAAYPSDQDNDVFGEKLIETSTPMEDFATEFYNNYSMQVREDERDYILDFEF
NYRIGKLALCFASLNKFAKRFGTTSGLFGSMAIVLLHATRNDTPFDPILKKVVTKSLEKE
YSENFPLNEISNNSFDWLNFYQEKFGKNDINGLLFLYRYRDDVPIGSSNLKEMIISSLSP
LEPHSQNEILQYYL
Sequence of entity 2 (B, H, N), FASTA
>4Y49_2 N-terminal acetyltransferase A complex catalytic subunit ARD1 (chains B, H, N)
MPINIRRATINDIICMQNANLHNLPENYMMKYYMYHILSWPEASFVATTTTLDCEDSDEQ
DENDKLELTLDGTNDGRTIKLDPTYLAPGEKLVGYVLVKMNDDPDQQNEPPNGHITSLSV
MRTYRRMGIAENLMRQALFALREVHQAEYVSLHVRQSNRAALHLYRDTLAFEVLSIEKSY
YQDGEDAYAMKKVLKLEELQISNFTHRRLKENEEKLEDDLESDLLEDIIKQGVNDIIV
Sequence of entity 3 (C, I, O), FASTA
>4Y49_3 N-terminal acetyltransferase A complex subunit NAT5 (chains C, I, O)
MGRDICTLDNVYANNLGMLTKLAHVTVPNLYQDAFFSALFAEDSLVAKNKKPSSKKDVHF
TQMAYYSEIPVGGLVAKLVPKKQNELSLKGIQIEFLGVLPNYRHKSIGSKLLKFAEDKCS
ECHQHNVFVYLPAVDDLTKQWFIAHGFEQVGETVNNFIKGVNGDEQDAILLKKHIS
Sequence of entity 4 (E, K, Q), FASTA
>4Y49_4 ALA-ALA-ALA-ALA-ALA-ALA (chains E, K, Q)
SYSMEHFR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ACO | Acetyl coenzyme *a | C23 H38 N7 O17 P3 S | 3 |
| CMC | Carboxymethyl coenzyme *a | C23 H38 N7 O18 P3 S | 3 |
| G4P | Guanosine-5',3'-tetraphosphate | C10 H17 N5 O17 P4 | 3 |
Primary citation
Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate. Dong, J., Wang, S., York, J.D. To be published.
Other PDB entries of the same protein (UniProt P12945 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4XNH 2.1 Å, Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a…
- 4HNY 2.25 Å, Apo N-terminal acetyltransferase complex A
- 4HNX 2.34 Å, The NatA Acetyltransferase Complex Bound To ppGpp
- 6O07 2.7 Å, Structure and mechanism of acetylation by the N-terminal dual enzyme NatA/Naa50 complex
- 4HNW 2.8 Å, The NatA Acetyltransferase Complex Bound To Inositol Hexakisphosphate
- 4XPD 2.81 Å, Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a…
- 6HD7 3.4 Å, Cryo-EM structure of the ribosome-NatA complex
- 6HD5 4.8 Å, Cryo-EM structure of the ribosome-NatA complex
Browse structure collections
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