7YTJ: VTC complex
Cryo-EM structure of VTC complex. Determined by electron microscopy at 3.0 Å resolution. Released 22 Feb 2023.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 5
- Atoms
- 13,137
- Mol. weight
- 238.13 kDa
- Ligands
- PO4, PC1, IHP
- Released
- 22 Feb 2023
Explore 7YTJ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7YTJ contains 62 α-helices and 26 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: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 41-42 | 2 | 3 |
| β-strand | 51-52 | 2 | 3 |
| α-helix | 57-87 | 31 | |
| α-helix | 90-123 | 34 | |
| α-helix | 133-155 | 23 | |
Chain B: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 57-87 | 31 | |
| α-helix | 92-123 | 32 | |
| α-helix | 133-155 | 23 | |
Chain C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 58-87 | 30 | |
| α-helix | 90-123 | 34 | |
| α-helix | 134-155 | 22 | |
Chain D: 25 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-10 | 7 | |
| α-helix | 23-36 | 14 | |
| α-helix | 43-87 | 45 | |
| α-helix | 88-90 | 3 | |
| α-helix | 96-138 | 43 | |
| α-helix | 144-153 | 10 | |
| α-helix | 162-179 | 18 | |
| β-strand | 196-204 | 9 | 1 |
| α-helix | 206-208 | 3 | |
| α-helix | 209-217 | 9 | |
| β-strand | 222-224 | 3 | 1 |
| β-strand | 237-244 | 8 | 1 |
| α-helix | 249-255 | 7 | |
| β-strand | 261-269 | 9 | 1 |
| β-strand | 276-287 | 12 | 1 |
| β-strand | 290-301 | 12 | 1 |
| α-helix | 302-310 | 9 | |
| α-helix | 315-318 | 4 | |
| α-helix | 320-325 | 6 | |
| α-helix | 330-350 | 21 | |
| β-strand | 353-366 | 14 | 1 |
| β-strand | 373-385 | 13 | 1 |
| β-strand | 418-420 | 3 | 1 |
| β-strand | 424-432 | 9 | 1 |
| α-helix | 433 | 1 | |
| α-helix | 440-446 | 7 | |
| β-strand | 452-453 | 2 | 1 |
| α-helix | 459-467 | 9 | |
| α-helix | 469-471 | 3 | |
| β-strand | 474-475 | 2 | 2 |
| α-helix | 479-481 | 3 | |
| α-helix | 608-609 | 2 | |
| β-strand | 613-614 | 2 | 2 |
| α-helix | 624-647 | 24 | |
| α-helix | 648-652 | 5 | |
| α-helix | 657-686 | 30 | |
| α-helix | 687-689 | 3 | |
| α-helix | 699-723 | 25 | |
Chain E: 28 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-38 | 6 | |
| α-helix | 42-47 | 6 | |
| α-helix | 51-63 | 13 | |
| α-helix | 75-111 | 37 | |
| α-helix | 117-121 | 5 | |
| α-helix | 125-163 | 39 | |
| α-helix | 171-179 | 9 | |
| α-helix | 189-190 | 2 | |
| α-helix | 191-206 | 16 | |
| β-strand | 233-241 | 9 | 1 |
| α-helix | 243-254 | 12 | |
| α-helix | 258 | 1 | |
| β-strand | 259-262 | 4 | 1 |
| α-helix | 264-266 | 3 | |
| α-helix | 323-324 | 2 | |
| β-strand | 325-331 | 7 | 1 |
| α-helix | 336-342 | 7 | |
| β-strand | 349-356 | 8 | 1 |
| α-helix | 359-361 | 3 | |
| β-strand | 365-372 | 8 | 1 |
| β-strand | 383-390 | 8 | 1 |
| α-helix | 395-399 | 5 | |
| α-helix | 405-416 | 12 | |
| α-helix | 421-441 | 21 | |
| β-strand | 444-457 | 14 | 1 |
| β-strand | 464-476 | 13 | 1 |
| α-helix | 504-507 | 4 | |
| β-strand | 513-515 | 3 | 1 |
| β-strand | 519-527 | 9 | 1 |
| α-helix | 537-543 | 7 | |
| β-strand | 549-550 | 2 | 1 |
| α-helix | 556-565 | 10 | |
| α-helix | 579-581 | 3 | |
| α-helix | 591-594 | 4 | |
| α-helix | 597-617 | 21 | |
| α-helix | 723-754 | 32 | |
| α-helix | 763-796 | 34 | |
| α-helix | 807-827 | 21 | |
| α-helix | 830-832 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Vacuolar transporter chaperone 4 | D | protein | 754 | Saccharomyces cerevisiae | P47075 (AlphaFold model) |
| Vacuolar transporter chaperone 1 | A, B, C | protein | 143 | Saccharomyces cerevisiae | P40046 (AlphaFold model) |
| Vacuolar transporter chaperone 3 | E | protein | 864 | Saccharomyces cerevisiae | Q02725 (AlphaFold model) |
Sequence of entity 1 (D), FASTA
>7YTJ_1 Vacuolar transporter chaperone 4 (chains D)
MAKFGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGQWTQELETDFLESLEIELDKV
YTFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDFEILEEELSDIIADVHDLAKF
SRLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTSGR
PIKGDSSAGGKQQNFVRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITS
IYFDNENLDLYYGRLRKDEGAEAHALAWYGGMSTDTIFVERKTHREDWTGEKSVKARFAL
KERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFY
NRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICR
FPYAVLNVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLP
QMDVDIRKPPLPTNIEITRPGRSDNEDNDFDEDDEDDAALVAAMTNAPGNSLDIEESVGY
GATSAPTSNTNHVVESANAAYYQRKIRNAENPISKKYYEIVAFFDHYFNGDQISKIPKGT
TFDTQIRAPPGKTICVPVRVEPKVYFATERTYLSWLSISILLGGVSTTLLTYGSPTAMIG
SIGFFITSLAVLIRTVMVYAKRVVNIRLKRAVDYEDKIGPGMVSVFLILSILFSFFCNLV
AKLESAWSHPQFEKGGGSGGGSGGSAWSHPQFEK
Sequence of entity 2 (A, B, C), FASTA
>7YTJ_2 Vacuolar transporter chaperone 1 (chains A, B, C)
MASSAPLLQRTPGKKIALPTRVEPKVFFANERTFLSWLNFTVMLGGLGVGLLNFGDKIGR
VSAGLFTFVAMGTMIYALVTYHWRAAAIRRRGSGPYDDRLGPTLLCFFLLVAVIINFILR
LKYNDANTKLLESAYPYDVPDYA
Sequence of entity 3 (E), FASTA
>7YTJ_3 Vacuolar transporter chaperone 3 (chains E)
MDYKDDDDKGDYKDDDDKIDYKDDDDKGSMLFGIKLANDVYPPWKDSYIDYERLKKLLKE
SVIHDGRSSVDSWSERNESDFVEALDKELEKVYTFQISKYNAVLRKLDDLEENTKSAEKI
QKINSEQFKNTLEECLDEAQRLDNFDRLNFTGFIKIVKKHDKLHPNYPSVKSLLQVRLKE
LPFNNSEEYSPLLYRISYLYEFLRSNYDHPNTVSKSLASTSKLSHFSNLEDASFKSYKFW
VHDDNIMEVKARILRHLPALVYASVPNENDDFVDNLESDVRVQPEARLNIGSKSNSLSSD
GNSNQDVEIGKSKSVIFPQSYDPTITTLYFDNDFFDLYNNRLLKISGAPTLRLRWIGKLL
DKPDIFLEKRTFTENTETGNSSFEEIRLQMKAKFINNFIFKNDPSYKNYLINQLRERGTQ
KEELEKLSRDFDNIQNFIVEEKLQPVLRATYNRTAFQIPGDQSIRVTIDSNIMYIREDSL
DKNRPIRNPENWHRDDIDSNIPNPLRFLRAGEYSKFPYSVMEIKVINQDNSQMPNYEWIK
DLTNSHLVNEVPKFSLYLQGVASLFGEDDKYVNILPFWLPDLETDIRKNPQEAYEEEKKT
LQKQKSIHDKLDNMRRLSKISVPDGKTTERQGQKDQNTRHVIADLEDHESSDEEGTALPK
KSAVKKGKKFKTNAAFLKILAGKNISENGNDPYSDDTDSASSFQLPPGVKKPVHLLKNAG
PVKVEAKVWLANERTFNRWLSVTTLLSVLTFSIYNSVQKAEFPQLADLLAYVYFFLTLFC
GVWAYRTYLKRLTLIKGRSGKHLDAPVGPILVAVVLIVTLVVNFSVAFKEAARRERGLVN
VSSQPSLPRTLKPIQDFIFNLVGE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PO4 | Phosphate ion | O4 P | 2 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 2 |
| IHP | Inositol hexakisphosphate | C6 H18 O24 P6 | 3 |
Primary citation
The cytoplasmic synthesis and coupled membrane translocation of eukaryotic polyphosphate by signal-activated VTC complex. Guan, Z., Chen, J., Liu, R. et al. Nat Commun (2023) 14:718-718. DOI 10.1038/s41467-023-36466-4 · PubMed
Other PDB entries of the same protein (UniProt P47075 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3G3T 1.85 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with orthophosphate
- 3G3R 2.0 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+
- 3G3U 2.07 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate
- 5IIT 2.13 Å, Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized…
- 3G3Q 2.64 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate…
- 5IIG 2.99 Å, Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase…
- 5IIQ 3.03 Å, Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase…
- 9UMG 3.04 Å, Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)
- 8I6V 3.06 Å, Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)
- 5LNC 3.29 Å, Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized…
Browse structure collections
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