5LQY: F-ATPase from Pichia angusta, in state2
Structure of F-ATPase from Pichia angusta, in state2. Determined by electron microscopy at 7.8 Å resolution. Released 16 Nov 2016.
- Method
- Electron microscopy
- Resolution
- 7.8 Å
- Organisms
- Ogataea angusta, Bos taurus
- Chains
- 30
- Atoms
- 24,170
- Mol. weight
- 557.71 kDa
- Ligands
- ATP, MG, ADP
- Released
- 16 Nov 2016
Explore 5LQY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5LQY contains 205 α-helices and 184 β-strands across 30 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 1: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1002-1029 | 28 | |
Chain 2: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1002-1024 | 23 | |
Chain 3: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1002-1015 | 14 | |
Chain 4: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1002-1025 | 24 | |
Chain A: 18 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-19 | 6 | |
| β-strand | 30-37 | 8 | 1 |
| β-strand | 40-45 | 6 | 1 |
| β-strand | 53-57 | 5 | 1 |
| β-strand | 62-68 | 7 | 1 |
| β-strand | 73-77 | 5 | 1 |
| β-strand | 89-96 | 8 | 1 |
| β-strand | 98-101 | 4 | 2 |
| α-helix | 103-105 | 3 | |
| β-strand | 109-110 | 2 | 3 |
| β-strand | 116 | 1 | 3 |
| β-strand | 127-130 | 4 | 2 |
| β-strand | 141 | 1 | 4 |
| β-strand | 147 | 1 | 5 |
| β-strand | 162 | 1 | 5 |
| β-strand | 166 | 1 | 3 |
| β-strand | 168-169 | 2 | 6 |
| β-strand | 171 | 1 | 7 |
| α-helix | 177-186 | 10 | |
| α-helix | 189-192 | 4 | |
| β-strand | 202-208 | 7 | 3 |
| α-helix | 212-224 | 13 | |
| β-strand | 231-236 | 6 | 3 |
| α-helix | 242-246 | 5 | |
| α-helix | 248-260 | 13 | |
| β-strand | 265-271 | 7 | 3 |
| α-helix | 273-285 | 13 | |
| α-helix | 300-308 | 9 | |
| β-strand | 314 | 1 | 4 |
| β-strand | 322-325 | 4 | 3 |
| β-strand | 330 | 1 | 7 |
| α-helix | 341-347 | 7 | |
| β-strand | 350-352 | 3 | 6 |
| β-strand | 373-374 | 2 | 6 |
| α-helix | 383-401 | 19 | |
| α-helix | 403-406 | 4 | |
| α-helix | 409-411 | 3 | |
| α-helix | 414-429 | 16 | |
| α-helix | 440-452 | 13 | |
| α-helix | 463-473 | 11 | |
| α-helix | 479-487 | 9 | |
| α-helix | 493-506 | 14 | |
Chain B: 19 helices, 30 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-17 | 7 | |
| β-strand | 32-37 | 6 | 1 |
| β-strand | 40-44 | 5 | 1 |
| β-strand | 53-56 | 4 | 1 |
| β-strand | 62-68 | 7 | 1 |
| β-strand | 73-77 | 5 | 1 |
| α-helix | 81-83 | 3 | |
| β-strand | 89 | 1 | 1 |
| β-strand | 91-96 | 6 | 1 |
| β-strand | 98-101 | 4 | 8 |
| β-strand | 104 | 1 | 9 |
| β-strand | 109-110 | 2 | 10 |
| β-strand | 116 | 1 | 10 |
| β-strand | 124 | 1 | 9 |
| β-strand | 127-130 | 4 | 8 |
| α-helix | 134-136 | 3 | |
| β-strand | 141 | 1 | 11 |
| β-strand | 147-148 | 2 | 12 |
| β-strand | 161-162 | 2 | 12 |
| β-strand | 166 | 1 | 10 |
| β-strand | 168 | 1 | 13 |
| β-strand | 169-171 | 3 | 14 |
| α-helix | 177-186 | 10 | |
| α-helix | 189-192 | 4 | |
| β-strand | 201-208 | 8 | 10 |
| α-helix | 212-224 | 13 | |
| β-strand | 231-236 | 6 | 10 |
| α-helix | 242-246 | 5 | |
| α-helix | 248-260 | 13 | |
| β-strand | 265-271 | 7 | 10 |
| α-helix | 273-285 | 13 | |
| α-helix | 300-309 | 10 | |
| β-strand | 313 | 1 | 10 |
| β-strand | 314 | 1 | 11 |
| β-strand | 322-327 | 6 | 10 |
| β-strand | 328-330 | 3 | 14 |
| α-helix | 339-345 | 7 | |
| β-strand | 350-351 | 2 | 13 |
| β-strand | 354 | 1 | 14 |
| α-helix | 356-359 | 4 | |
| β-strand | 367 | 1 | 14 |
| β-strand | 373-374 | 2 | 13 |
| α-helix | 383-388 | 6 | |
| α-helix | 392-404 | 13 | |
| α-helix | 414-429 | 16 | |
| α-helix | 440-451 | 12 | |
| α-helix | 463-473 | 11 | |
| α-helix | 479-487 | 9 | |
| α-helix | 493-507 | 15 | |
Chain C: 19 helices, 26 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-37 | 8 | 1 |
| β-strand | 40-45 | 6 | 1 |
| β-strand | 53-57 | 5 | 1 |
| β-strand | 62-68 | 7 | 1 |
| β-strand | 73-77 | 5 | 1 |
| β-strand | 89-96 | 8 | 1 |
| β-strand | 98-101 | 4 | 15 |
| β-strand | 104 | 1 | 16 |
| β-strand | 109-110 | 2 | 17 |
| β-strand | 116 | 1 | 17 |
| β-strand | 124 | 1 | 16 |
| β-strand | 127-130 | 4 | 15 |
| α-helix | 134-136 | 3 | |
| β-strand | 141 | 1 | 18 |
| α-helix | 153-156 | 4 | |
| β-strand | 166 | 1 | 17 |
| β-strand | 168 | 1 | 19 |
| β-strand | 169-171 | 3 | 20 |
| α-helix | 177-186 | 10 | |
| α-helix | 189-192 | 4 | |
| β-strand | 201-208 | 8 | 17 |
| α-helix | 212-223 | 12 | |
| β-strand | 231-236 | 6 | 17 |
| α-helix | 242-246 | 5 | |
| α-helix | 248-260 | 13 | |
| β-strand | 265-271 | 7 | 17 |
| α-helix | 273-285 | 13 | |
| α-helix | 300-309 | 10 | |
| β-strand | 314 | 1 | 18 |
| β-strand | 322-327 | 6 | 17 |
| β-strand | 328-330 | 3 | 20 |
| α-helix | 339-345 | 7 | |
| β-strand | 350-351 | 2 | 19 |
| β-strand | 354 | 1 | 20 |
| α-helix | 357-361 | 5 | |
| β-strand | 367 | 1 | 20 |
| β-strand | 373-374 | 2 | 19 |
| α-helix | 383-388 | 6 | |
| α-helix | 392-403 | 12 | |
| α-helix | 404-407 | 4 | |
| α-helix | 417-429 | 13 | |
| α-helix | 440-451 | 12 | |
| α-helix | 463-476 | 14 | |
| α-helix | 479-487 | 9 | |
| α-helix | 493-505 | 13 | |
Chain D: 17 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-17 | 8 | 1 |
| β-strand | 20-24 | 5 | 1 |
| β-strand | 36-38 | 3 | 1 |
| β-strand | 40 | 1 | 21 |
| β-strand | 46 | 1 | 21 |
| β-strand | 49-54 | 6 | 1 |
| β-strand | 59-64 | 6 | 1 |
| β-strand | 76-79 | 4 | 1 |
| β-strand | 85-87 | 3 | 22 |
| α-helix | 90-92 | 3 | |
| β-strand | 93 | 1 | 23 |
| β-strand | 96-97 | 2 | 23 |
| β-strand | 103 | 1 | 23 |
| β-strand | 115-117 | 3 | 22 |
| β-strand | 128 | 1 | 24 |
| β-strand | 134-135 | 2 | 25 |
| α-helix | 147 | 1 | |
| β-strand | 148-149 | 2 | 25 |
| β-strand | 153-155 | 3 | 23 |
| β-strand | 158 | 1 | 26 |
| α-helix | 164-172 | 9 | |
| β-strand | 183-187 | 5 | 23 |
| α-helix | 192-203 | 12 | |
| β-strand | 216-219 | 4 | 23 |
| α-helix | 227-231 | 5 | |
| α-helix | 233-246 | 14 | |
| β-strand | 252-257 | 6 | 23 |
| α-helix | 260-268 | 9 | |
| α-helix | 279-281 | 3 | |
| α-helix | 286-294 | 9 | |
| β-strand | 300 | 1 | 24 |
| β-strand | 305-310 | 6 | 23 |
| β-strand | 312 | 1 | 26 |
| β-strand | 332-333 | 2 | 23 |
| β-strand | 336 | 1 | 27 |
| α-helix | 338-341 | 4 | |
| β-strand | 349 | 1 | 27 |
| β-strand | 355 | 1 | 23 |
| α-helix | 366-389 | 24 | |
| α-helix | 394-396 | 3 | |
| α-helix | 399-414 | 16 | |
| α-helix | 423-426 | 4 | |
| α-helix | 429-430 | 2 | |
| α-helix | 435-445 | 11 | |
| α-helix | 464-474 | 11 | |
21 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 |
|---|
| ATP synthase subunit f | 1 | protein | 30 | Ogataea angusta | |
| ATP synthase subunit AAP1 | 2 | protein | 25 | Ogataea angusta | |
| ATP synthase subunit a | 3 | protein | 17 | Ogataea angusta | |
| ATP synthase subunit b | 4 | protein | 27 | Ogataea angusta | |
| ATP synthase alpha subunit | A, B, C | protein | 510 | Ogataea angusta | C0HK51 (AlphaFold model) |
| ATP synthase beta subunit | D, E, F | protein | 476 | Ogataea angusta | W1QA59 (AlphaFold model) |
| ATP synthase gamma subunit | G | protein | 269 | Ogataea angusta | C0HK53 (AlphaFold model) |
| ATP synthase delta subunit | H | protein | 138 | Ogataea angusta | W1QBD1 (AlphaFold model) |
| ATP synthase epsilon subunit | I | protein | 63 | Ogataea angusta | A0A1L1QK34 |
| ATP synthase inhibitor protein IF1 | J | protein | 66 | Bos taurus | P01096 |
| ATP synthase c subunit | K, L, M, N, O, P, Q, R, S, T | protein | 76 | Ogataea angusta | C0HK59, E7E832 |
| ATP synthase OSCP subunit | U | protein | 194 | Ogataea angusta | C0HK56 |
5 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>5LQY_1 ATP synthase subunit f (chains 1)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 2 (2), FASTA
>5LQY_2 ATP synthase subunit AAP1 (chains 2)
XXXXXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 3 (3), FASTA
>5LQY_3 ATP synthase subunit a (chains 3)
XXXXXXXXXXXXXXXXX
Sequence of entity 4 (4), FASTA
>5LQY_4 ATP synthase subunit b (chains 4)
XXXXXXXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 5 (A, B, C), FASTA
>5LQY_5 ATP synthase alpha subunit (chains A, B, C)
ATAKAAPTEVSSILESKIRGVSDEANLDETGRVLSVGDGIARVFGLNNCQAEELVEFASG
VKGMALNLEPGQVGIVLFGSDREVKEGEIVKRTGKIVDVPIGPGMLGRVVDALGNPIDGK
GPIEATGYAIAQLKAPGILPRRSVFEPMQTGLKAVDALVPIGRGQRELIIGDRQTGKTAV
ALDTILNQKRWNDGNDESKKLYCVYVAVGQKRSTVAQLVQTLEQNDAMKYSIVVAATASE
AAPLQYLAPFTACAIAEWFRDNGKHALIVYDDLSKQAVAYRQLSLLLRRPPGREAYPGDV
FYLHSRLLERAAKMSDANGGGSLTALPVIETQGGDVSAYIPTNVISITDGQIFLEAELFY
KGIRPAINVGLSVSRVGSAAQVKAMKQVAGSLKLFLAQYREVAAFAQFGSDLDASTKQTL
SRGERLTQLLKQKQYSPQASEEQVPVIYAGVNGFLDNIPIERIPEFEEQFIAYLKANEGD
ILEAIRTKGELSSELLDKLKSATETFVATF
Sequence of entity 6 (D, E, F), FASTA
>5LQY_6 ATP synthase beta subunit (chains D, E, F)
ATAGPASGKIRAVIGAVVDVQFEQGELPAILNALTIDQGNNQKLVLEVAQHLGENAVRAI
AMDGTEGLVRGQTVVDTGAPISVPVGRGTLGRIINVVGEPIDERGPIECKQRNPIHADPP
SFVEQSTEAEVLETGIKVVDLLAPYARGGKIGLFGGAGVGKTVFIQELINNIAKAHGGFS
VFTGVGERTREGNDLYREMKETGVINLEGESKVALVFGQMNEPPGARARVALTGLTIAEY
FRDEEGQDVLLFVDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGLLQERITTTRKG
SVTSVQAVYVPADDLTDPAPATTFAHLDATTVLSRGISELGIYPAVDPLDSKSRLLDVSV
VGQEHYDVATGVQQTLQAYKSLQDIIAILGMDELSEQDKLTVERARKIQRFLSQPFAVAE
VFTGIEGKLVRLKDTIASFKAVLEGKYDHLPENAFYMVGGIEDVVAKAEKIAAEAN
Sequence of entity 7 (G), FASTA
>5LQY_7 ATP synthase gamma subunit (chains G)
ATLREIETRLKSIKNIEKITNTMKVVASTRMGRAQRAMASSRAFREGDSDFFATAETSTP
ETAEKTLIIAVSSDKGLCGSIHSQIAKATRAKLQETPNADVVTIGDKIKAQMLRTHSSNV
VLSFNGVGKEAPTFWEASLIADEIRKLGDYDKIEVMYNKFVSGVAFEPSVFPSFSPISIE
ESPKLSEFELEEDQAIPTSLSQISLTNAILNAMAEGYASEISARRNAMDNASKNAGEMIN
KYSILYNRTRQAVITNELVDIITGASSLD
Sequence of entity 8 (H), FASTA
>5LQY_8 ATP synthase delta subunit (chains H)
AEAVNPDVLKVSLVAPHQAIFTNKEVSQVNLPASSGEMGVLANHVPTVEELAPGVVEVIE
SSGTASKYFVSGGFASILPGSKLSISTVEAHPLDAFSSENIKSLLAEAQKNASSADETVA
AEAAIEIEVLEALQAAVH
Sequence of entity 9 (I), FASTA
>5LQY_9 ATP synthase epsilon subunit (chains I)
SSWQKAGISFNKYLAIAARTVQRSLKNDLKVAAEKRYISDAKVQKLEKGNVVSTTDLASN
KSA
Sequence of entity 10 (J), FASTA
>5LQY_10 ATP synthase inhibitor protein IF1 (chains J)
GSESGDNVRSSAGAVRDAGGAFGKREQAEEERYFRARAKEQLAALKKHHENEISHHAKEI
HHHHHH
Sequence of entity 11 (K, L, M, N, O, P, Q, R, S, T), FASTA
>5LQY_11 ATP synthase c subunit (chains K, L, M, N, O, P, Q, R, S, T)
MQLVLAAKYIGAAIATIGLTGAGIGIAIVFAALINGTSRNPSLRNTLFPFAILGFALSEA
TGLFCLMISFLLLYGV
Sequence of entity 12 (U), FASTA
>5LQY_12 ATP synthase OSCP subunit (chains U)
ASAAPIKPPVQLFGLDGTYATALFSASAKDSSIEKTFQSVQKLSSTISKDAKVAQVLSNP
ALSLNSRKEVVSVLSKELKLEPVVSNLLTVLAENNRLSLFDSIAKQFSVLNDAYNGVVEA
TVVSAKPLDSKILNRLTKSITNSKYVGPGKTLKIKNEVDPEILGGLIVEVADKSVDLSLA
SKVNKLNKVLSETI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
| MG | Magnesium ion | Mg | 5 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 5 |
Primary citation
Structure of the mitochondrial ATP synthase fromPichia angustadetermined by electron cryo-microscopy. Vinothkumar, K.R., Montgomery, M.G., Liu, S. et al. Proc Natl Acad Sci U S A (2016) 113:12709-12714. DOI 10.1073/pnas.1615902113 · PubMed
Other PDB entries of the same protein (UniProt C0HK51 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5LQX 7.9 Å, Structure of F-ATPase from Pichia angusta, state3
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