6LY5: Fcpi-7
Organization and energy transfer in a huge diatom PSI-FCPI supercomplex. Determined by electron microscopy at 2.38 Å resolution. Released 21 Oct 2020.
- Method
- Electron microscopy
- Resolution
- 2.38 Å
- Organism
- Chaetoceros gracilis
- Chains
- 36
- Atoms
- 81,344
- Mol. weight
- 1277.92 kDa
- Ligands
- DD6, A86, CLA, KC1
- Released
- 21 Oct 2020
Explore 6LY5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6LY5 contains 292 α-helices and 101 β-strands across 36 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: 48 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-24 | 3 | 28 |
| α-helix | 33-35 | 3 | |
| α-helix | 44-46 | 3 | |
| β-strand | 50 | 1 | 29 |
| α-helix | 52-59 | 8 | |
| α-helix | 64-66 | 3 | |
| α-helix | 71-102 | 32 | |
| α-helix | 106-111 | 6 | |
| α-helix | 117-118 | 2 | |
| β-strand | 119-121 | 3 | 30 |
| α-helix | 129-132 | 4 | |
| β-strand | 134-135 | 2 | 31 |
| β-strand | 141-142 | 2 | 31 |
| β-strand | 143-144 | 2 | 30 |
| α-helix | 149-156 | 8 | |
| α-helix | 161-183 | 23 | |
| α-helix | 184-188 | 5 | |
| β-strand | 189-191 | 3 | 28 |
| α-helix | 192 | 1 | |
| α-helix | 193-196 | 4 | |
| α-helix | 199-205 | 7 | |
| α-helix | 206-212 | 7 | |
| α-helix | 213-221 | 9 | |
| α-helix | 222-226 | 5 | |
| α-helix | 227-235 | 9 | |
| α-helix | 239-241 | 3 | |
| α-helix | 243-244 | 2 | |
| α-helix | 247-250 | 4 | |
| α-helix | 252-258 | 7 | |
| α-helix | 267-270 | 4 | |
| α-helix | 274-277 | 4 | |
| α-helix | 296-313 | 18 | |
| β-strand | 317 | 1 | 32 |
| β-strand | 325 | 1 | 32 |
| α-helix | 327-333 | 7 | |
| α-helix | 346-352 | 7 | |
| α-helix | 354-378 | 25 | |
| α-helix | 389-416 | 28 | |
| α-helix | 417-421 | 5 | |
| α-helix | 425-427 | 3 | |
| α-helix | 431-437 | 7 | |
| α-helix | 439-469 | 31 | |
| α-helix | 473-475 | 3 | |
| α-helix | 487-498 | 12 | |
| β-strand | 500 | 1 | 33 |
| β-strand | 504 | 1 | 33 |
| α-helix | 513-515 | 3 | |
| β-strand | 520-522 | 3 | 34 |
| β-strand | 525-528 | 4 | 34 |
| α-helix | 535-560 | 26 | |
| α-helix | 571-574 | 4 | |
| α-helix | 593-622 | 30 | |
| β-strand | 625-627 | 3 | 34 |
| α-helix | 629-631 | 3 | |
| β-strand | 633-635 | 3 | 34 |
| α-helix | 648-650 | 3 | |
| α-helix | 651-657 | 7 | |
| α-helix | 658-660 | 3 | |
| α-helix | 661-664 | 4 | |
| α-helix | 672-693 | 22 | |
| α-helix | 696-712 | 17 | |
| β-strand | 720 | 1 | 29 |
| α-helix | 723-725 | 3 | |
| α-helix | 726-754 | 29 | |
Chain A: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36 | 1 | 1 |
| β-strand | 44 | 1 | 1 |
| α-helix | 45-46 | 2 | |
| α-helix | 63-66 | 4 | |
| α-helix | 69-92 | 24 | |
| α-helix | 107-109 | 3 | |
| α-helix | 117-131 | 15 | |
| α-helix | 167-197 | 31 | |
Chain b: 41 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17 | 1 | 35 |
| α-helix | 19-26 | 8 | |
| α-helix | 31-33 | 3 | |
| α-helix | 39-71 | 33 | |
| α-helix | 74-79 | 6 | |
| α-helix | 85-86 | 2 | |
| β-strand | 87-90 | 4 | 36 |
| α-helix | 98-103 | 6 | |
| β-strand | 112-114 | 3 | 36 |
| α-helix | 115 | 1 | |
| α-helix | 119-125 | 7 | |
| α-helix | 131-154 | 24 | |
| α-helix | 161-163 | 3 | |
| α-helix | 164-167 | 4 | |
| α-helix | 170-176 | 7 | |
| α-helix | 177-184 | 8 | |
| α-helix | 185-192 | 8 | |
| α-helix | 193-197 | 5 | |
| α-helix | 198-201 | 4 | |
| α-helix | 222-226 | 5 | |
| α-helix | 229-232 | 4 | |
| β-strand | 260 | 1 | 37 |
| β-strand | 267 | 1 | 37 |
| α-helix | 269-286 | 18 | |
| β-strand | 290 | 1 | 38 |
| β-strand | 298 | 1 | 38 |
| α-helix | 300-306 | 7 | |
| α-helix | 321-326 | 6 | |
| α-helix | 329-353 | 25 | |
| α-helix | 364-395 | 32 | |
| α-helix | 408-412 | 5 | |
| α-helix | 414-444 | 31 | |
| α-helix | 448-450 | 3 | |
| β-strand | 454 | 1 | 39 |
| α-helix | 457-465 | 9 | |
| α-helix | 476-478 | 3 | |
| α-helix | 483-491 | 9 | |
| α-helix | 493-501 | 9 | |
| α-helix | 513-538 | 26 | |
| α-helix | 549-551 | 3 | |
| α-helix | 562-564 | 3 | |
| α-helix | 571-602 | 32 | |
| α-helix | 606-611 | 6 | |
| α-helix | 615-618 | 4 | |
| α-helix | 619-624 | 6 | |
| α-helix | 628-631 | 4 | |
| β-strand | 634 | 1 | 40 |
| β-strand | 639 | 1 | 40 |
| α-helix | 643-664 | 22 | |
| α-helix | 667-683 | 17 | |
| β-strand | 695 | 1 | 35 |
| α-helix | 701-729 | 29 | |
Chain B: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-89 | 25 | |
| β-strand | 100 | 1 | 3 |
| α-helix | 103-106 | 4 | |
| α-helix | 108-110 | 3 | |
| β-strand | 111-113 | 3 | 4 |
| β-strand | 116-117 | 2 | 4 |
| α-helix | 118 | 1 | |
| β-strand | 119 | 1 | 3 |
| α-helix | 120-141 | 22 | |
| α-helix | 184-204 | 21 | |
| α-helix | 210-217 | 8 | |
Chain c: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 41 |
| α-helix | 16-20 | 5 | |
| β-strand | 27-30 | 4 | 42 |
| β-strand | 38-41 | 4 | 42 |
| α-helix | 45-47 | 3 | |
| α-helix | 53-57 | 5 | |
| β-strand | 65-68 | 4 | 41 |
| α-helix | 74-77 | 4 | |
Chain C: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36 | 1 | 7 |
| β-strand | 44 | 1 | 7 |
| α-helix | 45-46 | 2 | |
| α-helix | 72-97 | 26 | |
| α-helix | 119-135 | 17 | |
| α-helix | 137-140 | 4 | |
| α-helix | 145 | 1 | |
| α-helix | 161-192 | 32 | |
Chain d: 7 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 80-81 | 2 | |
| β-strand | 82 | 1 | 43 |
| β-strand | 90 | 1 | 44 |
| α-helix | 92-96 | 5 | |
| β-strand | 99-106 | 8 | 45 |
| β-strand | 111-112 | 2 | 43 |
| β-strand | 120-121 | 2 | 43 |
| α-helix | 122-123 | 2 | |
| β-strand | 125-131 | 7 | 45 |
| α-helix | 134-145 | 12 | |
| β-strand | 153-157 | 5 | 45 |
| β-strand | 163-165 | 3 | 45 |
| β-strand | 186 | 1 | 41 |
| α-helix | 191-193 | 3 | |
| α-helix | 194-196 | 3 | |
| α-helix | 207-209 | 3 | |
Chain D: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-64 | 3 | |
| α-helix | 68-94 | 27 | |
| α-helix | 112-114 | 3 | |
| α-helix | 115-118 | 4 | |
| α-helix | 122-145 | 24 | |
| α-helix | 169-199 | 31 | |
27 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 |
|---|
| Fcpi-7 | A | protein | 168 | Chaetoceros gracilis | A0A6J4B7P2 (AlphaFold model) |
| Fcpi-1 | B | protein | 223 | Chaetoceros gracilis | A0A1E7F4Y9 (AlphaFold model) |
| Fcpi-11 | C | protein | 198 | Chaetoceros gracilis | A0A6J4B024 (AlphaFold model) |
| Fcpi-6 | D | protein | 207 | Chaetoceros gracilis | A0A6J4B112 (AlphaFold model) |
| Fcpi-5 | E | protein | 222 | Chaetoceros gracilis | A0A6J4B3M5 |
| Fcpi-8 | F | protein | 215 | Chaetoceros gracilis | A0A6J4B492 |
| Fcpi-4 | G | protein | 245 | Chaetoceros gracilis | A0A6J4B0A4 |
| Fcpi-10 | H | protein | 203 | Chaetoceros gracilis | B8C0K4 |
| Fcpi-3 | I | protein | 195 | Chaetoceros gracilis | A0A6J4B150 |
| Fcpi-9 | J | protein | 200 | Chaetoceros gracilis | A0A6J4B2D5 |
| Fcpi-13 | K | protein | 207 | Chaetoceros gracilis | A0A6J4B0S3 |
| Fcpi-14 | L | protein | 229 | Chaetoceros gracilis | A0A6J4B037 |
21 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6LY5_1 FCPI-7 (chains A)
EMSKAVPFVKAPANTAGYVGDVGFDPLGFSDYFDMKWLRESEIKHGRASMLACLGFVVQQ
YITIPGYTHVDDSNLAPQAVGVSAMLQIVLWMGVLEFWTNKGNVTMETMFSSPDRVPGNL
GFDPMGLSVGKSQAEKDEMALKEIKNGRLAMLAIGGMIHHNWVTGEPL
Sequence of entity 2 (B), FASTA
>6LY5_2 FCPI-1 (chains B)
MAPFRSLITIFVSLSAVSAFSTNKQATSLKPSSLNIANPEMYEAAQAKWAEEFKPLAKYG
WGPSVHAEKWNGRHAMFGWFFICCTAYAKGHGLIPDMDVPLNLKEWGTLATITGKGTITN
GRAVILLANAHFFAISLMATICPLPFGDSLLLDPDDESYEKSMARNNEPFGYLPAFKSGL
TEEAEMINGRLAMLGLISLIFATAIEQKPMLDIVNEWTGGFYF
Sequence of entity 3 (C), FASTA
>6LY5_3 FCPI-11 (chains C)
MVRSVLLAALVGTAAAFAPASSMARSSSAVALKAEMSESLPFLPRPEKLDGSMAGDRGFD
PMGLSEIQQDLTYARWAELKHGRIAMLAIVGMIVQEYIHLPGEAYQNPDPFGAISTVGLG
VNGQIFAAIGCVELINFNKHYDGSEPGDIGWTGGLLKNKSPAEIMKAKEQEITHCRLAMI
AITGATVQTLLFHQPLLG
Sequence of entity 4 (D), FASTA
>6LY5_4 FCPI-6 (chains D)
MKLALLASLIASAAAFAPSSSTGARTSTALDAGKKSQALPFLPYPENLSGYVGDAGFDPF
RFSDFAPMDFLREAEIKHGRICMLAWLGFVAVDLGARIYPLPEAYEGLTSVTAHDALVQQ
GAMSQIFLWCSVFEAISTVSVIQMLYEESGREPGNFGFDPLGFLKGKSEAEVNEMKLKEI
KNGRLAMLAFSGVVTQAVLTQGPFPYV
Sequence of entity 5 (E), FASTA
>6LY5_5 FCPI-5 (chains E)
MFKTAAAITSLLAASASAFAPSSFNGRLSTAVAAEKSQSLPFMNRPALLDGSMAGDVGFD
PLGLSNIDDVGIDLYWLREAEVKHCRVAMLAVVGILQVEIFGPAPGCEMATDKCQMDAFW
QLWGAHPQYIAFGLIMIMMIEMISGIATTQGRESGERAPGDFGLDPLGYGKGDAAGFARL
QAQEIANGRLAMFAAAGEIVQGCTTHQGALENLMTALRDNSF
Sequence of entity 6 (F), FASTA
>6LY5_6 FCPI-8 (chains F)
MTKLSIALTTAAALLSSASAFAPSKDVRPVTSALSATGFEEVGGKPWDPLSLGKLEDAND
TFPNMFPKSQYLQESEIKHGRMSMLAWTGVWATHVGGMGLGMHIPGMPVESDWTKALGVF
AAEQPALFGAILLFISIAEGESVGHSGDNWRNMSTKEPGNLGFDWMGLTRKLSEEQVARY
KIVELKNGRAAMIAMASLFAMEAIPGSVPIMNVFN
Sequence of entity 7 (G), FASTA
>6LY5_7 FCPI-4 (chains G)
MKSALIAIALLSGSAAAFTSNAGSQSTSALKAMPERLWDSMVDKTQRSKAVPFLPRAVNL
DGSLPGDVGFDPFYLSSIPKDFSGFIQPPQWEEKGIPTLYWMREAELKHSRVAMLAWFGW
LATDGAFGVTLRFPGEIYSVENIPTAYEAHNALVSQGSMGFLLLAVGFIEFCTGAVLVEV
AKGDSDREAGDFKLDPLSFLKGKSEEEIKRMKTREIANGRLAMLAFGGVATQTALEGGNH
AFPYF
Sequence of entity 8 (H), FASTA
>6LY5_8 FCPI-10 (chains H)
MMKSVIIASLACSAAAFAPASNGRAATSLEASAKSKALPWLPNPSNLDGRIGANGFDPLG
ISEYFPVDYLVESEIKHGRVCMMAWAGYVAVDLGARIYPLPESMQGVTSATAHDPAVAFG
SMGNMFIWIALFEMVGWIGLSQTLQGSGREPGDFGWGKQFMGKTQAEIDTMKLKELTNGR
AAMLAFAGVVTQSVLYDKGFPYF
Sequence of entity 9 (I), FASTA
>6LY5_9 FCPI-3 (chains I)
MKTAAIISSLIASASAFAPVSQTNVRSSSSLQAWKDENIIGITAPMGFFDPLGLSSGKSD
EVMNLYREAELKHGRVAMAACLGWYITAAGVHPAFNSALSSDPLEAAKQLPTVGWLQFVL
GCGAIEWLAQQIKARPGYQPGDILGAAYWVDNSDEGWVDYQNKEINNGRLAMVAFMGIFV
QDLYFGNYGDQIFRN
Sequence of entity 10 (J), FASTA
>6LY5_10 FCPI-9 (chains J)
MKSVAILSLLTASAAAFAPASTTQSSSSTALAGSVFDNYVGAKDFRGAQFKFDPLKLSET
YEPFQGWFRESELRHGRTAMLAVVGYIATDFVRIPGEMYSFEAIPKSADAHDALVASGPM
SQLLLWIGLFDLVVTAPAVQAMGQGEREPGDFGWKWFAPSSKDAFDKKREAELLNGRLAM
FAIGGIATQSVLSGHGFPYL
Sequence of entity 11 (K), FASTA
>6LY5_11 FCPI-13 (chains K)
MKSVAILAALVGSATAFAPSQVSRTAASTSVRASLADMVGAEGPEPIPFAPSRTSKNFDP
VGFAERSPEWLPWYREAELKHGRAAMLATVGFVVPEFVRIPGEQFSFEAIPKVIDAHDAL
PESMIQIFGWISFLEACTFPAMAGLGGKYDRKPGDFSFDPLGLYPTDPEKQKKMQLAELK
NGRLAMIAIGGMVTGAAVTGHGFPYLP
Sequence of entity 12 (L), FASTA
>6LY5_12 FCPI-14 (chains L)
MKTAAVFALFAGSAAAFAPANVAPRASTVTHMSSINEAFGVSIETGNKCPPLGARILEDA
QPSAIKWFQNAEIKHGRIAMVATIGYLVQKLGVHFPLYLGPSGSNCFHPESETAWLLSSS
TGVTFSDIAKAAPLDAIQMVPVAGWMQIFFVAGWFESVAYYRQWVKDSPIPGDYGYDPLG
FTKREGGWDSEELTSLRLKEIKNGRLAMMTIAAWVSDEMIPGALPVWHP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| DD6 | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,… | C40 H54 O3 | 35 |
| A86 | (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-h… | C42 H58 O6 | 102 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 326 |
| KC1 | Chlorophyll c1 | C35 H30 Mg N4 O5 | 34 |
| SQD | 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol | C41 H78 O12 S | 2 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 26 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 3 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 22 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 16 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| BCR | Beta-carotene | C40 H56 | 18 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
Primary citation
Structural basis for energy transfer in a huge diatom PSI-FCPI supercomplex. Xu, C., Pi, X., Huang, Y. et al. Nat Commun (2020) 11:5081-5081. DOI 10.1038/s41467-020-18867-x · PubMed
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