7FIX: Photosystem I P700 chlorophyll a apoprotein A1
Cryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6. Determined by electron microscopy at 1.97 Å resolution. Released 21 Sept 2022.
- Method
- Electron microscopy
- Resolution
- 1.97 Å
- Organism
- Thermosynechococcus vestitus BP-1
- Chains
- 39
- Atoms
- 73,929
- Mol. weight
- 1125.8 kDa
- Ligands
- CL0, CLA, PQN, SF4
- Released
- 21 Sept 2022
Explore 7FIX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7FIX contains 402 α-helices and 216 β-strands across 39 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.
Chains A1, A2 and A3: 44 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-18 | 3 | 1 |
| α-helix | 27-29 | 3 | |
| β-strand | 44 | 1 | 2 |
| α-helix | 46-53 | 8 | |
| α-helix | 58-61 | 4 | |
| α-helix | 65-96 | 32 | |
| α-helix | 100-105 | 6 | |
| β-strand | 113-115 | 3 | 3 |
| α-helix | 123-126 | 4 | |
| β-strand | 128-129 | 2 | 4 |
| β-strand | 135-136 | 2 | 4 |
| β-strand | 137-138 | 2 | 3 |
| α-helix | 143-149 | 7 | |
| α-helix | 155-177 | 23 | |
| α-helix | 178-182 | 5 | |
| β-strand | 183-185 | 3 | 1 |
| α-helix | 186 | 1 | |
| α-helix | 187-191 | 5 | |
| α-helix | 193-198 | 6 | |
| α-helix | 199-207 | 9 | |
| α-helix | 208-215 | 8 | |
| α-helix | 216-220 | 5 | |
| α-helix | 221-229 | 9 | |
| α-helix | 237-238 | 2 | |
| α-helix | 241-244 | 4 | |
| α-helix | 246-252 | 7 | |
| α-helix | 272-277 | 6 | |
| α-helix | 294-310 | 17 | |
| β-strand | 315 | 1 | 5 |
| β-strand | 323 | 1 | 5 |
| α-helix | 325-331 | 7 | |
| α-helix | 344-350 | 7 | |
| α-helix | 352-374 | 23 | |
| α-helix | 387-414 | 28 | |
| α-helix | 415-419 | 5 | |
| α-helix | 429-434 | 6 | |
| α-helix | 437-467 | 31 | |
| α-helix | 471-473 | 3 | |
| β-strand | 475 | 1 | 6 |
| β-strand | 480 | 1 | 6 |
| α-helix | 485-495 | 11 | |
| α-helix | 511-513 | 3 | |
| β-strand | 518-520 | 3 | 7 |
| β-strand | 523-526 | 4 | 7 |
| α-helix | 533-558 | 26 | |
| α-helix | 569-572 | 4 | |
| α-helix | 591-620 | 30 | |
| β-strand | 623-625 | 3 | 7 |
| β-strand | 631-633 | 3 | 7 |
| α-helix | 639-642 | 4 | |
| α-helix | 646-648 | 3 | |
| α-helix | 649-655 | 7 | |
| α-helix | 656-657 | 2 | |
| α-helix | 659-662 | 4 | |
| α-helix | 670-691 | 22 | |
| α-helix | 694-710 | 17 | |
| β-strand | 718 | 1 | 2 |
| α-helix | 719 | 1 | |
| α-helix | 721-723 | 3 | |
| α-helix | 724-754 | 31 | |
Chains B1, B2 and B3: 44 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 15 |
| α-helix | 9-12 | 4 | |
| β-strand | 16 | 1 | 16 |
| α-helix | 18-25 | 8 | |
| α-helix | 30-32 | 3 | |
| α-helix | 38-70 | 33 | |
| α-helix | 73-78 | 6 | |
| β-strand | 86-89 | 4 | 17 |
| α-helix | 97-103 | 7 | |
| β-strand | 104 | 1 | 18 |
| β-strand | 111 | 1 | 18 |
| β-strand | 112-114 | 3 | 17 |
| α-helix | 119-125 | 7 | |
| α-helix | 131-154 | 24 | |
| α-helix | 158-160 | 3 | |
| α-helix | 164-168 | 5 | |
| α-helix | 170-175 | 6 | |
| α-helix | 176-184 | 9 | |
| α-helix | 185-192 | 8 | |
| α-helix | 193-197 | 5 | |
| α-helix | 198-201 | 4 | |
| α-helix | 222-226 | 5 | |
| α-helix | 229-233 | 5 | |
| α-helix | 236-238 | 3 | |
| β-strand | 260 | 1 | 19 |
| β-strand | 267 | 1 | 19 |
| α-helix | 269-286 | 18 | |
| β-strand | 290 | 1 | 20 |
| β-strand | 298 | 1 | 20 |
| α-helix | 300-305 | 6 | |
| β-strand | 308-309 | 2 | 21 |
| β-strand | 312-313 | 2 | 21 |
| α-helix | 317-319 | 3 | |
| α-helix | 325-331 | 7 | |
| α-helix | 333-357 | 25 | |
| α-helix | 368-399 | 32 | |
| α-helix | 404-406 | 3 | |
| α-helix | 410-416 | 7 | |
| α-helix | 418-448 | 31 | |
| α-helix | 452-454 | 3 | |
| β-strand | 458 | 1 | 22 |
| α-helix | 461-469 | 9 | |
| α-helix | 480-482 | 3 | |
| α-helix | 487-490 | 4 | |
| α-helix | 500-509 | 10 | |
| α-helix | 520-545 | 26 | |
| α-helix | 556-559 | 4 | |
| β-strand | 569 | 1 | 23 |
| α-helix | 578-608 | 31 | |
| α-helix | 612-616 | 5 | |
| α-helix | 622-624 | 3 | |
| α-helix | 625-631 | 7 | |
| α-helix | 632-633 | 2 | |
| α-helix | 637-639 | 3 | |
| β-strand | 641-642 | 2 | 24 |
| β-strand | 645-646 | 2 | 24 |
| α-helix | 650-671 | 22 | |
| α-helix | 674-690 | 17 | |
| β-strand | 702 | 1 | 16 |
| α-helix | 705-707 | 3 | |
| α-helix | 708-739 | 32 | |
Chains C1, C2 and C3: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 35 |
| α-helix | 15-19 | 5 | |
| β-strand | 26-29 | 4 | 36 |
| β-strand | 37-40 | 4 | 36 |
| α-helix | 44-46 | 3 | |
| α-helix | 52-56 | 5 | |
| β-strand | 64-67 | 4 | 35 |
Chains D1, D2 and D3: 8 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6 | 1 | 39 |
| β-strand | 9 | 1 | 40 |
| β-strand | 13 | 1 | 41 |
| β-strand | 17 | 1 | 42 |
| α-helix | 19-23 | 5 | |
| β-strand | 26-33 | 8 | 39 |
| β-strand | 37-40 | 4 | 40 |
| β-strand | 46-49 | 4 | 40 |
| α-helix | 50 | 1 | |
| β-strand | 52-58 | 7 | 39 |
| α-helix | 61-67 | 7 | |
| α-helix | 68-72 | 5 | |
| α-helix | 73-75 | 3 | |
| β-strand | 81-85 | 5 | 39 |
| β-strand | 91-93 | 3 | 39 |
| β-strand | 114-115 | 2 | 35 |
| α-helix | 119-121 | 3 | |
| α-helix | 122-124 | 3 | |
| α-helix | 125-128 | 4 | |
Chains E1, E2 and E3: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-9 | 4 | 47 |
| β-strand | 20-26 | 7 | 47 |
| β-strand | 36-39 | 4 | 47 |
| β-strand | 48 | 1 | 23 |
| β-strand | 57-60 | 4 | 47 |
| α-helix | 62-64 | 3 | |
| β-strand | 65-67 | 3 | 47 |
Chains F1, F2 and F3: 10 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-27 | 3 | |
| β-strand | 29-30 | 2 | 49 |
| α-helix | 35-41 | 7 | |
| α-helix | 53-61 | 9 | |
| β-strand | 65-66 | 2 | 49 |
| β-strand | 72 | 1 | 49 |
| β-strand | 74 | 1 | 22 |
| α-helix | 87-113 | 27 | |
| α-helix | 117-122 | 6 | |
| β-strand | 123 | 1 | 50 |
| α-helix | 126-134 | 9 | |
| α-helix | 136-138 | 3 | |
| α-helix | 139-149 | 11 | |
| α-helix | 154-155 | 2 | |
| α-helix | 156-158 | 3 | |
Chains I1, I2 and I3: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-16 | 7 | |
| α-helix | 17-21 | 5 | |
| α-helix | 22-34 | 13 | |
| β-strand | 37 | 1 | 15 |
Chains J1, J2 and J3: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-7 | 6 | |
| β-strand | 10 | 1 | 50 |
| α-helix | 11-32 | 22 | |
5 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 |
|---|
| Photosystem I P700 chlorophyll a apoprotein A1 | A1, A2, A3 | protein | 755 | Thermosynechococcus vestitus BP-1 | P0A405 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A2 | B1, B2, B3 | protein | 741 | Thermosynechococcus vestitus BP-1 | P0A407 (AlphaFold model) |
| Photosystem I iron-sulfur center | C1, C2, C3 | protein | 81 | Thermosynechococcus vestitus BP-1 | P0A415 (AlphaFold model) |
| Photosystem I reaction center subunit II | D1, D2, D3 | protein | 139 | Thermosynechococcus vestitus BP-1 | P0A420 (AlphaFold model) |
| Photosystem I reaction center subunit IV | E1, E2, E3 | protein | 76 | Thermosynechococcus vestitus BP-1 | P0A423 |
| Photosystem I reaction center subunit III | F1, F2, F3 | protein | 174 | Thermosynechococcus vestitus BP-1 | P0A401 |
| Photosystem I reaction center subunit VIII | I1, I2, I3 | protein | 38 | Thermosynechococcus vestitus BP-1 | P0A427 |
| Photosystem I reaction center subunit IX | J1, J2, J3 | protein | 41 | Thermosynechococcus vestitus BP-1 | P0A429 |
| Photosystem I reaction center subunit PsaK | K1, K2, K3 | protein | 83 | Thermosynechococcus vestitus BP-1 | P0A425 |
| Photosystem I reaction center subunit XI | L1, L2, L3 | protein | 155 | Thermosynechococcus vestitus BP-1 | Q8DGB4 |
| Photosystem I reaction center subunit XII | M1, M2, M3 | protein | 31 | Thermosynechococcus vestitus BP-1 | P0A403 |
| Ferredoxin-1 | R1, R2, R3 | protein | 98 | Thermosynechococcus vestitus BP-1 | P0A3C9 |
1 more molecules are not listed.
Sequence of entity 1 (A1, A2, A3), FASTA
>7FIX_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A1, A2, A3)
MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDT
HTSDLEDISRKIFSAHFGHLAVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPI
VGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYCTAIGGLVMAGLMLFAGWFHY
HKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPH
EFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHH
HLAIAVLFIIAGHMYRTNWGIGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINL
AMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWIGGFLVVGGAAHGAIFMVRDY
DPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGI
QLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHH
IHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLF
WMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFAQSAITINGWLRDFLWAQASQ
VIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPR
ALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG
Sequence of entity 2 (B1, B2, B3), FASTA
>7FIX_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B1, B2, B3)
MATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLW
VSGSLFHVAWQGNFEQWVQDPVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGV
YHWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPKFRPSLSWFKNAESRLNHHLA
GLFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTA
SHVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHS
IKEMMDAKDFFGTKVEGPFNMPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLP
PYAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVRDYDPAQNKGNVLDRVLQHKE
AIISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDT
LLSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLI
LVKGALDARGSKLMPDKKDFGYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFY
WHWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGTNNLSVWAWMFLFG
HLVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHF
SVGYILTYAAFLIASTAAKFG
Sequence of entity 3 (C1, C2, C3), FASTA
>7FIX_3 Photosystem I iron-sulfur center (chains C1, C2, C3)
MAHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPT
DFLSIRVYLGAETTRSMGLAY
Sequence of entity 4 (D1, D2, D3), FASTA
>7FIX_4 Photosystem I reaction center subunit II (chains D1, D2, D3)
MTTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFA
RKEQCLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSI
GQNPNPSQLKFTGKKPYDP
Sequence of entity 5 (E1, E2, E3), FASTA
>7FIX_5 Photosystem I reaction center subunit IV (chains E1, E2, E3)
MVQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNN
FALHEVQEVAPPKKGK
Sequence of entity 6 (F1, F2, F3), FASTA
>7FIX_6 Photosystem I reaction center subunit III (chains F1, F2, F3)
HHHHHHHHHHMRRFLALLLVLTLWLGFTPLASADVAGLVPCKDSPAFQKRAAAAVNTTAD
PASGQKRFERYSQALCGEDGLPHLVVDGRLSRAGDFLIPSVLFLYIAGWIGWVGRAYLIA
VRNSGEANEKEIIIDVPLAIKCMLTGFAWPLAALKELASGELTAKDNEITVSPR
Sequence of entity 7 (I1, I2, I3), FASTA
>7FIX_7 Photosystem I reaction center subunit VIII (chains I1, I2, I3)
MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA
Sequence of entity 8 (J1, J2, J3), FASTA
>7FIX_8 Photosystem I reaction center subunit IX (chains J1, J2, J3)
MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL
Sequence of entity 9 (K1, K2, K3), FASTA
>7FIX_9 Photosystem I reaction center subunit PsaK (chains K1, K2, K3)
MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELL
ATTSFGHLLAAGVVSGLQYAGAL
Sequence of entity 10 (L1, L2, L3), FASTA
>7FIX_10 Photosystem I reaction center subunit XI (chains L1, L2, L3)
MAEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLI
GPWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQ
FTAGFFVGAMGSAFVAFFLLENFSVVDGIMTGLFN
Sequence of entity 11 (M1, M2, M3), FASTA
>7FIX_11 Photosystem I reaction center subunit XII (chains M1, M2, M3)
MALTDTQVYVALVIALLPAVLAFRLSTELYK
Sequence of entity 12 (R1, R2, R3), FASTA
>7FIX_12 Ferredoxin-1 (chains R1, R2, R3)
MATYKVTLVRPDGSETTIDVPEDEYILDVAEEQGLDLPFSCRAGACSTCAGKLLEGEVDQ
SDQSFLDDDQIEKGFVLTCVAYPRSDCKILTNQEEELY
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CL0 | Chlorophyll a isomer | C55 H72 Mg N4 O5 | 3 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 285 |
| PQN | Phylloquinone | C31 H46 O2 | 6 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 9 |
| BCR | Beta-carotene | C40 H56 | 72 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 9 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 3 |
| CA | Calcium ion | Ca | 3 |
| GAK | [2Ga-2S] cluster | Ga2 S2 | 3 |
Water and common crystallization additives (UNL) are not listed.
Primary citation
Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97 angstrom resolution. Li, J., Hamaoka, N., Makino, F. et al. Commun Biol (2022) 5:951-951. DOI 10.1038/s42003-022-03926-4 · PubMed
Other PDB entries of the same protein (UniProt P0A405 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9QFP 1.74 Å, Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution
- 1JB0 2.5 Å, Crystal Structure of Photosystem I: a Photosynthetic Reaction Center and Core Antenna…
- 7M75 2.75 Å, Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two…
- 6TRA 2.85 Å, Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of…
- 6PFY 2.9 Å, Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I at…
- 6PGK 2.9 Å, Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I XFEL at…
- 6TRC 2.98 Å, Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of…
- 7M76 3.0 Å, Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two…
- 7M78 3.0 Å, Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two…
- 6TRD 3.16 Å, Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of…
- 6LU1 3.2 Å, Cyanobacterial PSI Monomer from T. elongatus by Single Particle CRYO-EM at 3.2 A…
- 10EG 3.4 Å, Thermosynechococcus vestitus (BP-1) Photosystem I Complexed with Platinum Nanoparticles
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