6PFY: Photosystem I P700 chlorophyll a apoprotein A1
Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I at synchrotron to 2.9 A. Determined by X-ray diffraction at 2.9 Å resolution. Released 20 Nov 2019.
- Method
- X-ray diffraction
- Resolution
- 2.9 Å
- Organism
- Thermosynechococcus elongatus (strain BP-1)
- Chains
- 36
- Atoms
- 72,737
- Mol. weight
- 1080.12 kDa
- Ligands
- CL0, CLA, PQN, SF4
- Released
- 20 Nov 2019
Explore 6PFY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6PFY contains 360 α-helices and 190 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: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 11 |
| α-helix | 15-18 | 4 | |
| β-strand | 26-29 | 4 | 12 |
| β-strand | 37-40 | 4 | 12 |
| α-helix | 52-55 | 4 | |
| β-strand | 64-67 | 4 | 11 |
Chain A: 39 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-18 | 3 | 1 |
| α-helix | 36-38 | 3 | |
| β-strand | 44 | 1 | 2 |
| α-helix | 46-53 | 8 | |
| α-helix | 58-60 | 3 | |
| α-helix | 65-96 | 32 | |
| α-helix | 101-104 | 4 | |
| β-strand | 114 | 1 | 3 |
| α-helix | 123-126 | 4 | |
| β-strand | 128-131 | 4 | 4 |
| β-strand | 134-136 | 3 | 4 |
| β-strand | 137 | 1 | 3 |
| α-helix | 143-149 | 7 | |
| α-helix | 156-177 | 22 | |
| α-helix | 178-182 | 5 | |
| β-strand | 183-185 | 3 | 1 |
| α-helix | 187-190 | 4 | |
| α-helix | 193-198 | 6 | |
| α-helix | 199-206 | 8 | |
| α-helix | 207-215 | 9 | |
| α-helix | 216-220 | 5 | |
| α-helix | 221-229 | 9 | |
| α-helix | 241-244 | 4 | |
| α-helix | 246-249 | 4 | |
| α-helix | 272-275 | 4 | |
| β-strand | 285 | 1 | 5 |
| β-strand | 292 | 1 | 5 |
| α-helix | 293 | 1 | |
| α-helix | 294-311 | 18 | |
| α-helix | 325-330 | 6 | |
| α-helix | 344-347 | 4 | |
| α-helix | 352-376 | 25 | |
| α-helix | 387-418 | 32 | |
| α-helix | 429-435 | 7 | |
| α-helix | 437-454 | 18 | |
| α-helix | 456-468 | 13 | |
| α-helix | 471-473 | 3 | |
| β-strand | 475 | 1 | 6 |
| β-strand | 480 | 1 | 6 |
| α-helix | 487-496 | 10 | |
| β-strand | 498 | 1 | 7 |
| β-strand | 502 | 1 | 7 |
| β-strand | 518-519 | 2 | 8 |
| β-strand | 523 | 1 | 9 |
| β-strand | 524-526 | 3 | 8 |
| α-helix | 533-558 | 26 | |
| α-helix | 591-620 | 30 | |
| β-strand | 623 | 1 | 10 |
| β-strand | 624 | 1 | 9 |
| β-strand | 633 | 1 | 10 |
| 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 | 670-690 | 21 | |
| α-helix | 694-710 | 17 | |
| β-strand | 718 | 1 | 2 |
| α-helix | 724-752 | 29 | |
Chain b: 10 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-4 | 3 | |
| β-strand | 6 | 1 | 21 |
| α-helix | 7-8 | 2 | |
| β-strand | 9 | 1 | 22 |
| β-strand | 17 | 1 | 64 |
| α-helix | 20-23 | 4 | |
| β-strand | 26-32 | 7 | 21 |
| β-strand | 37-40 | 4 | 22 |
| β-strand | 46-49 | 4 | 22 |
| β-strand | 53-58 | 6 | 21 |
| α-helix | 61-67 | 7 | |
| α-helix | 68-72 | 5 | |
| α-helix | 73-75 | 3 | |
| β-strand | 81-85 | 5 | 21 |
| β-strand | 91-93 | 3 | 21 |
| α-helix | 109-111 | 3 | |
| β-strand | 114-115 | 2 | 11 |
| α-helix | 119-121 | 3 | |
| α-helix | 123-124 | 2 | |
| α-helix | 125-128 | 4 | |
Chain B: 45 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 13 |
| α-helix | 9-12 | 4 | |
| β-strand | 16 | 1 | 14 |
| α-helix | 18-26 | 9 | |
| α-helix | 30-32 | 3 | |
| α-helix | 38-70 | 33 | |
| α-helix | 73-78 | 6 | |
| α-helix | 84-85 | 2 | |
| β-strand | 86-89 | 4 | 15 |
| α-helix | 97-103 | 7 | |
| β-strand | 104 | 1 | 16 |
| β-strand | 111 | 1 | 16 |
| β-strand | 112-114 | 3 | 15 |
| α-helix | 119-125 | 7 | |
| α-helix | 132-154 | 23 | |
| α-helix | 158-160 | 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 | 198-200 | 3 | |
| α-helix | 222-226 | 5 | |
| α-helix | 229-233 | 5 | |
| α-helix | 269-286 | 18 | |
| β-strand | 290 | 1 | 17 |
| β-strand | 298 | 1 | 17 |
| α-helix | 300-305 | 6 | |
| β-strand | 309 | 1 | 18 |
| β-strand | 312 | 1 | 18 |
| α-helix | 317-319 | 3 | |
| α-helix | 325-330 | 6 | |
| α-helix | 333-355 | 23 | |
| α-helix | 368-399 | 32 | |
| α-helix | 403-406 | 4 | |
| α-helix | 410-414 | 5 | |
| α-helix | 415-417 | 3 | |
| α-helix | 418-448 | 31 | |
| α-helix | 452-454 | 3 | |
| β-strand | 457-458 | 2 | 19 |
| α-helix | 462-469 | 8 | |
| α-helix | 487-490 | 4 | |
| α-helix | 500-508 | 9 | |
| α-helix | 520-545 | 26 | |
| α-helix | 556-558 | 3 | |
| α-helix | 578-609 | 32 | |
| α-helix | 613-618 | 6 | |
| α-helix | 622-625 | 4 | |
| α-helix | 626-631 | 6 | |
| α-helix | 632-633 | 2 | |
| α-helix | 637-639 | 3 | |
| β-strand | 641-642 | 2 | 20 |
| β-strand | 645-646 | 2 | 20 |
| α-helix | 650-671 | 22 | |
| α-helix | 674-690 | 17 | |
| α-helix | 694-696 | 3 | |
| β-strand | 702 | 1 | 14 |
| α-helix | 705-707 | 3 | |
| α-helix | 708-738 | 31 | |
Chain c: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-8 | 3 | 25 |
| β-strand | 20-26 | 7 | 25 |
| β-strand | 36-39 | 4 | 25 |
| β-strand | 48 | 1 | 79 |
| β-strand | 57-60 | 4 | 25 |
| α-helix | 62-64 | 3 | |
| β-strand | 67 | 1 | 25 |
Chain C: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 23 |
| α-helix | 17-19 | 3 | |
| β-strand | 26-29 | 4 | 24 |
| β-strand | 37-40 | 4 | 24 |
| α-helix | 52-56 | 5 | |
| β-strand | 64-67 | 4 | 23 |
Chain d: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-4 | 3 | |
| β-strand | 6-7 | 2 | 29 |
| α-helix | 12-16 | 5 | |
| α-helix | 30-37 | 8 | |
| β-strand | 42-43 | 2 | 29 |
| β-strand | 49-51 | 3 | 29 |
| α-helix | 57-59 | 3 | |
| α-helix | 64-89 | 26 | |
| α-helix | 96-98 | 3 | |
| β-strand | 100 | 1 | 30 |
| α-helix | 103-111 | 9 | |
| α-helix | 112-115 | 4 | |
| α-helix | 116-125 | 10 | |
Chain D: 9 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6 | 1 | 26 |
| α-helix | 7-8 | 2 | |
| β-strand | 9 | 1 | 27 |
| β-strand | 17 | 1 | 28 |
| α-helix | 20-23 | 4 | |
| β-strand | 26-33 | 8 | 26 |
| β-strand | 37-40 | 4 | 27 |
| β-strand | 46-49 | 4 | 27 |
| α-helix | 50 | 1 | |
| β-strand | 52-58 | 7 | 26 |
| α-helix | 61-67 | 7 | |
| α-helix | 68-72 | 5 | |
| α-helix | 73-75 | 3 | |
| β-strand | 81-85 | 5 | 26 |
| β-strand | 91-93 | 3 | 26 |
| β-strand | 114-115 | 2 | 23 |
| α-helix | 119-121 | 3 | |
| α-helix | 122-124 | 3 | |
| α-helix | 125-128 | 4 | |
25 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 | A, G, Y | protein | 755 | Thermosynechococcus elongatus (strain BP-1) | P0A405 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A2 | B, H, Z | protein | 741 | Thermosynechococcus elongatus (strain BP-1) | P0A407 (AlphaFold model) |
| Photosystem I iron-sulfur center | C, N, a | protein | 81 | Thermosynechococcus elongatus (strain BP-1) | P0A415 (AlphaFold model) |
| Photosystem I reaction center subunit II | D, O, b | protein | 139 | Thermosynechococcus elongatus (strain BP-1) | P0A420 (AlphaFold model) |
| Photosystem I reaction center subunit IV | E, P, c | protein | 76 | Thermosynechococcus elongatus (strain BP-1) | P0A423 |
| Photosystem I reaction center subunit III | F, Q, d | protein | 164 | Thermosynechococcus elongatus (strain BP-1) | P0A401 |
| Photosystem I reaction center subunit VIII | I, R, e | protein | 38 | Thermosynechococcus elongatus (strain BP-1) | P0A427 |
| Photosystem I reaction center subunit IX | J, S, f | protein | 41 | Thermosynechococcus elongatus (strain BP-1) | P0A429 |
| Photosystem I reaction center subunit PsaK | K, T, g | protein | 83 | Thermosynechococcus elongatus (strain BP-1) | P0A425 |
| Photosystem I reaction center subunit XI | L, U, h | protein | 155 | Thermosynechococcus elongatus (strain BP-1) | Q8DGB4 |
| Photosystem I reaction center subunit XII | M, V, i | protein | 31 | Thermosynechococcus elongatus (strain BP-1) | P0A403 |
| Photosystem I 4.8K protein | W, X, j | protein | 39 | Thermosynechococcus elongatus (strain BP-1) | Q8DKP6 |
Sequence of entity 1 (A, G, Y), FASTA
>6PFY_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A, G, Y)
MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDT
HTSDLEDISRKIFSAHFGHLAVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPI
VGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYCTAIGGLVMAGLMLFAGWFHY
HKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPH
EFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHH
HLAIAVLFIIAGHMYRTNWGIGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINL
AMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWIGGFLVVGGAAHGAIFMVRDY
DPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGI
QLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHH
IHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLF
WMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFAQSAITINGWLRDFLWAQASQ
VIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPR
ALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG
Sequence of entity 2 (B, H, Z), FASTA
>6PFY_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B, H, Z)
MATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLW
VSGSLFHVAWQGNFEQWVQDPVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGV
YHWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPKFRPSLSWFKNAESRLNHHLA
GLFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTA
SHVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHS
IKEMMDAKDFFGTKVEGPFNMPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLP
PYAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVRDYDPAQNKGNVLDRVLQHKE
AIISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDT
LLSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLI
LVKGALDARGSKLMPDKKDFGYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFY
WHWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGTNNLSVWAWMFLFG
HLVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHF
SVGYILTYAAFLIASTAAKFG
Sequence of entity 3 (C, N, a), FASTA
>6PFY_3 Photosystem I iron-sulfur center (chains C, N, a)
MAHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPT
DFLSIRVYLGAETTRSMGLAY
Sequence of entity 4 (D, O, b), FASTA
>6PFY_4 Photosystem I reaction center subunit II (chains D, O, b)
MTTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFA
RKEQCLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSI
GQNPNPSQLKFTGKKPYDP
Sequence of entity 5 (E, P, c), FASTA
>6PFY_5 Photosystem I reaction center subunit IV (chains E, P, c)
MVQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNN
FALHEVQEVAPPKKGK
Sequence of entity 6 (F, Q, d), FASTA
>6PFY_6 Photosystem I reaction center subunit III (chains F, Q, d)
MRRFLALLLVLTLWLGFTPLASADVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFER
YSQALCGEDGLPHLVVDGRLSRAGDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEK
EIIIDVPLAIKCMLTGFAWPLAALKELASGELTAKDNEITVSPR
Sequence of entity 7 (I, R, e), FASTA
>6PFY_7 Photosystem I reaction center subunit VIII (chains I, R, e)
MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA
Sequence of entity 8 (J, S, f), FASTA
>6PFY_8 Photosystem I reaction center subunit IX (chains J, S, f)
MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL
Sequence of entity 9 (K, T, g), FASTA
>6PFY_9 Photosystem I reaction center subunit PsaK (chains K, T, g)
MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELL
ATTSFGHLLAAGVVSGLQYAGAL
Sequence of entity 10 (L, U, h), FASTA
>6PFY_10 Photosystem I reaction center subunit XI (chains L, U, h)
MAEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLI
GPWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQ
FTAGFFVGAMGSAFVAFFLLENFLVVDGIMTGLFN
Sequence of entity 11 (M, V, i), FASTA
>6PFY_11 Photosystem I reaction center subunit XII (chains M, V, i)
MALTDTQVYVALVIALLPAVLAFRLSTELYK
Sequence of entity 12 (W, X, j), FASTA
>6PFY_12 Photosystem I 4.8K protein (chains W, X, j)
MSTMATKSAKPTYAFRTFWAVLLLAINFLVAAYYFGILK
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 | 282 |
| PQN | Phylloquinone | C31 H46 O2 | 6 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 9 |
| BCR | Beta-carotene | C40 H56 | 66 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 9 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 3 |
| CA | Calcium ion | Ca | 3 |
Primary citation
Membrane protein megahertz crystallography at the European XFEL. Gisriel, C., Coe, J., Letrun, R. et al. Nat Commun (2019) 10:5021-5021. DOI 10.1038/s41467-019-12955-3 · 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
- 7FIX 1.97 Å, Cryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and…
- 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…
- 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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