6TRA: Photosystem I P700 chlorophyll a apoprotein A1
Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of cytochrome c6. Determined by electron microscopy at 2.85 Å resolution. Released 16 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 2.85 Å
- Organism
- Thermosynechococcus elongatus (strain BP-1)
- Chains
- 12
- Atoms
- 25,197
- Mol. weight
- 361.54 kDa
- Ligands
- LMG, CA, SF4, LHG
- Released
- 16 Sept 2020
Explore 6TRA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6TRA contains 113 α-helices and 56 β-strands across 12 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: 40 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-18 | 3 | 1 |
| α-helix | 26-28 | 3 | |
| α-helix | 37-39 | 3 | |
| β-strand | 44 | 1 | 2 |
| α-helix | 46-53 | 8 | |
| α-helix | 58-61 | 4 | |
| α-helix | 65-95 | 31 | |
| α-helix | 100-103 | 4 | |
| β-strand | 113 | 1 | 3 |
| α-helix | 123-126 | 4 | |
| β-strand | 128-129 | 2 | 4 |
| β-strand | 135-136 | 2 | 4 |
| β-strand | 138 | 1 | 3 |
| α-helix | 143-148 | 6 | |
| α-helix | 155-177 | 23 | |
| α-helix | 178-182 | 5 | |
| β-strand | 183-185 | 3 | 1 |
| α-helix | 187-191 | 5 | |
| 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 | 237-238 | 2 | |
| α-helix | 241-244 | 4 | |
| α-helix | 247-251 | 5 | |
| α-helix | 265-268 | 4 | |
| α-helix | 272-275 | 4 | |
| α-helix | 294-311 | 18 | |
| β-strand | 315 | 1 | 5 |
| β-strand | 323 | 1 | 5 |
| α-helix | 327-331 | 5 | |
| 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 | 437-452 | 16 | |
| α-helix | 453-457 | 5 | |
| α-helix | 458-468 | 11 | |
| α-helix | 471-473 | 3 | |
| α-helix | 485-496 | 12 | |
| β-strand | 498 | 1 | 6 |
| β-strand | 502 | 1 | 6 |
| β-strand | 518-520 | 3 | 7 |
| β-strand | 523-526 | 4 | 7 |
| α-helix | 533-558 | 26 | |
| β-strand | 578 | 1 | 8 |
| β-strand | 587 | 1 | 8 |
| α-helix | 591-620 | 30 | |
| β-strand | 623-625 | 3 | 7 |
| β-strand | 631-633 | 3 | 7 |
| α-helix | 646-651 | 6 | |
| α-helix | 657-659 | 3 | |
| α-helix | 670-690 | 21 | |
| α-helix | 694-709 | 16 | |
| β-strand | 718 | 1 | 2 |
| α-helix | 724-754 | 31 | |
Chain B: 38 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16 | 1 | 9 |
| α-helix | 18-24 | 7 | |
| α-helix | 30-32 | 3 | |
| α-helix | 38-70 | 33 | |
| α-helix | 76-78 | 3 | |
| α-helix | 84-85 | 2 | |
| β-strand | 86-89 | 4 | 10 |
| α-helix | 97-102 | 6 | |
| β-strand | 112-114 | 3 | 10 |
| α-helix | 119-126 | 8 | |
| α-helix | 131-155 | 25 | |
| 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 | 207-210 | 4 | |
| α-helix | 222-226 | 5 | |
| α-helix | 229-233 | 5 | |
| α-helix | 269-286 | 18 | |
| β-strand | 290 | 1 | 11 |
| β-strand | 298 | 1 | 11 |
| α-helix | 300-304 | 5 | |
| α-helix | 317-319 | 3 | |
| α-helix | 325-330 | 6 | |
| α-helix | 333-354 | 22 | |
| α-helix | 368-395 | 28 | |
| α-helix | 396-400 | 5 | |
| α-helix | 410-415 | 6 | |
| α-helix | 418-448 | 31 | |
| α-helix | 452-454 | 3 | |
| β-strand | 458 | 1 | 12 |
| α-helix | 461-469 | 9 | |
| α-helix | 500-507 | 8 | |
| α-helix | 520-545 | 26 | |
| α-helix | 578-609 | 32 | |
| α-helix | 613-618 | 6 | |
| α-helix | 622-624 | 3 | |
| α-helix | 625-631 | 7 | |
| α-helix | 632-633 | 2 | |
| β-strand | 641-642 | 2 | 13 |
| β-strand | 645-646 | 2 | 13 |
| α-helix | 650-671 | 22 | |
| α-helix | 674-689 | 16 | |
| β-strand | 702 | 1 | 9 |
| α-helix | 708-737 | 30 | |
Chain C: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 14 |
| α-helix | 15-19 | 5 | |
| β-strand | 26-29 | 4 | 15 |
| β-strand | 37-40 | 4 | 15 |
| α-helix | 52-55 | 4 | |
| β-strand | 64-67 | 4 | 14 |
Chain D: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6 | 1 | 16 |
| α-helix | 7-8 | 2 | |
| β-strand | 13 | 1 | 17 |
| β-strand | 17 | 1 | 18 |
| α-helix | 20-23 | 4 | |
| β-strand | 26-33 | 8 | 16 |
| β-strand | 37-40 | 4 | 19 |
| β-strand | 46-49 | 4 | 19 |
| α-helix | 50 | 1 | |
| β-strand | 52-58 | 7 | 16 |
| α-helix | 61-67 | 7 | |
| α-helix | 68-72 | 5 | |
| α-helix | 73-75 | 3 | |
| β-strand | 80-85 | 6 | 16 |
| β-strand | 91-93 | 3 | 16 |
| β-strand | 114-115 | 2 | 14 |
| α-helix | 125-128 | 4 | |
Chain E: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-9 | 4 | 20 |
| β-strand | 20-26 | 7 | 20 |
| β-strand | 36-39 | 4 | 20 |
| β-strand | 57-60 | 4 | 20 |
| α-helix | 62-64 | 3 | |
| β-strand | 65-69 | 5 | 20 |
Chain F: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-7 | 2 | 21 |
| α-helix | 8-10 | 3 | |
| α-helix | 12-19 | 8 | |
| α-helix | 30-37 | 8 | |
| α-helix | 38-40 | 3 | |
| β-strand | 42-43 | 2 | 21 |
| β-strand | 49-50 | 2 | 21 |
| β-strand | 51 | 1 | 12 |
| α-helix | 60-89 | 30 | |
| β-strand | 100 | 1 | 22 |
| α-helix | 103-110 | 8 | |
| α-helix | 117-124 | 8 | |
| α-helix | 133-135 | 3 | |
Chain I: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 17-21 | 5 | |
| α-helix | 22-34 | 13 | |
Chain J: 2 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-8 | 7 | |
| β-strand | 10 | 1 | 22 |
| α-helix | 11-32 | 22 | |
4 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 | protein | 755 | Thermosynechococcus elongatus (strain BP-1) | P0A405 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A2 | B | protein | 741 | Thermosynechococcus elongatus (strain BP-1) | P0A407 (AlphaFold model) |
| Photosystem I iron-sulfur center | C | protein | 81 | Thermosynechococcus elongatus (strain BP-1) | P0A415 (AlphaFold model) |
| Photosystem I reaction center subunit II | D | protein | 139 | Thermosynechococcus elongatus (strain BP-1) | P0A420 (AlphaFold model) |
| Photosystem I reaction center subunit IV | E | protein | 76 | Thermosynechococcus elongatus (strain BP-1) | P0A423 |
| Photosystem I reaction center subunit III | F | protein | 141 | Thermosynechococcus elongatus (strain BP-1) | P0A401 |
| Photosystem I reaction center subunit VIII | I | protein | 38 | Thermosynechococcus elongatus (strain BP-1) | P0A427 |
| Photosystem I reaction center subunit IX | J | protein | 41 | Thermosynechococcus elongatus (strain BP-1) | P0A429 |
| Photosystem I reaction center subunit PsaK | K | protein | 83 | Thermosynechococcus elongatus (strain BP-1) | P0A425 |
| Photosystem I reaction center subunit XI | L | protein | 155 | Thermosynechococcus elongatus (strain BP-1) | Q8DGB4 |
| Photosystem I reaction center subunit XII | M | protein | 31 | Thermosynechococcus elongatus (strain BP-1) | P0A403 |
| Photosystem I 4.8K protein | X | protein | 36 | Thermosynechococcus elongatus (strain BP-1) | Q8DKP6 |
Sequence of entity 1 (A), FASTA
>6TRA_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDT
HTSDLEDISRKIFSAHFGHLAVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPI
VGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYCTAIGGLVMAGLMLFAGWFHY
HKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPH
EFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHH
HLAIAVLFIIAGHMYRTNWGIGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINL
AMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWIGGFLVVGGAAHGAIFMVRDY
DPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGI
QLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHH
IHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLF
WMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFAQSAITINGWLRDFLWAQASQ
VIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPR
ALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG
Sequence of entity 2 (B), FASTA
>6TRA_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
MATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLW
VSGSLFHVAWQGNFEQWVQDPVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGV
YHWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPKFRPSLSWFKNAESRLNHHLA
GLFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTA
SHVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHS
IKEMMDAKDFFGTKVEGPFNMPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLP
PYAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVRDYDPAQNKGNVLDRVLQHKE
AIISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDT
LLSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLI
LVKGALDARGSKLMPDKKDFGYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFY
WHWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGTNNLSVWAWMFLFG
HLVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHF
SVGYILTYAAFLIASTAAKFG
Sequence of entity 3 (C), FASTA
>6TRA_3 Photosystem I iron-sulfur center (chains C)
MAHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPT
DFLSIRVYLGAETTRSMGLAY
Sequence of entity 4 (D), FASTA
>6TRA_4 Photosystem I reaction center subunit II (chains D)
MTTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFA
RKEQCLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSI
GQNPNPSQLKFTGKKPYDP
Sequence of entity 5 (E), FASTA
>6TRA_5 Photosystem I reaction center subunit IV (chains E)
MVQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNN
FALHEVQEVAPPKKGK
Sequence of entity 6 (F), FASTA
>6TRA_6 Photosystem I reaction center subunit III (chains F)
DVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFERYSQALCGEDGLPHLVVDGRLSRA
GDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEKEIIIDVPLAIKCMLTGFAWPLAA
LKELASGELTAKDNEITVSPR
Sequence of entity 7 (I), FASTA
>6TRA_7 Photosystem I reaction center subunit VIII (chains I)
MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA
Sequence of entity 8 (J), FASTA
>6TRA_8 Photosystem I reaction center subunit IX (chains J)
MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL
Sequence of entity 9 (K), FASTA
>6TRA_9 Photosystem I reaction center subunit PsaK (chains K)
MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELL
ATTSFGHLLAAGVVSGLQYAGAL
Sequence of entity 10 (L), FASTA
>6TRA_10 Photosystem I reaction center subunit XI (chains L)
MAEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLI
GPWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQ
FTAGFFVGAMGSAFVAFFLLENFLVVDGIMTGLFN
Sequence of entity 11 (M), FASTA
>6TRA_11 Photosystem I reaction center subunit XII (chains M)
MALTDTQVYVALVIALLPAVLAFRLSTELYK
Sequence of entity 12 (X), FASTA
>6TRA_12 Photosystem I 4.8K protein (chains X)
MATKSAKPTYAFRTFWAVLLLAINFLVAAYYFGILK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 1 |
| CA | Calcium ion | Ca | 2 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 5 |
| BCR | Beta-carotene | C40 H56 | 24 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 96 |
| CL0 | Chlorophyll a isomer | C55 H72 Mg N4 O5 | 1 |
Primary citation
Current limits of structural biology: The transient interaction between cytochrome c6 and photosystem I. Koelsch, A., Radon, C., Golub, M. et al. Curr Opin Struct Biol (2020) 2:171-179. DOI 10.1016/j.crstbi.2020.08.003
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…
- 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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