7M76: Photosystem I P700 chlorophyll a apoprotein A1
Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two phylloquinones in Photosystem I. Determined by X-ray diffraction at 3.0 Å resolution. Released 24 Nov 2021.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organism
- Thermosynechococcus elongatus (strain BP-1)
- Chains
- 12
- Atoms
- 24,413
- Mol. weight
- 364.41 kDa
- Ligands
- LMT, DGD, CA, SF4
- Released
- 24 Nov 2021
Explore 7M76 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7M76 contains 122 α-helices and 60 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: 42 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-17 | 2 | 1 |
| α-helix | 36-39 | 4 | |
| β-strand | 44 | 1 | 2 |
| α-helix | 46-54 | 9 | |
| α-helix | 66-95 | 30 | |
| α-helix | 100-105 | 6 | |
| β-strand | 114 | 1 | 3 |
| α-helix | 123-126 | 4 | |
| β-strand | 128-129 | 2 | 4 |
| β-strand | 135-136 | 2 | 4 |
| β-strand | 137 | 1 | 3 |
| α-helix | 138-139 | 2 | |
| α-helix | 143-150 | 8 | |
| α-helix | 157-181 | 25 | |
| β-strand | 184-185 | 2 | 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 | 221-226 | 6 | |
| α-helix | 227-229 | 3 | |
| α-helix | 241-244 | 4 | |
| α-helix | 246-250 | 5 | |
| α-helix | 273-275 | 3 | |
| β-strand | 285-286 | 2 | 5 |
| β-strand | 291-292 | 2 | 5 |
| α-helix | 294-312 | 19 | |
| β-strand | 315 | 1 | 6 |
| β-strand | 323 | 1 | 6 |
| α-helix | 325-331 | 7 | |
| α-helix | 344-350 | 7 | |
| α-helix | 352-374 | 23 | |
| α-helix | 387-418 | 32 | |
| α-helix | 422-424 | 3 | |
| α-helix | 429-434 | 6 | |
| α-helix | 437-468 | 32 | |
| α-helix | 471-473 | 3 | |
| α-helix | 485-500 | 16 | |
| β-strand | 502 | 1 | 7 |
| α-helix | 511-513 | 3 | |
| β-strand | 518-519 | 2 | 8 |
| β-strand | 525-526 | 2 | 8 |
| α-helix | 533-558 | 26 | |
| α-helix | 569-572 | 4 | |
| α-helix | 582-584 | 3 | |
| α-helix | 591-619 | 29 | |
| β-strand | 623-625 | 3 | 9 |
| β-strand | 631-633 | 3 | 9 |
| α-helix | 639-642 | 4 | |
| α-helix | 646-649 | 4 | |
| α-helix | 650-655 | 6 | |
| 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 | 721-723 | 3 | |
| α-helix | 724-754 | 31 | |
Chain B: 43 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-12 | 4 | |
| β-strand | 16 | 1 | 10 |
| α-helix | 18-25 | 8 | |
| α-helix | 30-32 | 3 | |
| α-helix | 38-70 | 33 | |
| α-helix | 84-85 | 2 | |
| β-strand | 88-89 | 2 | 11 |
| α-helix | 97-103 | 7 | |
| β-strand | 112-113 | 2 | 11 |
| α-helix | 119-125 | 7 | |
| α-helix | 131-154 | 24 | |
| 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 | 198-201 | 4 | |
| α-helix | 223-226 | 4 | |
| β-strand | 260 | 1 | 12 |
| β-strand | 267 | 1 | 12 |
| α-helix | 269-286 | 18 | |
| β-strand | 290 | 1 | 13 |
| β-strand | 298 | 1 | 13 |
| α-helix | 300-305 | 6 | |
| β-strand | 308 | 1 | 14 |
| β-strand | 313 | 1 | 14 |
| α-helix | 317-319 | 3 | |
| α-helix | 325-331 | 7 | |
| α-helix | 333-357 | 25 | |
| α-helix | 364-366 | 3 | |
| α-helix | 368-395 | 28 | |
| α-helix | 396-400 | 5 | |
| α-helix | 410-416 | 7 | |
| α-helix | 418-448 | 31 | |
| α-helix | 452-454 | 3 | |
| β-strand | 457-458 | 2 | 15 |
| α-helix | 461-470 | 10 | |
| α-helix | 473-475 | 3 | |
| α-helix | 487-490 | 4 | |
| α-helix | 500-508 | 9 | |
| α-helix | 520-545 | 26 | |
| α-helix | 556-558 | 3 | |
| β-strand | 569 | 1 | 16 |
| α-helix | 578-608 | 31 | |
| α-helix | 612-618 | 7 | |
| 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 | 17 |
| β-strand | 645-646 | 2 | 17 |
| α-helix | 650-671 | 22 | |
| α-helix | 674-689 | 16 | |
| β-strand | 702 | 1 | 10 |
| α-helix | 705-707 | 3 | |
| α-helix | 708-737 | 30 | |
Chain C: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 18 |
| α-helix | 15-19 | 5 | |
| β-strand | 26-29 | 4 | 19 |
| β-strand | 37-40 | 4 | 19 |
| α-helix | 44-46 | 3 | |
| α-helix | 52-56 | 5 | |
| β-strand | 64-67 | 4 | 18 |
| α-helix | 74-76 | 3 | |
Chain D: 9 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6 | 1 | 20 |
| α-helix | 7-8 | 2 | |
| β-strand | 9 | 1 | 21 |
| β-strand | 13 | 1 | 22 |
| β-strand | 17 | 1 | 23 |
| α-helix | 19-23 | 5 | |
| β-strand | 26-33 | 8 | 20 |
| β-strand | 38-41 | 4 | 21 |
| β-strand | 45-48 | 4 | 21 |
| α-helix | 49-50 | 2 | |
| β-strand | 52-58 | 7 | 20 |
| α-helix | 61-67 | 7 | |
| α-helix | 68-72 | 5 | |
| α-helix | 73-75 | 3 | |
| β-strand | 81-85 | 5 | 20 |
| β-strand | 91-93 | 3 | 20 |
| α-helix | 109-111 | 3 | |
| β-strand | 114-115 | 2 | 18 |
| α-helix | 119-121 | 3 | |
| α-helix | 125-128 | 4 | |
Chain E: 0 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-8 | 3 | 24 |
| β-strand | 20-26 | 7 | 24 |
| β-strand | 36-39 | 4 | 24 |
| β-strand | 48 | 1 | 16 |
| β-strand | 57-60 | 4 | 24 |
| β-strand | 67 | 1 | 24 |
Chain F: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-7 | 2 | 25 |
| α-helix | 12-19 | 8 | |
| α-helix | 30-39 | 10 | |
| β-strand | 42-43 | 2 | 25 |
| β-strand | 49 | 1 | 25 |
| β-strand | 50-51 | 2 | 15 |
| α-helix | 64-89 | 26 | |
| α-helix | 94-97 | 4 | |
| α-helix | 103-111 | 9 | |
| α-helix | 112-115 | 4 | |
| α-helix | 116-126 | 11 | |
Chain I: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-16 | 7 | |
| α-helix | 17-21 | 5 | |
| α-helix | 22-35 | 14 | |
Chain J: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-7 | 6 | |
| 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 | 740 | Thermosynechococcus elongatus (strain BP-1) | P0A407 (AlphaFold model) |
| Photosystem I iron-sulfur center | C | protein | 80 | Thermosynechococcus elongatus (strain BP-1) | P0A415 (AlphaFold model) |
| Photosystem I reaction center subunit II | D | protein | 138 | Thermosynechococcus elongatus (strain BP-1) | P0A420 (AlphaFold model) |
| Photosystem I reaction center subunit IV | E | protein | 75 | Thermosynechococcus elongatus (strain BP-1) | P0A423 |
| Photosystem I reaction center subunit III | F | protein | 164 | 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 | 154 | 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 | 35 | Thermosynechococcus elongatus (strain BP-1) | Q8DKP6 |
Sequence of entity 1 (A), FASTA
>7M76_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
>7M76_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
ATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLWV
SGSLFHVAWQGNFEQWVQDPVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGVY
HWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPKFRPSLSWFKNAESRLNHHLAG
LFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTAS
HVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHSI
KEMMDAKDFFGTKVEGPFNMPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLPP
YAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVRDYDPAQNKGNVLDRVLQHKEA
IISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDTL
LSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLIL
VKGALDARGSKLMPDKKDFGYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFYW
HWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGTNNLSVWAWMFLFGH
LVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHFS
VGYILTYAAFLIASTAAKFG
Sequence of entity 3 (C), FASTA
>7M76_3 Photosystem I iron-sulfur center (chains C)
AHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTD
FLSIRVYLGAETTRSMGLAY
Sequence of entity 4 (D), FASTA
>7M76_4 Photosystem I reaction center subunit II (chains D)
TTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFAR
KEQCLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIG
QNPNPSQLKFTGKKPYDP
Sequence of entity 5 (E), FASTA
>7M76_5 Photosystem I reaction center subunit IV (chains E)
VQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNNF
ALHEVQEVAPPKKGK
Sequence of entity 6 (F), FASTA
>7M76_6 Photosystem I reaction center subunit III (chains F)
MRRFLALLLVLTLWLGFTPLASADVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFER
YSQALCGEDGLPHLVVDGRLSRAGDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEK
EIIIDVPLAIKCMLTGFAWPLAALKELASGELTAKDNEITVSPR
Sequence of entity 7 (I), FASTA
>7M76_7 Photosystem I reaction center subunit VIII (chains I)
MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA
Sequence of entity 8 (J), FASTA
>7M76_8 Photosystem I reaction center subunit IX (chains J)
MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL
Sequence of entity 9 (K), FASTA
>7M76_9 Photosystem I reaction center subunit PsaK (chains K)
MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELL
ATTSFGHLLAAGVVSGLQYAGAL
Sequence of entity 10 (L), FASTA
>7M76_10 Photosystem I reaction center subunit XI (chains L)
AEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLIG
PWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQF
TAGFFVGAMGSAFVAFFLLENFLVVDGIMTGLFN
Sequence of entity 11 (M), FASTA
>7M76_11 Photosystem I reaction center subunit XII (chains M)
MALTDTQVYVALVIALLPAVLAFRLSTELYK
Sequence of entity 12 (X), FASTA
>7M76_12 Photosystem I 4.8K protein (chains X)
ATKSAKPTYAFRTFWAVLLLAINFLVAAYYFGILK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 1 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 1 |
| CA | Calcium ion | Ca | 2 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 4 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 4 |
| BCR | Beta-carotene | C40 H56 | 22 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 95 |
| CL0 | Chlorophyll a isomer | C55 H72 Mg N4 O5 | 1 |
Primary citation
Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I. Keable, S.M., Kolsch, A., Simon, P.S. et al. Sci Rep (2021) 11:21787-21787. DOI 10.1038/s41598-021-00236-3 · 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…
- 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…
- 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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