5L8R: Plant photosystem I super-complex
The structure of plant photosystem I super-complex at 2.6 angstrom resolution. Determined by X-ray diffraction at 2.6 Å resolution. Released 15 Mar 2017.
- Method
- X-ray diffraction
- Resolution
- 2.6 Å
- Organism
- Pisum sativum
- Chains
- 16
- Atoms
- 37,583
- Mol. weight
- 564.88 kDa
- Ligands
- LUT, BCR, CLA, CHL
- Released
- 15 Mar 2017
Explore 5L8R in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5L8R contains 176 α-helices and 77 β-strands across 16 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 1: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-48 | 3 | |
| α-helix | 70-99 | 30 | |
| α-helix | 107-112 | 6 | |
| β-strand | 120-121 | 2 | 1 |
| β-strand | 124-125 | 2 | 1 |
| α-helix | 131-150 | 20 | |
| α-helix | 156-159 | 4 | |
| α-helix | 163-165 | 3 | |
| α-helix | 174-204 | 31 | |
| α-helix | 210-219 | 10 | |
| α-helix | 226-230 | 5 | |
Chain 2: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-66 | 3 | |
| α-helix | 72-74 | 3 | |
| α-helix | 96-128 | 33 | |
| α-helix | 137-139 | 3 | |
| α-helix | 149-172 | 24 | |
| β-strand | 192 | 1 | 2 |
| β-strand | 195 | 1 | 2 |
| α-helix | 198-201 | 4 | |
| α-helix | 213-241 | 29 | |
| α-helix | 246-255 | 10 | |
| α-helix | 262-264 | 3 | |
Chain 3: 9 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 61 | 1 | 3 |
| α-helix | 64-67 | 4 | |
| α-helix | 95-124 | 30 | |
| α-helix | 155-177 | 23 | |
| α-helix | 181-183 | 3 | |
| α-helix | 192-194 | 3 | |
| α-helix | 205-208 | 4 | |
| α-helix | 217-247 | 31 | |
| α-helix | 252-258 | 7 | |
| α-helix | 267-270 | 4 | |
Chain 4: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 61-63 | 3 | |
| α-helix | 85-118 | 34 | |
| α-helix | 138-161 | 24 | |
| β-strand | 168 | 1 | 4 |
| β-strand | 176 | 1 | 4 |
| β-strand | 181 | 1 | 5 |
| β-strand | 184 | 1 | 5 |
| α-helix | 187-189 | 3 | |
| α-helix | 200-225 | 26 | |
| α-helix | 229-238 | 10 | |
| α-helix | 245-248 | 4 | |
Chain A: 47 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-24 | 3 | 6 |
| α-helix | 44-46 | 3 | |
| β-strand | 50 | 1 | 7 |
| α-helix | 52-59 | 8 | |
| α-helix | 64-67 | 4 | |
| α-helix | 71-102 | 32 | |
| α-helix | 106-111 | 6 | |
| α-helix | 117-118 | 2 | |
| β-strand | 119-121 | 3 | 8 |
| α-helix | 129-132 | 4 | |
| β-strand | 134-135 | 2 | 9 |
| β-strand | 141-142 | 2 | 9 |
| β-strand | 143-144 | 2 | 8 |
| α-helix | 145 | 1 | |
| α-helix | 149-155 | 7 | |
| α-helix | 161-187 | 27 | |
| β-strand | 189-191 | 3 | 6 |
| α-helix | 192 | 1 | |
| α-helix | 193-197 | 5 | |
| α-helix | 199-204 | 6 | |
| α-helix | 205-212 | 8 | |
| α-helix | 213-221 | 9 | |
| α-helix | 222-226 | 5 | |
| α-helix | 227-234 | 8 | |
| α-helix | 243-244 | 2 | |
| α-helix | 247-250 | 4 | |
| α-helix | 252-258 | 7 | |
| α-helix | 260-263 | 4 | |
| α-helix | 267-270 | 4 | |
| α-helix | 274-279 | 6 | |
| β-strand | 287 | 1 | 10 |
| β-strand | 294 | 1 | 10 |
| α-helix | 296-313 | 18 | |
| β-strand | 317 | 1 | 11 |
| β-strand | 325 | 1 | 11 |
| α-helix | 327-333 | 7 | |
| α-helix | 346-350 | 5 | |
| α-helix | 354-378 | 25 | |
| α-helix | 389-416 | 28 | |
| α-helix | 417-421 | 5 | |
| β-strand | 423 | 1 | 12 |
| β-strand | 427 | 1 | 12 |
| α-helix | 430-437 | 8 | |
| α-helix | 439-453 | 15 | |
| α-helix | 454-458 | 5 | |
| α-helix | 459-469 | 11 | |
| α-helix | 473-475 | 3 | |
| α-helix | 487-498 | 12 | |
| β-strand | 500 | 1 | 13 |
| β-strand | 504 | 1 | 13 |
| β-strand | 521-523 | 3 | 14 |
| β-strand | 526-529 | 4 | 14 |
| α-helix | 536-561 | 26 | |
| α-helix | 572-575 | 4 | |
| α-helix | 594-623 | 30 | |
| β-strand | 626-628 | 3 | 14 |
| β-strand | 634-636 | 3 | 14 |
| α-helix | 642-645 | 4 | |
| α-helix | 649-651 | 3 | |
| α-helix | 652-658 | 7 | |
| α-helix | 659-660 | 2 | |
| α-helix | 662-665 | 4 | |
| α-helix | 673-694 | 22 | |
| α-helix | 697-713 | 17 | |
| β-strand | 721 | 1 | 7 |
| α-helix | 724-726 | 3 | |
| α-helix | 727-757 | 31 | |
Chain B: 45 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-13 | 4 | |
| β-strand | 17 | 1 | 15 |
| α-helix | 19-26 | 8 | |
| α-helix | 31-33 | 3 | |
| α-helix | 39-71 | 33 | |
| α-helix | 74-79 | 6 | |
| β-strand | 87-90 | 4 | 16 |
| α-helix | 98-104 | 7 | |
| β-strand | 113-115 | 3 | 16 |
| α-helix | 116 | 1 | |
| α-helix | 120-127 | 8 | |
| α-helix | 132-155 | 24 | |
| α-helix | 163-164 | 2 | |
| α-helix | 165-168 | 4 | |
| α-helix | 171-177 | 7 | |
| α-helix | 178-185 | 8 | |
| α-helix | 186-193 | 8 | |
| α-helix | 194-198 | 5 | |
| α-helix | 199-202 | 4 | |
| α-helix | 224-227 | 4 | |
| α-helix | 230-234 | 5 | |
| α-helix | 270-287 | 18 | |
| β-strand | 291 | 1 | 17 |
| β-strand | 299 | 1 | 17 |
| α-helix | 301-307 | 7 | |
| α-helix | 311-313 | 3 | |
| α-helix | 322-327 | 6 | |
| α-helix | 330-354 | 25 | |
| α-helix | 365-392 | 28 | |
| α-helix | 393-397 | 5 | |
| α-helix | 407-413 | 7 | |
| α-helix | 415-445 | 31 | |
| α-helix | 449-451 | 3 | |
| β-strand | 455 | 1 | 18 |
| α-helix | 458-466 | 9 | |
| β-strand | 477 | 1 | 19 |
| β-strand | 480 | 1 | 19 |
| α-helix | 484-489 | 6 | |
| α-helix | 494-501 | 8 | |
| α-helix | 514-539 | 26 | |
| α-helix | 550-553 | 4 | |
| α-helix | 563-565 | 3 | |
| α-helix | 572-602 | 31 | |
| α-helix | 606-612 | 7 | |
| α-helix | 616-619 | 4 | |
| α-helix | 620-625 | 6 | |
| α-helix | 626-627 | 2 | |
| α-helix | 629-632 | 4 | |
| β-strand | 635-636 | 2 | 20 |
| β-strand | 639-640 | 2 | 20 |
| α-helix | 644-665 | 22 | |
| α-helix | 668-683 | 16 | |
| α-helix | 688-690 | 3 | |
| β-strand | 696 | 1 | 15 |
| α-helix | 699-701 | 3 | |
| α-helix | 702-732 | 31 | |
Chain C: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 21 |
| α-helix | 16-20 | 5 | |
| β-strand | 27-30 | 4 | 22 |
| β-strand | 38-41 | 4 | 22 |
| α-helix | 45-47 | 3 | |
| α-helix | 53-57 | 5 | |
| β-strand | 65-68 | 4 | 21 |
Chain D: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-75 | 4 | |
| β-strand | 83 | 1 | 23 |
| β-strand | 91 | 1 | 24 |
| α-helix | 93-97 | 5 | |
| β-strand | 100-107 | 8 | 25 |
| β-strand | 111-114 | 4 | 23 |
| β-strand | 120-123 | 4 | 23 |
| α-helix | 124 | 1 | |
| β-strand | 126-132 | 7 | 25 |
| α-helix | 135-147 | 13 | |
| β-strand | 153-158 | 6 | 25 |
| β-strand | 164-168 | 5 | 25 |
| α-helix | 182-184 | 3 | |
| β-strand | 187-188 | 2 | 21 |
| α-helix | 192-194 | 3 | |
| α-helix | 195-197 | 3 | |
| α-helix | 198-201 | 4 | |
8 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 |
|---|
| Lhca1 | 1 | protein | 193 | Pisum sativum | E1C9L2 (AlphaFold model) |
| Chlorophyll a-b binding protein, chloroplastic | 2 | protein | 269 | Pisum sativum | Q41038 (AlphaFold model) |
| Chlorophyll a-b binding protein 3, chloroplastic | 3 | protein | 275 | Pisum sativum | Q32904 (AlphaFold model) |
| Chlorophyll a-b binding protein P4, chloroplastic | 4 | protein | 198 | Pisum sativum | Q9SQL2 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A1 | A | protein | 758 | Pisum sativum | P05310 |
| Photosystem I P700 chlorophyll a apoprotein A2 | B | protein | 734 | Pisum sativum | A0A0F6NGI2 |
| Photosystem I iron-sulfur center | C | protein | 81 | Pisum sativum | P10793 |
| PsaD | D | protein | 143 | Pisum sativum | E1C9K8 |
| Putative uncharacterized protein | E | protein | 66 | Pisum sativum | E1C9K6 |
| Photosystem I reaction center subunit III | F | protein | 154 | Pisum sativum | A0A0M3KL12 |
| PsaG | G | protein | 97 | Pisum sativum | Q9S7N7 |
| Photosystem I reaction center subunit VI | H | protein | 88 | Pisum sativum | A0A0M3KL10 |
4 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>5L8R_1 Lhca1 (chains 1)
DWMPGQPRPSYLDGSAPGDFGFDPLRLGEVPENLERFKESELIHCRWAMLAVPGILVPEA
LGLGNWVKAQEWAALPGGQATYLGNPVPWGTLPTILVIEFLSIAFVEHQRSMEKDPEKKK
YPGGAFDPLGYSKDPKKFHEYKIKEVKNGRLALLAFVGICVQQSAYPGTGPLENLATHLA
DPWHNTIGNVLIP
Sequence of entity 2 (2), FASTA
>5L8R_2 Chlorophyll a-b binding protein, chloroplastic (chains 2)
MASACASSAIAAVAISTPSSQKNGSPSGTSKAFLGRKLKVNSSTASPSRVRSTSTVCTVA
EPDRPLWFPGSTPPPWLDGSLPGDFGFDPLGLGSDPESLRWNVQAELVHSRWAMLGAAGI
FIPEFLTKLGILNTPSWYTAGEQEYFTDTTTLFIVELVFIGWAEGRRWADILNPGCVNTD
PIFPNNKLTGTDVGYPGGLWFDPLGWGSASPQKLKELRTKEIKNGRLAMLAVMGAWFQHI
YTGTGPIDNLFAHLADPGHATIFAAFTPK
Sequence of entity 3 (3), FASTA
>5L8R_3 Chlorophyll a-b binding protein 3, chloroplastic (chains 3)
MATQALVSSSSLTFAAEAVRQSFRARSLPSSVGCSRKGLVRAAATPPVKQGGVDRPLWFA
SKQSLSYLDGSLPGDYGFDPLGLSDPEGTGGFIEPRWLAYGEVINGRFAMLGAVGAIAPE
YLGKVGLIPQETALAWFQTGVIPPAGTYNYWADNYTLFVLEMALMGFAEHRRFQDWAKPG
SMGKQYFLGLEKGFGGSGNPAYPGGPFFNPLGFGKDEKSLKELKLKEVKNGRLAMLAILG
YFIQGLVTGVGPYQNLLDHVADPVNNNVLTSLKFH
Sequence of entity 4 (4), FASTA
>5L8R_4 Chlorophyll a-b binding protein P4, chloroplastic (chains 4)
KKGEWLPGLASPGYLTGSLPGDNGFDPLGLAEDPENLKWFVQAELVNGRWAMLGVAGMLL
PEVFTSIGIINVPKWYDAGKEEYFASSSTLFVIEFILFHYVEIRRWQDIKNPGSVNQDPI
FKQYSLPAGEVGYPGGIFNPLNFAPTLEAKEKEIANGRLAMLAFLGFIIQHNVTGKGPFD
NLLQHISDPWHNTIVQTL
Sequence of entity 5 (A), FASTA
>5L8R_5 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
MIIRSPEPKVQILADPEVKILVDRDPIKTSFEQWAKPGHFSRTIAKGPDTTTWIWNLHAD
AHDFDSHTSDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLNDPTHIRPSA
QVVWPIVGQEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAALMLF
AGWFHYHKAAPKLVWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPK
EIPLPHEFILNRDLLAQLYPSFAEGATPFFTLNWSKYADFLTFRGGLDPLTGGLWLTDIA
HHHLAIAILFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSI
NLAMLGSLTIIVAHHMYAMPPYPYLATDYGTQLSLFTHHMWIGGFLIVGAAAHAAIFMVR
DYDPTTRYNDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDT
AIQLQPVFAQWIQNTHALAPGTTAPGATTSTSLTWGGGDLVSVGGKVALLPIPLGTADFL
VHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFL
GLFWMYNAISVVIFHFSWKMQSDVWGSINDQGVVTHITGGNFAQSSITINGWLRDFLWAQ
ASQVIQSYGSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAT
QPRALSIVQGRAVGVTHYLLGGIATTWAFFLARIIAVG
Sequence of entity 6 (B), FASTA
>5L8R_6 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
MALRFPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEGRLYQNIFASHFGQLAIIFLW
TSGNLFHVAWQGNFEAWVQDPLHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGV
YQWWYTIGLRTNEDLYTGAIFLLFLSFISLLAGWLHLQPKWKPSVSWFKNAESRLNHHLS
GLFGVSSLAWAGHLVHVAIPGSRGEYVRWNNFLSVLPHPQGLGPLFTGQWNLYAQNPDSS
NHLFSTSQGAGTAILTLLGGFHPQTQSLWLTDMAHHHLAIAILFLIGGHMYRTNFGIGHS
IKYILEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAF
IAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNPEQNADNVLARMLEHKEAIIS
HLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSS
TNSPALNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALD
ARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHIT
LWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMFLFGHLVWATG
FMFLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVALSIVQARLVGLVHFSVGYIFT
YAAFLIASTSGKFG
Sequence of entity 7 (C), FASTA
>5L8R_7 Photosystem I iron-sulfur center (chains C)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY
Sequence of entity 8 (D), FASTA
>5L8R_8 PsaD (chains D)
GFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPN
LLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGVN
FRSIGKNVSPIEVKFTGKQPYDL
Sequence of entity 9 (E), FASTA
>5L8R_9 Putative uncharacterized protein (chains E)
PPIGPKRGAKVKILRQESYWYKGTGSVVAVDQDPNTRYPVVVRFNKVNYANVSTNNYALD
EVEEVK
Sequence of entity 10 (F), FASTA
>5L8R_10 Photosystem I reaction center subunit III (chains F)
DIAGLTPCKDSKQFAKREKQSIKKLESSLKLYAPDSAPALAINATIEKTKRRFDNYGKQG
LLCGADGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDDKKPTQKEII
IDVPLATRLVFRGFSWPIAAYRELLNGELVAKDV
Sequence of entity 11 (G), FASTA
>5L8R_11 PsaG (chains G)
LNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDTRAKEYVSLLKS
NDPVGFNIVDVLAWGSIGHIVAYYILATSSNGYDPKF
Sequence of entity 12 (H), FASTA
>5L8R_12 Photosystem I reaction center subunit VI (chains H)
VYFDLEDLGNTTGQWDLYGSDAPSPYNSLQSKFFETFAAPFTKRGLLLKFLILGGGSTLA
YFSATASGDILPIKKGPQLPPQLGPRLG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| LUT | (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | C40 H56 O2 | 7 |
| BCR | Beta-carotene | C40 H56 | 27 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 142 |
| CHL | Chlorophyll B | C55 H70 Mg N4 O6 | 13 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 7 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 20 |
| XAT | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-… | C40 H56 O4 | 2 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 10 |
| CA | Calcium ion | Ca | 2 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 5 |
| CL0 | Chlorophyll a isomer | C55 H72 Mg N4 O5 | 1 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| ZEX | (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylc… | C40 H56 O2 | 1 |
Primary citation
Structure of the plant photosystem I supercomplex at 2.6 angstrom resolution. Mazor, Y., Borovikova, A., Caspy, I. et al. Nat Plants (2017) 3:17014-17014. DOI 10.1038/nplants.2017.14 · PubMed
Other PDB entries of the same protein (UniProt E1C9L2 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4Y28 2.8 Å, The structure of plant photosystem I super-complex at 2.8 angstrom resolution.
- 4RKU 3.0 Å, Crystal structure of plant Photosystem I at 3 Angstrom resolution
- 3LW5 3.3 Å, Improved model of plant photosystem I
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