6YEZ: Plant PSI-ferredoxin-plastocyanin supercomplex
Plant PSI-ferredoxin-plastocyanin supercomplex. Determined by electron microscopy at 2.7 Å resolution. Released 30 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organism
- Pisum sativum
- Chains
- 18
- Atoms
- 39,217
- Mol. weight
- 573.56 kDa
- Ligands
- CL0, CLA, PQN, BCR
- Released
- 30 Sept 2020
Explore 6YEZ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6YEZ contains 172 α-helices and 87 β-strands across 18 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 | 107-109 | 3 | |
| α-helix | 111-113 | 3 | |
| β-strand | 121 | 1 | 29 |
| β-strand | 124 | 1 | 29 |
| α-helix | 131-150 | 20 | |
| α-helix | 163-165 | 3 | |
| α-helix | 176-204 | 29 | |
| α-helix | 210-219 | 10 | |
| α-helix | 227-230 | 4 | |
Chain 2: 8 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 | 138-141 | 4 | |
| α-helix | 149-171 | 23 | |
| β-strand | 192 | 1 | 30 |
| β-strand | 195 | 1 | 30 |
| α-helix | 198-201 | 4 | |
| α-helix | 213-241 | 29 | |
| α-helix | 246-255 | 10 | |
Chain 3: 8 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 61 | 1 | 25 |
| α-helix | 62-67 | 6 | |
| α-helix | 95-117 | 23 | |
| α-helix | 143-145 | 3 | |
| α-helix | 156-177 | 22 | |
| α-helix | 205-208 | 4 | |
| α-helix | 217-247 | 31 | |
| α-helix | 252-261 | 10 | |
| α-helix | 269-272 | 4 | |
Chain 4: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 61-63 | 3 | |
| α-helix | 85-117 | 33 | |
| α-helix | 138-161 | 24 | |
| β-strand | 181 | 1 | 31 |
| β-strand | 184 | 1 | 31 |
| α-helix | 187-189 | 3 | |
| α-helix | 198-224 | 27 | |
| α-helix | 229-238 | 10 | |
| α-helix | 240-242 | 3 | |
| α-helix | 245-248 | 4 | |
Chain A: 47 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-24 | 3 | 1 |
| α-helix | 32-35 | 4 | |
| α-helix | 42-46 | 5 | |
| β-strand | 50 | 1 | 2 |
| 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 | 1 | 3 |
| α-helix | 129-132 | 4 | |
| β-strand | 134-135 | 2 | 4 |
| β-strand | 141-142 | 2 | 4 |
| α-helix | 143 | 1 | |
| β-strand | 144 | 1 | 3 |
| α-helix | 145 | 1 | |
| α-helix | 149-156 | 8 | |
| α-helix | 161-187 | 27 | |
| β-strand | 189-191 | 3 | 1 |
| α-helix | 193-196 | 4 | |
| α-helix | 200-205 | 6 | |
| α-helix | 206-212 | 7 | |
| α-helix | 213-221 | 9 | |
| α-helix | 222-226 | 5 | |
| α-helix | 227-234 | 8 | |
| α-helix | 239-241 | 3 | |
| α-helix | 243-244 | 2 | |
| α-helix | 245-250 | 6 | |
| α-helix | 253-258 | 6 | |
| α-helix | 260-262 | 3 | |
| α-helix | 267-271 | 5 | |
| α-helix | 274-277 | 4 | |
| α-helix | 296-313 | 18 | |
| β-strand | 317 | 1 | 5 |
| β-strand | 325 | 1 | 5 |
| α-helix | 327-333 | 7 | |
| α-helix | 346-349 | 4 | |
| α-helix | 354-378 | 25 | |
| α-helix | 389-420 | 32 | |
| β-strand | 423 | 1 | 6 |
| β-strand | 427 | 1 | 6 |
| α-helix | 430-437 | 8 | |
| α-helix | 439-455 | 17 | |
| α-helix | 458-469 | 12 | |
| α-helix | 473-475 | 3 | |
| α-helix | 487-497 | 11 | |
| α-helix | 499-502 | 4 | |
| β-strand | 504 | 1 | 7 |
| β-strand | 521-523 | 3 | 8 |
| β-strand | 526-529 | 4 | 8 |
| α-helix | 531-533 | 3 | |
| α-helix | 536-561 | 26 | |
| α-helix | 594-623 | 30 | |
| β-strand | 626-627 | 2 | 8 |
| β-strand | 635-636 | 2 | 8 |
| α-helix | 642-645 | 4 | |
| α-helix | 649-651 | 3 | |
| α-helix | 652-658 | 7 | |
| α-helix | 659-665 | 7 | |
| α-helix | 673-694 | 22 | |
| α-helix | 697-712 | 16 | |
| β-strand | 721 | 1 | 2 |
| α-helix | 724-726 | 3 | |
| α-helix | 727-757 | 31 | |
Chain B: 42 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-13 | 4 | |
| β-strand | 17 | 1 | 9 |
| α-helix | 19-26 | 8 | |
| α-helix | 31-33 | 3 | |
| α-helix | 39-71 | 33 | |
| α-helix | 74-77 | 4 | |
| α-helix | 85-86 | 2 | |
| β-strand | 87-90 | 4 | 10 |
| α-helix | 98-104 | 7 | |
| β-strand | 113-115 | 3 | 10 |
| α-helix | 120-127 | 8 | |
| α-helix | 132-155 | 24 | |
| α-helix | 162-164 | 3 | |
| 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 | 199-201 | 3 | |
| α-helix | 212-214 | 3 | |
| α-helix | 223-227 | 5 | |
| α-helix | 230-234 | 5 | |
| α-helix | 237-239 | 3 | |
| α-helix | 270-287 | 18 | |
| β-strand | 291 | 1 | 11 |
| β-strand | 299 | 1 | 11 |
| α-helix | 301-307 | 7 | |
| α-helix | 322-327 | 6 | |
| α-helix | 330-354 | 25 | |
| α-helix | 365-396 | 32 | |
| α-helix | 407-413 | 7 | |
| α-helix | 415-445 | 31 | |
| α-helix | 449-451 | 3 | |
| β-strand | 455 | 1 | 12 |
| α-helix | 458-466 | 9 | |
| α-helix | 484-488 | 5 | |
| α-helix | 494-501 | 8 | |
| α-helix | 514-539 | 26 | |
| α-helix | 550-553 | 4 | |
| α-helix | 573-601 | 29 | |
| α-helix | 606-612 | 7 | |
| α-helix | 616-618 | 3 | |
| α-helix | 619-625 | 7 | |
| α-helix | 626-628 | 3 | |
| α-helix | 629-632 | 4 | |
| β-strand | 635-636 | 2 | 13 |
| β-strand | 639-640 | 2 | 13 |
| α-helix | 644-665 | 22 | |
| α-helix | 668-683 | 16 | |
| β-strand | 696 | 1 | 9 |
| α-helix | 702-732 | 31 | |
Chain C: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 14 |
| β-strand | 27-30 | 4 | 15 |
| β-strand | 38-41 | 4 | 15 |
| α-helix | 45-47 | 3 | |
| α-helix | 53-57 | 5 | |
| β-strand | 65-68 | 4 | 14 |
Chain D: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-75 | 4 | |
| β-strand | 83 | 1 | 16 |
| β-strand | 87 | 1 | 17 |
| β-strand | 91 | 1 | 18 |
| α-helix | 93-97 | 5 | |
| β-strand | 100-105 | 6 | 19 |
| β-strand | 111-114 | 4 | 16 |
| β-strand | 120-123 | 4 | 16 |
| β-strand | 128-132 | 5 | 19 |
| α-helix | 135-143 | 9 | |
| α-helix | 144-148 | 5 | |
| β-strand | 154-158 | 5 | 19 |
| β-strand | 164-168 | 5 | 19 |
| β-strand | 187-188 | 2 | 14 |
| α-helix | 192-194 | 3 | |
| α-helix | 195-197 | 3 | |
| α-helix | 198-201 | 4 | |
10 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 | 743 | Pisum sativum | A0A0F6NFW5 (AlphaFold model) |
| Photosystem I P700 chlorophyll a apoprotein A2 | B | protein | 733 | Pisum sativum | A0A0F6NGI2 (AlphaFold model) |
| Photosystem I iron-sulfur center | C | protein | 80 | Pisum sativum | P10793 (AlphaFold model) |
| PsaD | D | protein | 143 | Pisum sativum | E1C9K8 (AlphaFold model) |
| PsaE | E | protein | 66 | Pisum sativum | E1C9K6 |
| PsaF | F | protein | 154 | Pisum sativum | A0A0M3KL12 |
| PsaG | G | protein | 97 | Pisum sativum | |
| PsaH | H | protein | 93 | Pisum sativum | A0A0M3KL10 |
| Photosystem I reaction center subunit VIII | I | protein | 31 | Pisum sativum | P17227 |
| PsaJ | J | protein | 42 | Pisum sativum | D5MAL3 |
| Photosystem I reaction center subunit X psaK | K | protein | 81 | Pisum sativum | E1C9L3 |
| PsaL | L | protein | 159 | Pisum sativum | E1C9L1 |
6 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>6YEZ_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
PEVKILVDRDPIKTSFEQWAKPGHFSRTIAKGPDTTTWIWNLHADAHDFDSHTSDLEEIS
RKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLNDPTHIRPSAQVVWPIVGQEILNGD
VGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAALMLFAGWFHYHKAAPKLVW
FQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPKEIPLPHEFILNRDLL
AQLYPSFAEGATPFFTLNWSKYADFLTFRGGLDPLTGGLWLTDIAHHHLAIAILFLIAGH
MYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSINLAMLGSLTIIVAHH
MYAMPPYPYLATDYGTQLSLFTHHMWIGGFLIVGAAAHAAIFMVRDYDPTTRYNDLLDRV
LRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVFAQWIQNT
HALAPGTTAPGATTSTSLTWGGGDLVSVGGKVALLPIPLGTADFLVHHIHAFTIHVTVLI
LLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNAISVVIFH
FSWKMQSDVWGSINDQGVVTHITGGNFAQSSITINGWLRDFLWAQASQVIQSYGSSLSAY
GLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSIVQGRAVGV
THYLLGGIATTWAFFLARIIAVG
Sequence of entity 2 (B), FASTA
>6YEZ_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
ALRFPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEGRLYQNIFASHFGQLAIIFLWT
SGNLFHVAWQGNFEAWVQDPLHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGVY
QWWYTIGLRTNEDLYTGAIFLLFLSFISLLAGWLHLQPKWKPSVSWFKNAESRLNHHLSG
LFGVSSLAWAGHLVHVAIPGSRGEYVRWNNFLSVLPHPQGLGPLFTGQWNLYAQNPDSSN
HLFSTSQGAGTAILTLLGGFHPQTQSLWLTDMAHHHLAIAILFLIGGHMYRTNFGIGHSI
KYILEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAFI
AQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNPEQNADNVLARMLEHKEAIISH
LSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSST
NSPALNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDA
RGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHITL
WQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMFLFGHLVWATGF
MFLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVALSIVQARLVGLVHFSVGYIFTY
AAFLIASTSGKFG
Sequence of entity 3 (C), FASTA
>6YEZ_3 Photosystem I iron-sulfur center (chains C)
SHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPTD
FLSVRVYLWHETTRSMGLAY
Sequence of entity 4 (D), FASTA
>6YEZ_4 PsaD (chains D)
GFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPN
LLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGVN
FRSIGKNVSPIEVKFTGKQPYDL
Sequence of entity 5 (E), FASTA
>6YEZ_5 PsaE (chains E)
PPIGPKRGAKVKILRQESYWYKGTGSVVAVDQDPNTRYPVVVRFNKVNYANVSTNNYALD
EVEEVK
Sequence of entity 6 (F), FASTA
>6YEZ_6 PsaF (chains F)
DIAGLTPCKDSKQFAKREKQSIKKLESSLKLYAPDSAPALAINATIEKTKRRFDNYGKQG
LLCGADGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDDKKPTQKEII
IDVPLATGLVFRGFSWPIAAYRELLNGELVAKDV
Sequence of entity 7 (G), FASTA
>6YEZ_7 PsaG (chains G)
LNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDTRAKEYVSLLKS
NDPVGFNIVDVLAWGSIGHIVAYYILATSSNGYDPKF
Sequence of entity 8 (H), FASTA
>6YEZ_8 PsaH (chains H)
YGDKSVYFDLEDLGNTTGQWDLYGSDAPSPYNSLQSKFFETFAAPFTKRGLLLKFLILGG
GSTLAYFSATASGDILPIKKGPQLPPQLGPRLG
Sequence of entity 9 (I), FASTA
>6YEZ_9 Photosystem I reaction center subunit VIII (chains I)
INLPSLFVPLVGLLFPAVAMASLFLHVEKRL
Sequence of entity 10 (J), FASTA
>6YEZ_10 PsaJ (chains J)
MRDLKTYLSVAPVASTLWFAALAGLLIEINRFFPDALTFPFF
Sequence of entity 11 (K), FASTA
>6YEZ_11 Photosystem I reaction center subunit X psaK (chains K)
FIGSPTNLIMVTSTSLMLFAGRFGLAPSANRKATAGLKLEARDSGLQTGDPAGFTLADTL
ACGVVGHIIGVGVVLGLKNIG
Sequence of entity 12 (L), FASTA
>6YEZ_12 PsaL (chains L)
YQVVQPINGDPFIGSLETPVTSSPLVAWYLSNLPGYRTAVNPLLRGIEVGLAHGFLLVGP
FVKAGPLRNTEIAGQAGSLAAGGLVVILSICLTIYGISSFNEGDPSTAPSLTLTGRKKQP
DQLQTADGWAKFTGGFFFGGISGVTWAFFLLYVLDLPYF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CL0 | Chlorophyll a isomer | C55 H72 Mg N4 O5 | 1 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 141 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| BCR | Beta-carotene | C40 H56 | 27 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 8 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 6 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 19 |
| CA | Calcium ion | Ca | 2 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 7 |
| LUT | (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | C40 H56 O2 | 7 |
| CHL | Chlorophyll B | C55 H70 Mg N4 O6 | 15 |
| XAT | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-… | C40 H56 O4 | 2 |
| 3PH | 1,2-diacyl-glycerol-3-sn-phosphate | C39 H77 O8 P | 1 |
| C7Z | (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},… | C40 H56 O2 | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 1 |
| CU | Copper (II) ion | Cu | 1 |
Primary citation
The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin. Caspy, I., Borovikova-Sheinker, A., Klaiman, D. et al. Nat Plants (2020) 6:1300-1305. DOI 10.1038/s41477-020-00779-9 · PubMed
Other PDB entries of the same protein (UniProt A0A0F6NFW5 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6YAC 2.5 Å, Plant PSI-ferredoxin supercomplex
- 6ZOO 2.74 Å, Photosystem I reduced Plastocyanin Complex
- 6ZXS 3.0 Å, Cold grown Pea Photosystem I
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