7DKZ: Lhca1
Structure of plant photosystem I-light harvesting complex I supercomplex. Determined by X-ray diffraction at 2.39 Å resolution. Released 31 Mar 2021.
- Method
- X-ray diffraction
- Resolution
- 2.39 Å
- Organism
- Pisum sativum
- Chains
- 16
- Atoms
- 36,093
- Mol. weight
- 543.37 kDa
- Ligands
- CLA, CHL, LUT, XAT
- Released
- 31 Mar 2021
Explore 7DKZ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7DKZ contains 175 α-helices and 73 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: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-44 | 3 | |
| α-helix | 62-64 | 3 | |
| α-helix | 66-95 | 30 | |
| α-helix | 103-105 | 3 | |
| β-strand | 116-117 | 2 | 1 |
| β-strand | 120-121 | 2 | 1 |
| α-helix | 127-146 | 20 | |
| α-helix | 151-155 | 5 | |
| α-helix | 159-161 | 3 | |
| α-helix | 170-200 | 31 | |
| α-helix | 206-215 | 10 | |
| α-helix | 223-226 | 4 | |
Chain 2: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 86-117 | 32 | |
| α-helix | 139-162 | 24 | |
| β-strand | 169 | 1 | 2 |
| β-strand | 177 | 1 | 2 |
| α-helix | 188-191 | 4 | |
| α-helix | 201-231 | 31 | |
| α-helix | 236-245 | 10 | |
Chain 3: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 54 | 1 | 3 |
| β-strand | 72 | 1 | 3 |
| β-strand | 84 | 1 | 4 |
| β-strand | 87 | 1 | 4 |
| α-helix | 89-109 | 21 | |
| α-helix | 112-119 | 8 | |
| α-helix | 130-132 | 3 | |
| α-helix | 148-171 | 24 | |
| α-helix | 184-187 | 4 | |
| α-helix | 199-202 | 4 | |
| α-helix | 211-242 | 32 | |
| α-helix | 246-255 | 10 | |
Chain 4: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 85-118 | 34 | |
| α-helix | 138-161 | 24 | |
| β-strand | 168 | 1 | 5 |
| β-strand | 176 | 1 | 5 |
| α-helix | 177-178 | 2 | |
| α-helix | 187-189 | 3 | |
| α-helix | 198-225 | 28 | |
| α-helix | 229-238 | 10 | |
Chain A: 48 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-24 | 3 | 6 |
| α-helix | 42-45 | 4 | |
| 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 | 134-137 | 4 | 9 |
| β-strand | 140-142 | 3 | 9 |
| β-strand | 143-144 | 2 | 8 |
| α-helix | 145 | 1 | |
| α-helix | 149-155 | 7 | |
| α-helix | 161-183 | 23 | |
| α-helix | 184-188 | 5 | |
| 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 | 227-235 | 9 | |
| α-helix | 239-241 | 3 | |
| α-helix | 243-244 | 2 | |
| α-helix | 247-250 | 4 | |
| α-helix | 252-258 | 7 | |
| α-helix | 260-264 | 5 | |
| α-helix | 267-270 | 4 | |
| α-helix | 274-277 | 4 | |
| 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 | 327-332 | 6 | |
| α-helix | 346-349 | 4 | |
| α-helix | 354-378 | 25 | |
| α-helix | 389-420 | 32 | |
| α-helix | 430-436 | 7 | |
| α-helix | 439-455 | 17 | |
| α-helix | 458-469 | 12 | |
| α-helix | 473-475 | 3 | |
| β-strand | 477 | 1 | 12 |
| β-strand | 482 | 1 | 12 |
| α-helix | 487-497 | 11 | |
| β-strand | 521-523 | 3 | 13 |
| β-strand | 526-529 | 4 | 13 |
| α-helix | 536-561 | 26 | |
| α-helix | 572-575 | 4 | |
| α-helix | 594-619 | 26 | |
| α-helix | 620-624 | 5 | |
| β-strand | 626-627 | 2 | 13 |
| β-strand | 635-636 | 2 | 13 |
| 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: 47 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-13 | 4 | |
| β-strand | 17 | 1 | 14 |
| α-helix | 19-27 | 9 | |
| α-helix | 31-33 | 3 | |
| α-helix | 39-71 | 33 | |
| α-helix | 74-79 | 6 | |
| α-helix | 85-86 | 2 | |
| β-strand | 87-90 | 4 | 15 |
| α-helix | 98-103 | 6 | |
| β-strand | 113-115 | 3 | 15 |
| α-helix | 116 | 1 | |
| α-helix | 120-126 | 7 | |
| α-helix | 132-155 | 24 | |
| α-helix | 159-161 | 3 | |
| 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 | 199-202 | 4 | |
| α-helix | 223-227 | 5 | |
| α-helix | 230-234 | 5 | |
| α-helix | 237-239 | 3 | |
| β-strand | 261-262 | 2 | 16 |
| β-strand | 267-268 | 2 | 16 |
| α-helix | 270-287 | 18 | |
| β-strand | 291 | 1 | 17 |
| β-strand | 299 | 1 | 17 |
| α-helix | 301-307 | 7 | |
| 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 | |
| α-helix | 477-479 | 3 | |
| 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 | 607-612 | 6 | |
| α-helix | 616-618 | 3 | |
| α-helix | 619-625 | 7 | |
| α-helix | 626-627 | 2 | |
| α-helix | 631-633 | 3 | |
| β-strand | 635-636 | 2 | 19 |
| β-strand | 639-640 | 2 | 19 |
| α-helix | 644-665 | 22 | |
| α-helix | 668-683 | 16 | |
| β-strand | 696 | 1 | 14 |
| α-helix | 699-701 | 3 | |
| α-helix | 702-730 | 29 | |
Chain C: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-8 | 5 | 20 |
| α-helix | 16-20 | 5 | |
| β-strand | 27-30 | 4 | 21 |
| β-strand | 38-41 | 4 | 21 |
| α-helix | 45-47 | 3 | |
| α-helix | 53-57 | 5 | |
| β-strand | 65-68 | 4 | 20 |
Chain D: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 78-81 | 4 | |
| β-strand | 82 | 1 | 22 |
| β-strand | 90 | 1 | 23 |
| α-helix | 92-96 | 5 | |
| β-strand | 99-106 | 8 | 24 |
| β-strand | 110-113 | 4 | 22 |
| β-strand | 119-122 | 4 | 22 |
| α-helix | 123 | 1 | |
| β-strand | 124-131 | 8 | 24 |
| α-helix | 134-143 | 10 | |
| α-helix | 144-148 | 5 | |
| β-strand | 152-157 | 6 | 24 |
| β-strand | 163-167 | 5 | 24 |
| α-helix | 181-183 | 3 | |
| β-strand | 186-187 | 2 | 20 |
| α-helix | 191-193 | 3 | |
| α-helix | 194-196 | 3 | |
| α-helix | 197-200 | 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 | 195 | Pisum sativum | |
| 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 (AlphaFold model) |
| 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 |
| PsaE | E | protein | 66 | Pisum sativum | E1C9K6 |
| Psi-F | F | protein | 154 | Pisum sativum | A0A0M3KL12 |
| PsaG | G | protein | 97 | Pisum sativum | |
| PsaH | H | protein | 88 | Pisum sativum | A0A0M3KL10 |
4 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>7DKZ_1 Lhca1 (chains 1)
ADWMPGQPRPSYLDGSAPGDFGFDPLRLGEVPENLERFKESELIHCRWAMLAVPGILVPE
ALGLGNWVKAQEWAALPGGQATYLGNPVPWGTLPTILVIEFLSIAFVEHQRSMEKDPEKK
KYPGGAFDPLGYSKDPKKFHEYKIKEVKNGRLALLAFVGICVQQSAYPGTGPLENLATHL
ADPWHNTIGNVLIPA
Sequence of entity 2 (2), FASTA
>7DKZ_2 Chlorophyll a-b binding protein, chloroplastic (chains 2)
MASACASSAIAAVAISTPSSQKNGSPSGTSKAFLGRKLKVNSSTASPSRVRSTSTVCTVA
EPDRPLWFPGSTPPPWLDGSLPGDFGFDPLGLGSDPESLRWNVQAELVHSRWAMLGAAGI
FIPEFLTKLGILNTPSWYTAGEQEYFTDTTTLFIVELVFIGWAEGRRWADILNPGCVNTD
PIFPNNKLTGTDVGYPGGLWFDPLGWGSASPQKLKELRTKEIKNGRLAMLAVMGAWFQHI
YTGTGPIDNLFAHLADPGHATIFAAFTPK
Sequence of entity 3 (3), FASTA
>7DKZ_3 Chlorophyll a-b binding protein 3, chloroplastic (chains 3)
MATQALVSSSSLTFAAEAVRQSFRARSLPSSVGCSRKGLVRAAATPPVKQGGVDRPLWFA
SKQSLSYLDGSLPGDYGFDPLGLSDPEGTGGFIEPRWLAYGEVINGRFAMLGAVGAIAPE
YLGKVGLIPQETALAWFQTGVIPPAGTYNYWADNYTLFVLEMALMGFAEHRRFQDWAKPG
SMGKQYFLGLEKGFGGSGNPAYPGGPFFNPLGFGKDEKSLKELKLKEVKNGRLAMLAILG
YFIQGLVTGVGPYQNLLDHVADPVNNNVLTSLKFH
Sequence of entity 4 (4), FASTA
>7DKZ_4 Chlorophyll a-b binding protein P4, chloroplastic (chains 4)
KKGEWLPGLASPGYLTGSLPGDNGFDPLGLAEDPENLKWFVQAELVNGRWAMLGVAGMLL
PEVFTSIGIINVPKWYDAGKEEYFASSSTLFVIEFILFHYVEIRRWQDIKNPGSVNQDPI
FKQYSLPAGEVGYPGGIFNPLNFAPTLEAKEKEIANGRLAMLAFLGFIIQHNVTGKGPFD
NLLQHISDPWHNTIVQTL
Sequence of entity 5 (A), FASTA
>7DKZ_5 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
MIIRSPEPKVQILADPEVKILVDRDPIKTSFEQWAKPGHFSRTIAKGPDTTTWIWNLHAD
AHDFDSHTSDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLNDPTHIRPSA
QVVWPIVGQEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAALMLF
AGWFHYHKAAPKLVWFQDVESMLNHHLAGLLGLGSLSWAGHQIHVSLPINQFLNAGVDPK
EIPLPHEFILNRDLLAQLYPSFAEGATPFFTLNWSKYADFLTFRGGLDPLTGGLWLTDIA
HHHLAIAILFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSI
NLAMLGSLTIIVAHHMYAMPPYPYLATDYGTQLSLFTHHMWIGGFLIVGAAAHAAIFMVR
DYDPTTRYNDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDT
AIQLQPVFAQWIQNTHALAPGTTAPGATTSTSLTWGGGDLVSVGGKVALLPIPLGTADFL
VHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFL
GLFWMYNAISVVIFHFSWKMQSDVWGSINDQGVVTHITGGNFAQSSITINGWLRDFLWAQ
ASQVIQSYGSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAT
QPRALSIVQGRAVGVTHYLLGGIATTWAFFLARIIAVG
Sequence of entity 6 (B), FASTA
>7DKZ_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
>7DKZ_7 Photosystem I iron-sulfur center (chains C)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY
Sequence of entity 8 (D), FASTA
>7DKZ_8 PsaD (chains D)
GFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPN
LLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGVN
FRSIGKNVSPIEVKFTGKQPYDL
Sequence of entity 9 (E), FASTA
>7DKZ_9 PsaE (chains E)
PPIGPKRGAKVKILRQESYWYKGTGSVVAVDQDPNTRYPVVVRFNKVNYANVSTNNYALD
EVEEVK
Sequence of entity 10 (F), FASTA
>7DKZ_10 PSI-F (chains F)
DIAGLTPCKDSKQFAKREKQSIKKLESSLKLYAPDSAPALAINATIEKTKRRFDNYGKQG
LLCGADGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDDKKPTQKEII
IDVPLATRLVFRGFSWPIAAYRELLNGELVAKDV
Sequence of entity 11 (G), FASTA
>7DKZ_11 PsaG (chains G)
LNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDTRAKEYVSLLKS
NDPVGFNIVDVLAWGSIGHIVAYYILATSSNGYDPKF
Sequence of entity 12 (H), FASTA
>7DKZ_12 PsaH (chains H)
VYFDLEDLGNTTGQWDLYGSDAPSPYNSLQSKFFETFAAPFTKRGLLLKFLILGGGSTLA
YFSATASGDILPIKKGPQLPPQLGPRLG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 140 |
| CHL | Chlorophyll B | C55 H70 Mg N4 O6 | 12 |
| LUT | (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | C40 H56 O2 | 4 |
| XAT | (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-… | C40 H56 O4 | 4 |
| BCR | Beta-carotene | C40 H56 | 26 |
| LHG | 1,2-dipalmitoyl-phosphatidyl-glycerole | C38 H75 O10 P | 7 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 2 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 5 |
| HTG | heptyl 1-thio-beta-D-glucopyranoside | C13 H26 O5 S | 8 |
| DGD | Digalactosyl diacyl glycerol (DGDG) | C51 H96 O15 | 2 |
| PQN | Phylloquinone | C31 H46 O2 | 2 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 3 |
Primary citation
Structure of plant photosystem I-light harvesting complex I supercomplex at 2.4 angstrom resolution. Wang, J., Yu, L.J., Wang, W. et al. J Integr Plant Biol (2021) 63:1367-1381. DOI 10.1111/jipb.13095 · PubMed
Other PDB entries of the same protein (UniProt Q41038 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6YAC 2.5 Å, Plant PSI-ferredoxin supercomplex
- 5L8R 2.6 Å, The structure of plant photosystem I super-complex at 2.6 angstrom resolution.
- 6YEZ 2.7 Å, Plant PSI-ferredoxin-plastocyanin supercomplex
- 6ZOO 2.74 Å, Photosystem I reduced Plastocyanin Complex
- 4XK8 2.8 Å, Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution
- 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
- 6ZXS 3.0 Å, Cold grown Pea Photosystem I
- 2WSC 3.3 Å, Improved Model of Plant Photosystem I
- 3LW5 3.3 Å, Improved model of plant photosystem I
- 2O01 3.4 Å, The Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution
- 2WSF 3.48 Å, Improved Model of Plant Photosystem I
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