6YAC: Plant PSI-ferredoxin supercomplex

Plant PSI-ferredoxin supercomplex. Determined by electron microscopy at 2.5 Å resolution. Released 30 Sept 2020.

Method
Electron microscopy
Resolution
2.5 Å
Organism
Pisum sativum
Chains
17
Atoms
38,469
Mol. weight
562.54 kDa
Ligands
LMG, CA, DGD, FES
Released
30 Sept 2020

Explore 6YAC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YAC contains 173 α-helices and 83 β-strands across 17 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: 8 helices, 2 β-strands

ElementResiduesLengthSheet
α-helix46-483
α-helix70-9930
α-helix107-1093
α-helix111-1133
β-strand120130
β-strand125130
α-helix131-15020
α-helix176-20429
α-helix210-2189
α-helix227-2304
Chain 2: 6 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix96-12833
α-helix139-1413
α-helix150-17223
β-strand192131
β-strand195131
α-helix198-2014
α-helix214-24128
α-helix246-25510
Chain 3: 9 helices, 1 β-strand
ElementResiduesLengthSheet
β-strand61128
α-helix64-674
α-helix95-11521
α-helix118-1225
α-helix130-1323
α-helix143-1453
α-helix156-17722
α-helix217-24731
α-helix252-26110
α-helix268-2725
Chain 4: 9 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix61-633
α-helix85-11733
α-helix126-1294
α-helix138-16124
β-strand181132
β-strand184132
α-helix187-1893
α-helix198-22427
α-helix229-2379
α-helix240-2423
α-helix245-2484
Chain A: 43 helices, 20 β-strands
ElementResiduesLengthSheet
β-strand22-2431
α-helix42-454
β-strand5012
α-helix52-598
α-helix64-674
α-helix71-10232
α-helix106-1116
α-helix117-1182
β-strand11913
α-helix129-1324
β-strand134-13524
β-strand141-14224
β-strand14413
α-helix149-1568
α-helix161-18727
β-strand189-19131
α-helix193-1964
α-helix199-2057
α-helix206-2127
α-helix213-2219
α-helix222-2265
α-helix227-2348
α-helix243-2442
α-helix245-2506
α-helix253-2586
α-helix260-2634
α-helix267-2715
α-helix274-2774
β-strand28715
β-strand29415
α-helix296-31318
β-strand31716
β-strand32516
α-helix327-3337
α-helix354-37825
α-helix389-42032
β-strand42317
β-strand42717
α-helix430-4378
α-helix439-45517
α-helix458-46912
α-helix473-4753
α-helix487-49812
β-strand50018
β-strand50418
β-strand521-52339
β-strand526-52949
α-helix531-5344
α-helix536-56126
α-helix572-5754
α-helix594-62330
β-strand626-62839
β-strand634-63639
α-helix642-6454
α-helix649-6524
α-helix653-6586
α-helix659-6602
α-helix664-6663
α-helix673-69422
α-helix697-71216
β-strand72112
α-helix724-7263
α-helix727-75630
Chain B: 44 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix10-134
β-strand17110
α-helix19-257
α-helix31-333
α-helix39-7133
α-helix74-796
α-helix85-862
β-strand87-90411
α-helix98-1036
β-strand113-115311
α-helix120-1278
α-helix132-15524
α-helix162-1643
α-helix171-1777
α-helix178-1858
α-helix186-1938
α-helix194-1985
α-helix199-2013
α-helix212-2143
α-helix223-2275
α-helix230-2345
α-helix237-2393
β-strand261112
β-strand268112
α-helix270-28718
β-strand291113
β-strand299113
α-helix301-3077
α-helix322-3287
α-helix330-35425
α-helix365-39632
α-helix401-4033
α-helix407-4137
α-helix415-44531
α-helix449-4513
β-strand455114
α-helix458-4669
α-helix484-4896
α-helix494-5018
α-helix514-53926
α-helix550-5534
α-helix563-5653
α-helix572-60231
α-helix606-6127
α-helix616-6183
α-helix619-6257
α-helix626-6283
α-helix629-6324
β-strand635-636215
β-strand639-640215
α-helix644-66522
α-helix668-68316
β-strand696110
α-helix699-7013
α-helix702-73231
Chain C: 4 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand4-8516
α-helix16-205
β-strand27-30417
β-strand38-41417
α-helix45-473
α-helix55-573
β-strand65-68416
α-helix74-774
Chain D: 8 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix71-755
β-strand83118
β-strand87119
β-strand91120
α-helix93-975
β-strand100-105621
β-strand111-114418
β-strand120-123418
α-helix1241
β-strand128-132521
α-helix135-14713
β-strand154-158521
β-strand166-168321
β-strand187-188216
α-helix192-1943
α-helix195-1973
α-helix198-2003
α-helix208-2103

9 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Photosystem I P700 chlorophyll a apoprotein A1Aprotein743Pisum sativumA0A0F6NFW5 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A2Bprotein733Pisum sativumA0A0F6NGI2 (AlphaFold model)
Photosystem I iron-sulfur centerCprotein80Pisum sativumP10793 (AlphaFold model)
PsaDDprotein143Pisum sativumE1C9K8 (AlphaFold model)
PsaEEprotein66Pisum sativumE1C9K6
PsaFFprotein154Pisum sativumA0A0M3KL12
PsaGGprotein97Pisum sativum
PsaHHprotein88Pisum sativumA0A0M3KL10
Photosystem I reaction center subunit VIIIIprotein31Pisum sativumP17227
Photosystem I reaction center subunit IXJprotein42Pisum sativumD5MAL3
Photosystem I reaction center subunit X psaKKprotein81Pisum sativumE1C9L3
PsaLLprotein157Pisum sativumE1C9L1

5 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>6YAC_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
>6YAC_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
>6YAC_3 Photosystem I iron-sulfur center (chains C)
SHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPTD
FLSVRVYLWHETTRSMGLAY
Sequence of entity 4 (D), FASTA
>6YAC_4 PsaD (chains D)
GFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPN
LLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGVN
FRSIGKNVSPIEVKFTGKQPYDL
Sequence of entity 5 (E), FASTA
>6YAC_5 PsaE (chains E)
PPIGPKRGAKVKILRQESYWYKGTGSVVAVDQDPNTRYPVVVRFNKVNYANVSTNNYALD
EVEEVK
Sequence of entity 6 (F), FASTA
>6YAC_6 PsaF (chains F)
DIAGLTPCKDSKQFAKREKQSIKKLESSLKLYAPDSAPALAINATIEKTKRRFDNYGKQG
LLCGADGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDDKKPTQKEII
IDVPLATGLVFRGFSWPIAAYRELLNGELVAKDV
Sequence of entity 7 (G), FASTA
>6YAC_7 PsaG (chains G)
LNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDTRAKEYVSLLKS
NDPVGFNIVDVLAWGSIGHIVAYYILATSSNGYDPKF
Sequence of entity 8 (H), FASTA
>6YAC_8 PsaH (chains H)
VYFDLEDLGNTTGQWDLYGSDAPSPYNSLQSKFFETFAAPFTKRGLLLKFLILGGGSTLA
YFSATASGDILPIKKGPQLPPQLGPRLG
Sequence of entity 9 (I), FASTA
>6YAC_9 Photosystem I reaction center subunit VIII (chains I)
INLPSLFVPLVGLLFPAVAMASLFLHVEKRL
Sequence of entity 10 (J), FASTA
>6YAC_10 Photosystem I reaction center subunit IX (chains J)
MRDLKTYLSVAPVASTLWFAALAGLLIEINRFFPDALTFPFF
Sequence of entity 11 (K), FASTA
>6YAC_11 Photosystem I reaction center subunit X psaK (chains K)
FIGSPTNLIMVTSTSLMLFAGRFGLAPSANRKATAGLKLEARDSGLQTGDPAGFTLADTL
ACGVVGHIIGVGVVLGLKNIG
Sequence of entity 12 (L), FASTA
>6YAC_12 PsaL (chains L)
YQVVQPINGDPFIGSLETPVTSSPLVAWYLSNLPGYRTAVNPLLRGIEVGLAHGFLLVGP
FVKAGPLRNTEIAGQAGSLAAGGLVVILSICLTIYGISSFNEGDPSTAPSLTLTGRKKQP
DQLQTADGWAKFTGGFFFGGISGVIWAFFLLYVLDLP

Ligands and cofactors

IDNameFormulaCopies
LMG1,2-distearoyl-monogalactosyl-diglycerideC45 H86 O1019
CACalcium ionCa2
DGDDigalactosyl diacyl glycerol (DGDG)C51 H96 O158
FESFE2/S2 (inorganic) clusterFe2 S21
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 O21
XAT(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-…C40 H56 O42
CHLChlorophyll BC55 H70 Mg N4 O615
LUT(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diolC40 H56 O27
LMTDodecyl-beta-D-maltosideC24 H46 O116
LHG1,2-dipalmitoyl-phosphatidyl-glyceroleC38 H75 O10 P8
BCRBeta-caroteneC40 H5627
SF4Iron/sulfur clusterFe4 S43
PQNPhylloquinoneC31 H46 O22
CLAChlorophyll aC55 H72 Mg N4 O5141
CL0Chlorophyll a isomerC55 H72 Mg N4 O51

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:

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