8J6Z: Chlorophyll a-b binding protein 6, chloroplastic

Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2). Determined by electron microscopy at 2.79 Å resolution. Released 15 Nov 2023.

Method
Electron microscopy
Resolution
2.79 Å
Organism
Arabidopsis thaliana
Chains
20
Atoms
43,924
Mol. weight
740.83 kDa
Ligands
CHL, CLA, XAT, LHG
Released
15 Nov 2023

Explore 8J6Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J6Z contains 218 α-helices and 86 β-strands across 20 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: 11 helices, 2 β-strands

ElementResiduesLengthSheet
α-helix52-554
α-helix77-10630
α-helix114-1163
α-helix118-1203
β-strand127-12821
β-strand131-13221
α-helix138-15720
α-helix163-1653
α-helix170-1723
α-helix177-1793
α-helix181-21131
α-helix217-22610
α-helix234-2374
Chain 2: 5 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix84-11633
α-helix137-16024
β-strand16712
β-strand17512
β-strand18013
β-strand18313
α-helix186-1894
α-helix199-23032
α-helix234-24310
Chain 3: 11 helices, 3 β-strands
ElementResiduesLengthSheet
β-strand5914
α-helix62-643
β-strand8815
β-strand9115
α-helix93-11321
α-helix116-1227
α-helix134-1363
α-helix141-1433
α-helix152-17524
α-helix179-1813
α-helix203-2064
α-helix215-24632
α-helix250-25910
α-helix266-2694
Chain 4: 8 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix62-643
α-helix82-843
α-helix86-11934
α-helix139-16224
β-strand16916
β-strand17716
α-helix178-1803
α-helix188-1903
α-helix199-22628
α-helix230-23910
Chain A: 47 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand14-1637
α-helix24-274
β-strand4218
α-helix44-518
α-helix56-594
α-helix63-9432
α-helix98-1014
β-strand111-11339
α-helix121-1244
β-strand127110
β-strand133110
β-strand135-13629
α-helix1371
α-helix141-1477
α-helix153-17927
β-strand181-18337
α-helix1841
α-helix185-1884
α-helix191-1977
α-helix198-2047
α-helix205-2139
α-helix214-2185
α-helix219-2279
α-helix231-2333
α-helix235-2362
α-helix239-2424
α-helix244-2507
α-helix252-2565
α-helix259-2624
α-helix266-2716
α-helix288-30518
β-strand309111
β-strand317111
α-helix319-3246
α-helix338-3414
α-helix346-37025
α-helix381-41232
α-helix422-4287
α-helix431-46232
α-helix465-4673
α-helix479-48911
β-strand492112
β-strand496112
α-helix505-5073
β-strand513-515313
β-strand518-521413
α-helix528-55326
α-helix564-5674
α-helix586-61126
α-helix612-6165
β-strand618-620313
β-strand626-628313
α-helix634-6374
α-helix641-6433
α-helix644-6507
α-helix651-6522
α-helix654-6574
α-helix665-68016
α-helix682-6865
α-helix689-70517
β-strand71318
α-helix716-7183
α-helix719-74830
Chain B: 44 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix10-134
β-strand17114
α-helix19-268
α-helix31-333
α-helix39-7133
α-helix74-796
α-helix81-833
β-strand87-90415
α-helix98-1036
β-strand113-115315
α-helix120-1267
α-helix132-15524
α-helix159-1613
α-helix162-1643
α-helix165-1684
α-helix171-1777
α-helix178-1858
α-helix186-1938
α-helix194-1985
α-helix199-2024
α-helix223-2275
α-helix230-2334
α-helix270-28718
β-strand291116
β-strand299116
α-helix301-3066
α-helix322-3276
α-helix330-35425
α-helix365-39632
α-helix407-4137
α-helix415-44531
α-helix449-4513
β-strand455117
α-helix458-4669
α-helix477-4793
α-helix484-4896
α-helix494-5018
α-helix514-53926
α-helix550-5534
α-helix563-5653
α-helix572-60332
α-helix607-6126
α-helix616-6194
α-helix620-6256
α-helix626-6272
α-helix631-6333
β-strand635-636218
β-strand639-640218
α-helix644-66522
α-helix668-68316
β-strand696114
α-helix699-7013
α-helix702-73332
Chain C: 3 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand4-8519
α-helix16-205
β-strand27-30420
β-strand38-41420
α-helix45-473
α-helix53-575
β-strand65-68419
Chain D: 10 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix64-685
α-helix72-754
β-strand76121
β-strand84122
α-helix86-905
β-strand93-100823
β-strand104-107421
β-strand113-116421
α-helix1171
β-strand119-125723
α-helix128-13710
α-helix138-1425
β-strand146-151623
β-strand157-161523
α-helix175-1773
β-strand180-181219
α-helix185-1873
α-helix188-1903
α-helix191-1944

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Chlorophyll a-b binding protein 6, chloroplastic1protein241Arabidopsis thalianaQ01667 (AlphaFold model)
Photosystem I chlorophyll a/b-binding protein 2, chloroplastic2protein257Arabidopsis thalianaQ9SYW8 (AlphaFold model)
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic3protein273Arabidopsis thalianaQ9SY97 (AlphaFold model)
Chlorophyll a-b binding protein 4, chloroplastic4protein251Arabidopsis thalianaP27521 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A1Aprotein750Arabidopsis thalianaP56766
Photosystem I P700 chlorophyll a apoprotein A2Bprotein734Arabidopsis thalianaP56767
Photosystem I iron-sulfur centerCprotein81Arabidopsis thalianaP62090
Photosystem I reaction center subunit II-2, chloroplasticDprotein204Arabidopsis thalianaQ9SA56
Photosystem I reaction center subunit IV A, chloroplasticEprotein143Arabidopsis thalianaQ9S831
Photosystem I reaction center subunit III, chloroplasticFprotein221Arabidopsis thalianaQ9SHE8
Photosystem I reaction center subunit V, chloroplasticGprotein160Arabidopsis thalianaQ9S7N7
Photosystem I reaction center subunit VI-2, chloroplasticHprotein145Arabidopsis thalianaQ9SUI6

7 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>8J6Z_1 Chlorophyll a-b binding protein 6, chloroplastic (chains 1)
MASNSLMSCGIAAVYPSLLSSSKSKFVSAGVPLPNAGNVGRIRMAAHWMPGEPRPAYLDG
SAPGDFGFDPLGLGEVPANLERYKESELIHCRWAMLAVPGILVPEALGYGNWVKAQEWAA
LPGGQATYLGNPVPWGTLPTILAIEFLAIAFVEHQRSMEKDPEKKKYPGGAFDPLGYSKD
PKKLEELKVKEIKNGRLALLAFVGFCVQQSAYPGTGPLENLATHLADPWHNNIGDIVIPF
N
Sequence of entity 2 (2), FASTA
>8J6Z_2 Photosystem I chlorophyll a/b-binding protein 2, chloroplastic (chains 2)
MASSLCASSAIAAISSPSFLGGKKLRLKKKLTVPAVSRPDASVRAVAADPDRPIWFPGST
PPEWLDGSLPGDFGFDPLGLSSDPDSLKWNVQAEIVHCRWAMLGAAGIFIPEFLTKIGIL
NTPSWYTAGEQEYFTDKTTLFVVELILIGWAEGRRWADIIKPGSVNTDPVFPNNKLTGTD
VGYPGGLWFDPLGWGSGSPAKLKELRTKEIKNGRLAMLAVMGAWFQHIYTGTGPIDNLFA
HLADPGHATIFAAFTPK
Sequence of entity 3 (3), FASTA
>8J6Z_3 Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic (chains 3)
MAAQALVSSSLTSSVQTARQIFGSKPVASASQKKSSFVVKAAATPPVKQGANRPLWFASS
QSLSYLDGSLPGDYGFDPLGLSDPEGTGGFIEPRWLAYGEIINGRFAMLGAAGAIAPEIL
GKAGLIPAETALPWFQTGVIPPAGTYTYWADNYTLFVLEMALMGFAEHRRLQDWYNPGSM
GKQYFLGLEKGLAGSGNPAYPGGPFFNPLGFGKDEKSLKELKLKEVKNGRLAMLAILGYF
IQGLVTGVGPYQNLLDHLADPVNNNVLTSLKFH
Sequence of entity 4 (4), FASTA
>8J6Z_4 Chlorophyll a-b binding protein 4, chloroplastic (chains 4)
MATVTTHASASIFRPCTSKPRFLTGSSGRLNRDLSFTSIGSSAKTSSFKVEAKKGEWLPG
LASPDYLTGSLAGDNGFDPLGLAEDPENLKWFVQAELVNGRWAMLGVAGMLLPEVFTKIG
IINVPEWYDAGKEQYFASSSTLFVIEFILFHYVEIRRWQDIKNPGSVNQDPIFKQYSLPK
GEVGYPGGIFNPLNFAPTQEAKEKELANGRLAMLAFLGFVVQHNVTGKGPFENLLQHLSD
PWHNTIVQTFN
Sequence of entity 5 (A), FASTA
>8J6Z_5 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
MIIRSPEPEVKILVDRDPIKTSFEEWAKPGHFSRTIAKGPDTTTWIWNLHADAHDFDSHT
SDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLSDPTHIGPSAQVVWPIVG
QEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAALMLFAGWFHYHK
AAPKLAWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPKEIPLPHEF
ILNRDLLAQLYPSFAEGATPFFTLNWSKYSEFLTFRGGLDPVTGGLWLTDIAHHHLAIAI
LFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSLNLAMLGSL
TIIVAHHMYSMPPYPYLATDYATQLSLFTHHMWIGGFLIVGAAAHAAIFMVRDYDPTNRY
NDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVF
AQWIQNTHALAPGVTAPGETASTSLTWGGGELVAVGGKVALLPIPLGTADFLVHHIHAFT
IHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNA
ISVVIFHFSWKMQSDVWGSISDQGVVTHITGGNFAQSSITINGWLRDFLWAQASQVIQSY
GSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSII
QGRAVGVTHYLLGGIATTWAFFLARIIAVG
Sequence of entity 6 (B), FASTA
>8J6Z_6 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
MALRFPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEERLYQNIFASHFGQLAIIFLW
TSGNLFHVAWQGNFETWVQDPLHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGV
YQWWYTIGLRTNEDLYTGALFLLFLSALSLIGGWLHLQPKWKPRVSWFKNAESRLNHHLS
GLFGVSSLAWTGHLVHVAIPASRGEYVRWNNFLNVLPHPQGLGPLFTGQWNLYAQNPDSS
SHLFGTSQGSGTAILTLLGGFHPQTQSLWLTDMAHHHLAIAILFLIAGHMYRTNFGIGHS
IKDLLEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAF
IAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNPEQNEDNVLARMLDHKEAIIS
HLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSS
TSGPAFNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALD
ARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHIT
LWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMFLFGHLVWATG
FMFLISWRGYWQELIETLAWAHERTPLANLIRWKDKPVALSIVQARLVGLAHFSVGYIFT
YAAFLIASTSGKFG
Sequence of entity 7 (C), FASTA
>8J6Z_7 Photosystem I iron-sulfur center (chains C)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY
Sequence of entity 8 (D), FASTA
>8J6Z_8 Photosystem I reaction center subunit II-2, chloroplastic (chains D)
MATQAAGIFSPAITTTTSAVKKLHLFSSSHRPKSLSFTKTAIRAEKTESSSAAPAVKEAP
VGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAIMREGP
NLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPGREGVGL
NMRSIGKNVSPIEVKFTGKQSYDL
Sequence of entity 9 (E), FASTA
>8J6Z_9 Photosystem I reaction center subunit IV A, chloroplastic (chains E)
MAMTTASTVFVLPANVTSVAGASSSRSSVSFLPMRNAGSRLVVRAAEDPAPASSSSKDSP
AAAAAPDGATATKPKPPPIGPKRGSKVKILRRESYWFKNVGSVVAVDQDPKTRYPVVVRF
AKVNYANISTNNYALDEVEEVAA
Sequence of entity 10 (F), FASTA
>8J6Z_10 Photosystem I reaction center subunit III, chloroplastic (chains F)
MSLTIPANLVLNPRSNKSLTQSVPKSSARFVCSDDKSSSSTPQSMKAFSAAVALSSILLS
APMPAVADISGLTPCKDSKQFAKREKQQIKKLESSLKLYAPESAPALALNAQIEKTKRRF
DNYGKYGLLCGSDGLPHLIVNGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAISGEKK
PAMKEIIIDVPLASRIIFRGFIWPVAAYREFLNGDLIAKDV
Sequence of entity 11 (G), FASTA
>8J6Z_11 Photosystem I reaction center subunit V, chloroplastic (chains G)
MATSASALLSPTTFSTAISHKNPNSISFHGLRPLRLGGSSSALPKLSTTGRKSSSAVVRA
ELSPSIVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGKTHFEAGDDRAKEYVSLLK
SNDPIGFNIVDVLAWGSIGHIVAYYILATSSNGYDPSFFG
Sequence of entity 12 (H), FASTA
>8J6Z_12 Photosystem I reaction center subunit VI-2, chloroplastic (chains H)
MASFATIAAVQPSAAVKGLGGSSLAGAKLFIKPSRQSFKTKSTRAGAVVAKYGDKSVYFD
LEDLGNTTGQWDVYGSDAPSPYNPLQSKFFETFAAPFTKRGLLLKFLILGGGSLLTYVSA
NSTGDVLPIKRGPQEPPKLGPRGKL

Ligands and cofactors

IDNameFormulaCopies
CHLChlorophyll BC55 H70 Mg N4 O630
CLAChlorophyll aC55 H72 Mg N4 O5168
XAT(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-…C40 H56 O46
LHG1,2-dipalmitoyl-phosphatidyl-glyceroleC38 H75 O10 P9
LUT(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diolC40 H56 O211
BCRBeta-caroteneC40 H5627
LMG1,2-distearoyl-monogalactosyl-diglycerideC45 H86 O102
CL0Chlorophyll a isomerC55 H72 Mg N4 O51
SF4Iron/sulfur clusterFe4 S43
PQNPhylloquinoneC31 H46 O22
DGDDigalactosyl diacyl glycerol (DGDG)C51 H96 O151
NEX(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimeth…C40 H56 O43

Primary citation

Regulatory dynamics of the higher-plant PSI-LHCI supercomplex during state transitions. Wu, J., Chen, S., Wang, C. et al. Mol Plant (2023) 16:1937-1950. DOI 10.1016/j.molp.2023.11.002 · PubMed

Other PDB entries of the same protein (UniProt Q01667 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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