5ZF0: Photosystem I P700 chlorophyll a apoprotein A1

X-ray Structure of the Electron Transfer Complex between Ferredoxin and Photosystem I. Determined by X-ray diffraction at 4.2 Å resolution. Released 11 Apr 2018.

Method
X-ray diffraction
Resolution
4.2 Å
Organisms
Thermosynechococcus elongatus BP-1, Thermosynechococcus elongatus
Chains
78
Atoms
148,494
Mol. weight
2223.59 kDa
Ligands
CLA, PQN, BCR, LHG
Released
11 Apr 2018

Explore 5ZF0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZF0 contains 839 α-helices and 411 β-strands across 78 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 A1: 42 helices, 18 β-strands

ElementResiduesLengthSheet
β-strand16-1831
α-helix36-383
β-strand4412
α-helix46-538
α-helix54-563
α-helix58-603
α-helix65-9632
α-helix100-1056
β-strand113-11423
α-helix123-1264
β-strand128-13144
β-strand134-13634
β-strand137-13823
α-helix1391
α-helix143-1508
α-helix155-17723
α-helix178-1825
β-strand183-18531
α-helix187-1904
α-helix193-1986
α-helix199-2079
α-helix208-2158
α-helix216-2205
α-helix221-2299
α-helix241-2444
α-helix246-2516
α-helix272-2754
α-helix294-31118
β-strand31515
β-strand32315
α-helix325-3317
α-helix344-3507
α-helix352-37625
α-helix387-41832
α-helix422-4254
α-helix429-4346
α-helix437-46832
α-helix471-4733
β-strand47516
β-strand48016
α-helix485-49612
β-strand49817
β-strand50217
β-strand518-52038
β-strand523-52648
α-helix533-55826
α-helix569-5724
α-helix591-62030
β-strand623-62538
β-strand631-63338
α-helix639-6424
α-helix646-6483
α-helix649-6557
α-helix656-6572
α-helix659-6624
α-helix670-69122
α-helix694-71017
β-strand71812
α-helix721-7233
α-helix724-75431
Chains A2 and A3: 41 helices, 18 β-strands
ElementResiduesLengthSheet
β-strand16-18376
α-helix36-383
β-strand44177
α-helix46-538
α-helix58-603
α-helix65-9632
α-helix100-1056
β-strand113-114278
α-helix123-1264
β-strand128-131479
β-strand134-136379
β-strand137-138278
α-helix1391
α-helix143-1508
α-helix155-17723
α-helix178-1825
β-strand183-185376
α-helix187-1904
α-helix193-1986
α-helix199-2079
α-helix208-2158
α-helix216-2205
α-helix221-2299
α-helix241-2444
α-helix246-2516
α-helix272-2754
α-helix294-31118
β-strand315180
β-strand323180
α-helix325-3317
α-helix344-3507
α-helix352-37625
α-helix387-41832
α-helix422-4254
α-helix429-4346
α-helix437-46832
α-helix471-4733
β-strand475181
β-strand480181
α-helix485-49612
β-strand498182
β-strand502182
β-strand518-520383
β-strand523-526483
α-helix533-55826
α-helix569-5724
α-helix591-62030
β-strand623-625383
β-strand631-633383
α-helix639-6424
α-helix646-6483
α-helix649-6557
α-helix656-6572
α-helix659-6624
α-helix670-69122
α-helix694-71017
β-strand718177
α-helix721-7233
α-helix724-75431
Chain A4: 41 helices, 18 β-strands
ElementResiduesLengthSheet
β-strand16-18355
α-helix36-383
β-strand44156
α-helix46-538
α-helix58-603
α-helix65-9632
α-helix100-1056
β-strand113-114257
α-helix123-1264
β-strand128-131458
β-strand134-136358
β-strand137-138257
α-helix1391
α-helix143-1508
α-helix155-17723
α-helix178-1825
β-strand183-185355
α-helix187-1904
α-helix193-1986
α-helix199-2079
α-helix208-2158
α-helix216-2205
α-helix221-2277
α-helix241-2444
α-helix246-2516
α-helix272-2754
α-helix294-31118
β-strand315159
β-strand323159
α-helix325-3317
α-helix344-3507
α-helix352-37625
α-helix387-41832
α-helix422-4254
α-helix429-4346
α-helix437-46832
α-helix471-4733
β-strand475160
β-strand480160
α-helix485-49612
β-strand498161
β-strand502161
β-strand518-520362
β-strand523-526462
α-helix533-55826
α-helix569-5724
α-helix591-62030
β-strand623-625362
β-strand631-633362
α-helix639-6424
α-helix646-6483
α-helix649-6557
α-helix656-6572
α-helix659-6624
α-helix670-69122
α-helix694-71017
β-strand718156
α-helix721-7233
α-helix724-75431
Chain A5: 42 helices, 18 β-strands
ElementResiduesLengthSheet
β-strand16-18339
α-helix36-383
β-strand44140
α-helix46-538
α-helix58-603
α-helix65-9632
α-helix100-1056
β-strand113-114241
α-helix123-1264
β-strand128-131442
β-strand134-136342
β-strand137-138241
α-helix1391
α-helix143-1508
α-helix155-17723
α-helix178-1825
β-strand183-185339
α-helix187-1904
α-helix193-1986
α-helix199-2079
α-helix208-2158
α-helix216-2205
α-helix221-2299
α-helix237-2382
α-helix241-2444
α-helix246-2516
α-helix272-2754
α-helix294-31118
β-strand315143
β-strand323143
α-helix325-3317
α-helix344-3507
α-helix352-37625
α-helix387-41832
α-helix422-4254
α-helix429-4346
α-helix437-46832
α-helix471-4733
β-strand475144
β-strand480144
α-helix485-49612
β-strand498145
β-strand502145
β-strand518-520346
β-strand523-526446
α-helix533-55826
α-helix569-5724
α-helix591-62030
β-strand623-625346
β-strand631-633346
α-helix639-6424
α-helix646-6483
α-helix649-6557
α-helix656-6572
α-helix659-6624
α-helix670-69122
α-helix694-71017
β-strand718140
α-helix721-7233
α-helix724-75431
Chain A6: 42 helices, 18 β-strands
ElementResiduesLengthSheet
β-strand16-183119
α-helix36-383
β-strand441120
α-helix46-538
α-helix58-603
α-helix65-9632
α-helix100-1056
β-strand113-1142121
α-helix123-1264
β-strand128-1314122
β-strand134-1363122
β-strand137-1382121
α-helix1391
α-helix143-1508
α-helix155-17723
α-helix178-1825
β-strand183-1853119
α-helix187-1904
α-helix193-1986
α-helix199-2079
α-helix208-2158
α-helix216-2205
α-helix221-2277
α-helix237-2382
α-helix241-2444
α-helix246-2516
α-helix272-2754
α-helix294-31118
β-strand3151123
β-strand3231123
α-helix325-3317
α-helix344-3474
α-helix352-37625
α-helix387-41832
α-helix422-4254
α-helix429-4346
α-helix437-46832
α-helix471-4733
β-strand4751124
β-strand4801124
α-helix485-49612
β-strand4981125
β-strand5021125
β-strand518-5203126
β-strand523-5264126
α-helix533-55826
α-helix569-5724
α-helix591-62030
β-strand623-6253126
β-strand631-6333126
α-helix639-6424
α-helix646-6483
α-helix649-6557
α-helix656-6572
α-helix659-6624
α-helix670-69122
α-helix694-71017
β-strand7181120
α-helix721-7233
α-helix724-75431
Chain B1: 48 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand2112
α-helix9-135
β-strand16113
α-helix18-269
α-helix30-323
α-helix38-7033
α-helix73-786
α-helix84-852
β-strand86-89414
α-helix97-1037
β-strand112-114314
α-helix119-1257
α-helix131-15424
α-helix158-1603
α-helix164-1674
α-helix170-1756
α-helix176-1849
α-helix185-1928
α-helix193-1975
α-helix198-2014
α-helix211-2133
α-helix222-2254
α-helix229-2335
α-helix269-28618
β-strand290115
β-strand298115
α-helix300-3056
β-strand309116
β-strand312116
α-helix317-3193
α-helix325-3317
α-helix333-35725
α-helix364-3663
α-helix368-39528
α-helix396-4005
α-helix410-4167
α-helix418-44831
α-helix452-4543
β-strand458117
α-helix461-4699
α-helix473-4753
α-helix487-4904
α-helix500-5089
α-helix520-54526
α-helix556-5594
α-helix569-5713
α-helix578-60932
α-helix612-6187
α-helix622-6254
α-helix626-6316
α-helix632-6332
α-helix637-6393
β-strand641-642218
β-strand645-646218
α-helix650-67122
α-helix674-68916
α-helix694-6963
β-strand702113
α-helix705-7073
α-helix708-73629
Chains B2, B3 and B4: 49 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand2187
α-helix9-124
β-strand16188
α-helix18-269
α-helix30-323
α-helix38-7033
α-helix73-786
α-helix83-853
β-strand86-89489
α-helix97-1037
β-strand112-114389
α-helix119-1257
α-helix131-15424
α-helix158-1603
α-helix161-1633
α-helix164-1674
α-helix170-1756
α-helix176-1849
α-helix185-1928
α-helix193-1975
α-helix198-2014
α-helix211-2133
α-helix222-2254
α-helix229-2335
α-helix269-28618
β-strand290190
β-strand298190
α-helix300-3056
β-strand309191
β-strand312191
α-helix317-3193
α-helix325-3317
α-helix333-35725
α-helix364-3663
α-helix368-39528
α-helix396-4005
α-helix410-4167
α-helix418-44831
α-helix452-4543
β-strand458192
α-helix461-4699
α-helix473-4753
α-helix487-4904
α-helix500-5089
α-helix520-54526
α-helix556-5594
α-helix569-5713
α-helix578-60932
α-helix612-6187
α-helix622-6254
α-helix626-6316
α-helix632-6332
α-helix637-6393
β-strand641-642293
β-strand645-646293
α-helix650-67122
α-helix674-68916
α-helix694-6963
β-strand702188
α-helix705-7073
α-helix708-73629
Chain B5: 50 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand2148
α-helix9-124
β-strand16149
α-helix18-269
α-helix30-323
α-helix38-7033
α-helix73-786
α-helix83-853
β-strand86-89450
α-helix97-1037
β-strand112-114350
α-helix119-1257
α-helix131-15424
α-helix158-1603
α-helix161-1633
α-helix164-1674
α-helix170-1756
α-helix176-1849
α-helix185-1928
α-helix193-1975
α-helix198-2014
α-helix211-2133
α-helix222-2254
α-helix229-2335
α-helix269-28618
β-strand290151
β-strand298151
α-helix300-3056
β-strand309152
β-strand312152
α-helix317-3193
α-helix325-3317
α-helix333-35725
α-helix364-3663
α-helix368-39528
α-helix396-4005
α-helix404-4063
α-helix410-4167
α-helix418-44831
α-helix452-4543
β-strand458153
α-helix461-4699
α-helix473-4753
α-helix487-4904
α-helix500-5089
α-helix520-54526
α-helix556-5594
α-helix569-5713
α-helix578-60932
α-helix612-6187
α-helix622-6254
α-helix626-6316
α-helix632-6332
α-helix637-6393
β-strand641-642254
β-strand645-646254
α-helix650-67122
α-helix674-68916
α-helix694-6963
β-strand702149
α-helix705-7073
α-helix708-73629

32 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 A1A1, A2, A3, A4, A5, A6protein755Thermosynechococcus elongatus BP-1P0A405 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A2B1, B2, B3, B4, B5, B6protein740Thermosynechococcus elongatus BP-1P0A407 (AlphaFold model)
Photosystem I iron-sulfur centerC1, C2, C3, C4, C5, C6protein80Thermosynechococcus elongatus BP-1P0A415 (AlphaFold model)
Photosystem I reaction center subunit IID1, D2, D3, D4, D5, D6protein138Thermosynechococcus elongatus BP-1P0A420 (AlphaFold model)
Photosystem I reaction center subunit IVE1, E2, E3, E4, E5, E6protein75Thermosynechococcus elongatus BP-1P0A423
Photosystem I reaction center subunit IIIF1, F2, F3, F4, F5, F6protein164Thermosynechococcus elongatus BP-1P0A401
Photosystem I reaction center subunit VIIII1, I2, I3, I4, I5, I6protein38Thermosynechococcus elongatus BP-1P0A427
Photosystem I reaction center subunit IXJ1, J2, J3, J4, J5, J6protein41Thermosynechococcus elongatus BP-1P0A429
Photosystem I reaction center subunit PsaKK1, K2, K3, K4, K5, K6protein83Thermosynechococcus elongatus BP-1P0A425
Photosystem I reaction center subunit XIL1, L2, L3, L4, L5, L6protein154Thermosynechococcus elongatus BP-1Q8DGB4
Photosystem I reaction center subunit XIIM1, M2, M3, M4, M5, M6protein31Thermosynechococcus elongatus BP-1P0A403
PsaXX1, X2, X3, X4, X5, X6protein35Thermosynechococcus elongatus

1 more molecules are not listed.

Sequence of entity 1 (A1, A2, A3, A4, A5, A6), FASTA
>5ZF0_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A1, A2, A3, A4, A5, A6)
MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDT
HTSDLEDISRKIFSAHFGHLAVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPI
VGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYCTAIGGLVMAGLMLFAGWFHY
HKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPH
EFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHH
HLAIAVLFIIAGHMYRTNWGIGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINL
AMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWIGGFLVVGGAAHGAIFMVRDY
DPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGI
QLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHH
IHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLF
WMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFAQSAITINGWLRDFLWAQASQ
VIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPR
ALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG
Sequence of entity 2 (B1, B2, B3, B4, B5, B6), FASTA
>5ZF0_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B1, B2, B3, B4, B5, B6)
ATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLWV
SGSLFHVAWQGNFEQWVQDPVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGVY
HWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPKFRPSLSWFKNAESRLNHHLAG
LFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTAS
HVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHSI
KEMMDAKDFFGTKVEGPFNMPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLPP
YAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVRDYDPAQNKGNVLDRVLQHKEA
IISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDTL
LSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLIL
VKGALDARGSKLMPDKKDFGYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFYW
HWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGTNNLSVWAWMFLFGH
LVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHFS
VGYILTYAAFLIASTAAKFG
Sequence of entity 3 (C1, C2, C3, C4, C5, C6), FASTA
>5ZF0_3 Photosystem I iron-sulfur center (chains C1, C2, C3, C4, C5, C6)
AHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPTD
FLSIRVYLGAETTRSMGLAY
Sequence of entity 4 (D1, D2, D3, D4, D5, D6), FASTA
>5ZF0_4 Photosystem I reaction center subunit II (chains D1, D2, D3, D4, D5, D6)
TTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFAR
KEQCLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSIG
QNPNPSQLKFTGKKPYDP
Sequence of entity 5 (E1, E2, E3, E4, E5, E6), FASTA
>5ZF0_5 Photosystem I reaction center subunit IV (chains E1, E2, E3, E4, E5, E6)
VQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNNF
ALHEVQEVAPPKKGK
Sequence of entity 6 (F1, F2, F3, F4, F5, F6), FASTA
>5ZF0_6 Photosystem I reaction center subunit III (chains F1, F2, F3, F4, F5, F6)
MRRFLALLLVLTLWLGFTPLASADVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFER
YSQALCGEDGLPHLVVDGRLSRAGDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEK
EIIIDVPLAIKCMLTGFAWPLAALKELASGELTAKDNEITVSPR
Sequence of entity 7 (I1, I2, I3, I4, I5, I6), FASTA
>5ZF0_7 Photosystem I reaction center subunit VIII (chains I1, I2, I3, I4, I5, I6)
MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA
Sequence of entity 8 (J1, J2, J3, J4, J5, J6), FASTA
>5ZF0_8 Photosystem I reaction center subunit IX (chains J1, J2, J3, J4, J5, J6)
MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL
Sequence of entity 9 (K1, K2, K3, K4, K5, K6), FASTA
>5ZF0_9 Photosystem I reaction center subunit PsaK (chains K1, K2, K3, K4, K5, K6)
MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELL
ATTSFGHLLAAGVVSGLQYAGAL
Sequence of entity 10 (L1, L2, L3, L4, L5, L6), FASTA
>5ZF0_10 Photosystem I reaction center subunit XI (chains L1, L2, L3, L4, L5, L6)
AEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLIG
PWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQF
TAGFFVGAMGSAFVAFFLLENFLVVDGIMTGLFN
Sequence of entity 11 (M1, M2, M3, M4, M5, M6), FASTA
>5ZF0_11 Photosystem I reaction center subunit XII (chains M1, M2, M3, M4, M5, M6)
MALTDTQVYVALVIALLPAVLAFRLSTELYK
Sequence of entity 12 (X1, X2, X3, X4, X5, X6), FASTA
>5ZF0_12 PsaX (chains X1, X2, X3, X4, X5, X6)
ATKSAKPTYAFRTFWAVLLLAINFLVAAYYFAAAA

Ligands and cofactors

IDNameFormulaCopies
CLAChlorophyll aC55 H72 Mg N4 O5576
PQNPhylloquinoneC31 H46 O212
BCRBeta-caroteneC40 H56132
LHG1,2-dipalmitoyl-phosphatidyl-glyceroleC38 H75 O10 P18
SF4Iron/sulfur clusterFe4 S418
LMG1,2-distearoyl-monogalactosyl-diglycerideC45 H86 O106
CACalcium ionCa6
FESFE2/S2 (inorganic) clusterFe2 S26

Primary citation

X-ray structure of an asymmetrical trimeric ferredoxin-photosystem I complex. Kubota-Kawai, H., Mutoh, R., Shinmura, K. et al. Nat Plants (2018) 4:218-224. DOI 10.1038/s41477-018-0130-0 · PubMed

Other PDB entries of the same protein (UniProt P0A405 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 5ZF0 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.