7FIX: Photosystem I P700 chlorophyll a apoprotein A1

Cryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and cytochrome c6. Determined by electron microscopy at 1.97 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 1.97 Å
Organism: Thermosynechococcus vestitus BP-1
Chains: 39
Atoms: 73,929
Mol. weight: 1125.8 kDa
Ligands: CL0, CLA, PQN, SF4
Released: 21 Sept 2022

Explore 7FIX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7FIX contains 402 α-helices and 216 β-strands across 39 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.

Chains A1, A2 and A3: 44 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	16-18	3	1
α-helix	27-29	3
β-strand	44	1	2
α-helix	46-53	8
α-helix	58-61	4
α-helix	65-96	32
α-helix	100-105	6
β-strand	113-115	3	3
α-helix	123-126	4
β-strand	128-129	2	4
β-strand	135-136	2	4
β-strand	137-138	2	3
α-helix	143-149	7
α-helix	155-177	23
α-helix	178-182	5
β-strand	183-185	3	1
α-helix	186	1
α-helix	187-191	5
α-helix	193-198	6
α-helix	199-207	9
α-helix	208-215	8
α-helix	216-220	5
α-helix	221-229	9
α-helix	237-238	2
α-helix	241-244	4
α-helix	246-252	7
α-helix	272-277	6
α-helix	294-310	17
β-strand	315	1	5
β-strand	323	1	5
α-helix	325-331	7
α-helix	344-350	7
α-helix	352-374	23
α-helix	387-414	28
α-helix	415-419	5
α-helix	429-434	6
α-helix	437-467	31
α-helix	471-473	3
β-strand	475	1	6
β-strand	480	1	6
α-helix	485-495	11
α-helix	511-513	3
β-strand	518-520	3	7
β-strand	523-526	4	7
α-helix	533-558	26
α-helix	569-572	4
α-helix	591-620	30
β-strand	623-625	3	7
β-strand	631-633	3	7
α-helix	639-642	4
α-helix	646-648	3
α-helix	649-655	7
α-helix	656-657	2
α-helix	659-662	4
α-helix	670-691	22
α-helix	694-710	17
β-strand	718	1	2
α-helix	719	1
α-helix	721-723	3
α-helix	724-754	31

Chains B1, B2 and B3: 44 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	15
α-helix	9-12	4
β-strand	16	1	16
α-helix	18-25	8
α-helix	30-32	3
α-helix	38-70	33
α-helix	73-78	6
β-strand	86-89	4	17
α-helix	97-103	7
β-strand	104	1	18
β-strand	111	1	18
β-strand	112-114	3	17
α-helix	119-125	7
α-helix	131-154	24
α-helix	158-160	3
α-helix	164-168	5
α-helix	170-175	6
α-helix	176-184	9
α-helix	185-192	8
α-helix	193-197	5
α-helix	198-201	4
α-helix	222-226	5
α-helix	229-233	5
α-helix	236-238	3
β-strand	260	1	19
β-strand	267	1	19
α-helix	269-286	18
β-strand	290	1	20
β-strand	298	1	20
α-helix	300-305	6
β-strand	308-309	2	21
β-strand	312-313	2	21
α-helix	317-319	3
α-helix	325-331	7
α-helix	333-357	25
α-helix	368-399	32
α-helix	404-406	3
α-helix	410-416	7
α-helix	418-448	31
α-helix	452-454	3
β-strand	458	1	22
α-helix	461-469	9
α-helix	480-482	3
α-helix	487-490	4
α-helix	500-509	10
α-helix	520-545	26
α-helix	556-559	4
β-strand	569	1	23
α-helix	578-608	31
α-helix	612-616	5
α-helix	622-624	3
α-helix	625-631	7
α-helix	632-633	2
α-helix	637-639	3
β-strand	641-642	2	24
β-strand	645-646	2	24
α-helix	650-671	22
α-helix	674-690	17
β-strand	702	1	16
α-helix	705-707	3
α-helix	708-739	32

Chains C1, C2 and C3: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	35
α-helix	15-19	5
β-strand	26-29	4	36
β-strand	37-40	4	36
α-helix	44-46	3
α-helix	52-56	5
β-strand	64-67	4	35

Chains D1, D2 and D3: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	39
β-strand	9	1	40
β-strand	13	1	41
β-strand	17	1	42
α-helix	19-23	5
β-strand	26-33	8	39
β-strand	37-40	4	40
β-strand	46-49	4	40
α-helix	50	1
β-strand	52-58	7	39
α-helix	61-67	7
α-helix	68-72	5
α-helix	73-75	3
β-strand	81-85	5	39
β-strand	91-93	3	39
β-strand	114-115	2	35
α-helix	119-121	3
α-helix	122-124	3
α-helix	125-128	4

Chains E1, E2 and E3: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	47
β-strand	20-26	7	47
β-strand	36-39	4	47
β-strand	48	1	23
β-strand	57-60	4	47
α-helix	62-64	3
β-strand	65-67	3	47

Chains F1, F2 and F3: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	29-30	2	49
α-helix	35-41	7
α-helix	53-61	9
β-strand	65-66	2	49
β-strand	72	1	49
β-strand	74	1	22
α-helix	87-113	27
α-helix	117-122	6
β-strand	123	1	50
α-helix	126-134	9
α-helix	136-138	3
α-helix	139-149	11
α-helix	154-155	2
α-helix	156-158	3

Chains I1, I2 and I3: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	10-16	7
α-helix	17-21	5
α-helix	22-34	13
β-strand	37	1	15

Chains J1, J2 and J3: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-7	6
β-strand	10	1	50
α-helix	11-32	22

5 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	A1, A2, A3	protein	755	Thermosynechococcus vestitus BP-1	P0A405 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A2	B1, B2, B3	protein	741	Thermosynechococcus vestitus BP-1	P0A407 (AlphaFold model)
Photosystem I iron-sulfur center	C1, C2, C3	protein	81	Thermosynechococcus vestitus BP-1	P0A415 (AlphaFold model)
Photosystem I reaction center subunit II	D1, D2, D3	protein	139	Thermosynechococcus vestitus BP-1	P0A420 (AlphaFold model)
Photosystem I reaction center subunit IV	E1, E2, E3	protein	76	Thermosynechococcus vestitus BP-1	P0A423
Photosystem I reaction center subunit III	F1, F2, F3	protein	174	Thermosynechococcus vestitus BP-1	P0A401
Photosystem I reaction center subunit VIII	I1, I2, I3	protein	38	Thermosynechococcus vestitus BP-1	P0A427
Photosystem I reaction center subunit IX	J1, J2, J3	protein	41	Thermosynechococcus vestitus BP-1	P0A429
Photosystem I reaction center subunit PsaK	K1, K2, K3	protein	83	Thermosynechococcus vestitus BP-1	P0A425
Photosystem I reaction center subunit XI	L1, L2, L3	protein	155	Thermosynechococcus vestitus BP-1	Q8DGB4
Photosystem I reaction center subunit XII	M1, M2, M3	protein	31	Thermosynechococcus vestitus BP-1	P0A403
Ferredoxin-1	R1, R2, R3	protein	98	Thermosynechococcus vestitus BP-1	P0A3C9

1 more molecules are not listed.

Sequence of entity 1 (A1, A2, A3), FASTA

>7FIX_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A1, A2, A3)
MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDT
HTSDLEDISRKIFSAHFGHLAVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPI
VGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYCTAIGGLVMAGLMLFAGWFHY
HKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPH
EFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHH
HLAIAVLFIIAGHMYRTNWGIGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINL
AMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWIGGFLVVGGAAHGAIFMVRDY
DPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGI
QLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHH
IHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLF
WMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFAQSAITINGWLRDFLWAQASQ
VIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPR
ALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG

Sequence of entity 2 (B1, B2, B3), FASTA

>7FIX_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B1, B2, B3)
MATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLW
VSGSLFHVAWQGNFEQWVQDPVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGV
YHWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPKFRPSLSWFKNAESRLNHHLA
GLFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTA
SHVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHS
IKEMMDAKDFFGTKVEGPFNMPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLP
PYAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVRDYDPAQNKGNVLDRVLQHKE
AIISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDT
LLSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLI
LVKGALDARGSKLMPDKKDFGYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFY
WHWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGTNNLSVWAWMFLFG
HLVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHF
SVGYILTYAAFLIASTAAKFG

Sequence of entity 3 (C1, C2, C3), FASTA

>7FIX_3 Photosystem I iron-sulfur center (chains C1, C2, C3)
MAHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPT
DFLSIRVYLGAETTRSMGLAY

Sequence of entity 4 (D1, D2, D3), FASTA

>7FIX_4 Photosystem I reaction center subunit II (chains D1, D2, D3)
MTTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFA
RKEQCLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSI
GQNPNPSQLKFTGKKPYDP

Sequence of entity 5 (E1, E2, E3), FASTA

>7FIX_5 Photosystem I reaction center subunit IV (chains E1, E2, E3)
MVQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNN
FALHEVQEVAPPKKGK

Sequence of entity 6 (F1, F2, F3), FASTA

>7FIX_6 Photosystem I reaction center subunit III (chains F1, F2, F3)
HHHHHHHHHHMRRFLALLLVLTLWLGFTPLASADVAGLVPCKDSPAFQKRAAAAVNTTAD
PASGQKRFERYSQALCGEDGLPHLVVDGRLSRAGDFLIPSVLFLYIAGWIGWVGRAYLIA
VRNSGEANEKEIIIDVPLAIKCMLTGFAWPLAALKELASGELTAKDNEITVSPR

Sequence of entity 7 (I1, I2, I3), FASTA

>7FIX_7 Photosystem I reaction center subunit VIII (chains I1, I2, I3)
MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA

Sequence of entity 8 (J1, J2, J3), FASTA

>7FIX_8 Photosystem I reaction center subunit IX (chains J1, J2, J3)
MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL

Sequence of entity 9 (K1, K2, K3), FASTA

>7FIX_9 Photosystem I reaction center subunit PsaK (chains K1, K2, K3)
MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELL
ATTSFGHLLAAGVVSGLQYAGAL

Sequence of entity 10 (L1, L2, L3), FASTA

>7FIX_10 Photosystem I reaction center subunit XI (chains L1, L2, L3)
MAEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLI
GPWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQ
FTAGFFVGAMGSAFVAFFLLENFSVVDGIMTGLFN

Sequence of entity 11 (M1, M2, M3), FASTA

>7FIX_11 Photosystem I reaction center subunit XII (chains M1, M2, M3)
MALTDTQVYVALVIALLPAVLAFRLSTELYK

Sequence of entity 12 (R1, R2, R3), FASTA

>7FIX_12 Ferredoxin-1 (chains R1, R2, R3)
MATYKVTLVRPDGSETTIDVPEDEYILDVAEEQGLDLPFSCRAGACSTCAGKLLEGEVDQ
SDQSFLDDDQIEKGFVLTCVAYPRSDCKILTNQEEELY

Ligands and cofactors

ID	Name	Formula	Copies
CL0	Chlorophyll a isomer	C55 H72 Mg N4 O5	3
CLA	Chlorophyll a	C55 H72 Mg N4 O5	285
PQN	Phylloquinone	C31 H46 O2	6
SF4	Iron/sulfur cluster	Fe4 S4	9
BCR	Beta-carotene	C40 H56	72
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	9
DGD	Digalactosyl diacyl glycerol (DGDG)	C51 H96 O15	3
CA	Calcium ion	Ca	3
GAK	[2Ga-2S] cluster	Ga2 S2	3

Water and common crystallization additives (UNL) are not listed.

Primary citation

Structure of cyanobacterial photosystem I complexed with ferredoxin at 1.97 angstrom resolution. Li, J., Hamaoka, N., Makino, F. et al. Commun Biol (2022) 5:951-951. DOI 10.1038/s42003-022-03926-4 · PubMed

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

9QFP 1.74 Å, Monomeric Photosystem I Cryo-EM structure at 1.8 A resolution
1JB0 2.5 Å, Crystal Structure of Photosystem I: a Photosynthetic Reaction Center and Core Antenna…
7M75 2.75 Å, Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two…
6TRA 2.85 Å, Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of…
6PFY 2.9 Å, Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I at…
6PGK 2.9 Å, Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I XFEL at…
6TRC 2.98 Å, Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of…
7M76 3.0 Å, Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two…
7M78 3.0 Å, Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two…
6TRD 3.16 Å, Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of…
6LU1 3.2 Å, Cyanobacterial PSI Monomer from T. elongatus by Single Particle CRYO-EM at 3.2 A…
10EG 3.4 Å, Thermosynechococcus vestitus (BP-1) Photosystem I Complexed with Platinum Nanoparticles

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