6TRD: Photosystem I P700 chlorophyll a apoprotein A1

Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of cytochrome c6. Determined by electron microscopy at 3.16 Å resolution. Released 16 Sept 2020.

Method: Electron microscopy
Resolution: 3.16 Å
Organism: Thermosynechococcus elongatus BP-1
Chains: 36
Atoms: 74,991
Mol. weight: 1084.61 kDa
Ligands: PQN, BCR, LHG, LMG
Released: 16 Sept 2020

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

Secondary structure: helices and β-sheets

6TRD contains 348 α-helices and 190 β-strands across 36 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 0 and L: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	35
β-strand	8	1	36
β-strand	11	1	36
β-strand	14	1	21
β-strand	15	1	20
β-strand	17-18	2	35
α-helix	26-31	6
α-helix	43-57	15
α-helix	60-65	6
α-helix	74-100	27
α-helix	110-112	3
α-helix	114-140	27
α-helix	142-150	9

Chains 1, a and A: 41 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	65
β-strand	44	1	66
α-helix	46-53	8
α-helix	58-61	4
α-helix	65-96	32
α-helix	100-105	6
β-strand	115	1	67
α-helix	123-126	4
β-strand	128-129	2	68
β-strand	135-136	2	68
β-strand	137	1	67
α-helix	138-139	2
α-helix	143-150	8
α-helix	155-177	23
α-helix	178-182	5
β-strand	185	1	65
α-helix	187-191	5
α-helix	193-199	7
α-helix	200-206	7
α-helix	207-215	9
α-helix	216-220	5
α-helix	221-227	7
α-helix	239-242	4
α-helix	246-250	5
α-helix	265-268	4
α-helix	272-275	4
α-helix	294-311	18
β-strand	315	1	69
β-strand	323	1	69
α-helix	327-331	5
α-helix	344-350	7
α-helix	352-374	23
α-helix	387-418	32
α-helix	429-434	6
α-helix	437-468	32
α-helix	471-473	3
α-helix	485-496	12
β-strand	498	1	70
β-strand	502	1	70
α-helix	511-513	3
β-strand	518-520	3	71
β-strand	523-526	4	71
α-helix	528-530	3
α-helix	533-558	26
α-helix	569-572	4
β-strand	578	1	72
β-strand	587	1	72
α-helix	591-620	30
β-strand	623-626	4	71
β-strand	630-633	4	71
α-helix	639-642	4
α-helix	646-648	3
α-helix	649-655	7
α-helix	656-657	2
α-helix	670-690	21
α-helix	694-710	17
β-strand	718	1	66
α-helix	721-723	3
α-helix	724-754	31

Chains 2, b and B: 43 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	73
α-helix	9-12	4
β-strand	16	1	74
α-helix	18-25	8
α-helix	30-32	3
α-helix	38-70	33
α-helix	73-77	5
α-helix	84-85	2
β-strand	86-89	4	75
α-helix	98-103	6
β-strand	112-114	3	75
α-helix	119-125	7
α-helix	131-154	24
α-helix	164-168	5
α-helix	170-176	7
α-helix	177-184	8
α-helix	185-192	8
α-helix	193-197	5
α-helix	198-202	5
α-helix	207-210	4
α-helix	222-225	4
α-helix	236-238	3
β-strand	260	1	76
β-strand	267	1	76
α-helix	269-286	18
β-strand	290	1	77
β-strand	298	1	77
α-helix	300-305	6
β-strand	308-309	2	78
β-strand	312-313	2	78
α-helix	317-319	3
α-helix	325-331	7
α-helix	333-354	22
α-helix	364-366	3
α-helix	368-399	32
α-helix	410-415	6
α-helix	418-448	31
β-strand	457-458	2	79
α-helix	461-470	10
α-helix	480-482	3
α-helix	487-490	4
α-helix	500-508	9
α-helix	520-545	26
α-helix	546-548	3
α-helix	578-609	32
α-helix	613-618	6
α-helix	622-624	3
α-helix	625-631	7
α-helix	632-633	2
α-helix	638-640	3
β-strand	641	1	80
β-strand	646	1	80
α-helix	650-671	22
α-helix	675-690	16
β-strand	702	1	74
α-helix	705-707	3
α-helix	708-735	28

Chains 3, c and C: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
α-helix	15-19	5
β-strand	26-29	4	10
β-strand	37-40	4	10
α-helix	52-56	5
β-strand	64-67	4	9

Chains 4 and D: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	19
β-strand	13	1	20
β-strand	17	1	21
β-strand	26-33	8	22
β-strand	37-40	4	19
β-strand	46-49	4	19
α-helix	50	1
β-strand	52-58	7	22
α-helix	61-67	7
α-helix	68-72	5
α-helix	73-75	3
β-strand	80-85	6	22
β-strand	91-93	3	22
β-strand	114-115	2	9
α-helix	125-127	3

Chains 5, e and E: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	25
β-strand	17	1	25
β-strand	22-26	5	25
β-strand	36-39	4	25
β-strand	57-60	4	25
α-helix	62-64	3
β-strand	65-69	5	25

Chains 6, f and F: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	12-19	8
α-helix	30-37	8
α-helix	38-40	3
β-strand	43	1	30
β-strand	49	1	30
β-strand	50-51	2	79
α-helix	60-89	30
α-helix	94-99	6
β-strand	100	1	31
α-helix	103-111	9
α-helix	116-124	9

Chains 7, i and I: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	9-16	8
α-helix	17-21	5
α-helix	22-34	13
β-strand	37	1	73

7 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	1, A, a	protein	755	Thermosynechococcus elongatus BP-1	P0A405 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A2	2, B, b	protein	741	Thermosynechococcus elongatus BP-1	P0A407 (AlphaFold model)
Photosystem I iron-sulfur center	3, C, c	protein	81	Thermosynechococcus elongatus BP-1	P0A415 (AlphaFold model)
Photosystem I reaction center subunit II	4, D, d	protein	139	Thermosynechococcus elongatus BP-1	P0A420 (AlphaFold model)
Photosystem I reaction center subunit IV	5, E, e	protein	76	Thermosynechococcus elongatus BP-1	P0A423
Photosystem I reaction center subunit III	6, F, f	protein	141	Thermosynechococcus elongatus BP-1	P0A401
Photosystem I reaction center subunit VIII	7, I, i	protein	38	Thermosynechococcus elongatus BP-1	P0A427
Photosystem I reaction center subunit IX	8, J, j	protein	41	Thermosynechococcus elongatus BP-1	P0A429
Photosystem I reaction center subunit PsaK	9, K, k	protein	83	Thermosynechococcus elongatus BP-1	P0A425
Photosystem I reaction center subunit XI	0, L, l	protein	155	Thermosynechococcus elongatus BP-1	Q8DGB4
Photosystem I reaction center subunit XII	M, m, y	protein	31	Thermosynechococcus elongatus BP-1	P0A403
Photosystem I 4.8K protein	X, x, z	protein	36	Thermosynechococcus elongatus BP-1	Q8DKP6

Sequence of entity 1 (1, A, a), FASTA

>6TRD_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains 1, A, a)
MTISPPEREPKVRVVVDNDPVPTSFEKWAKPGHFDRTLARGPQTTTWIWNLHALAHDFDT
HTSDLEDISRKIFSAHFGHLAVVFIWLSGMYFHGAKFSNYEAWLADPTGIKPSAQVVWPI
VGQGILNGDVGGGFHGIQITSGLFQLWRASGITNEFQLYCTAIGGLVMAGLMLFAGWFHY
HKRAPKLEWFQNVESMLNHHLAGLLGLGSLAWAGHQIHVSLPINKLLDAGVAAKDIPLPH
EFILNPSLMAELYPKVDWGFFSGVIPFFTFNWAAYSDFLTFNGGLNPVTGGLWLSDTAHH
HLAIAVLFIIAGHMYRTNWGIGHSLKEILEAHKGPFTGAGHKGLYEVLTTSWHAQLAINL
AMMGSLSIIVAQHMYAMPPYPYLATDYPTQLSLFTHHMWIGGFLVVGGAAHGAIFMVRDY
DPAMNQNNVLDRVLRHRDAIISHLNWVCIFLGFHSFGLYVHNDTMRAFGRPQDMFSDTGI
QLQPVFAQWVQNLHTLAPGGTAPNAAATASVAFGGDVVAVGGKVAMMPIVLGTADFMVHH
IHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSGWDHVFLGLF
WMYNCISVVIFHFSWKMQSDVWGTVAPDGTVSHITGGNFAQSAITINGWLRDFLWAQASQ
VIGSYGSALSAYGLLFLGAHFIWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAIQPR
ALSIIQGRAVGVAHYLLGGIATTWAFFLARIISVG

Sequence of entity 2 (2, B, b), FASTA

>6TRD_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains 2, B, b)
MATKFPKFSQDLAQDPTTRRIWYAIAMAHDFESHDGMTEENLYQKIFASHFGHLAIIFLW
VSGSLFHVAWQGNFEQWVQDPVNTRPIAHAIWDPQFGKAAVDAFTQAGASNPVDIAYSGV
YHWWYTIGMRTNGDLYQGAIFLLILASLALFAGWLHLQPKFRPSLSWFKNAESRLNHHLA
GLFGVSSLAWAGHLIHVAIPESRGQHVGWDNFLSTMPHPAGLAPFFTGNWGVYAQNPDTA
SHVFGTAQGAGTAILTFLGGFHPQTESLWLTDMAHHHLAIAVLFIVAGHMYRTQFGIGHS
IKEMMDAKDFFGTKVEGPFNMPHQGIYETYNNSLHFQLGWHLACLGVITSLVAQHMYSLP
PYAFIAQDHTTMAALYTHHQYIAGFLMVGAFAHGAIFLVRDYDPAQNKGNVLDRVLQHKE
AIISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAHGKLLYGFDT
LLSNPDSIASTAWPNYGNVWLPGWLDAINSGTNSLFLTIGPGDFLVHHAIALGLHTTTLI
LVKGALDARGSKLMPDKKDFGYAFPCDGPGRGGTCDISAWDAFYLAMFWMLNTIGWVTFY
WHWKHLGVWEGNVAQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGTNNLSVWAWMFLFG
HLVWATGFMFLISWRGYWQELIETLVWAHERTPLANLVRWKDKPVALSIVQARLVGLAHF
SVGYILTYAAFLIASTAAKFG

Sequence of entity 3 (3, C, c), FASTA

>6TRD_3 Photosystem I iron-sulfur center (chains 3, C, c)
MAHTVKIYDTCIGCTQCVRACPTDVLEMVPWDGCKAGQIASSPRTEDCVGCKRCETACPT
DFLSIRVYLGAETTRSMGLAY

Sequence of entity 4 (4, D, d), FASTA

>6TRD_4 Photosystem I reaction center subunit II (chains 4, D, d)
MTTLTGQPPLYGGSTGGLLSAADTEEKYAITWTSPKEQVFEMPTAGAAVMREGENLVYFA
RKEQCLALAAQQLRPRKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSVPRSI
GQNPNPSQLKFTGKKPYDP

Sequence of entity 5 (5, E, e), FASTA

>6TRD_5 Photosystem I reaction center subunit IV (chains 5, E, e)
MVQRGSKVKILRPESYWYNEVGTVASVDQTPGVKYPVIVRFDKVNYTGYSGSASGVNTNN
FALHEVQEVAPPKKGK

Sequence of entity 6 (6, F, f), FASTA

>6TRD_6 Photosystem I reaction center subunit III (chains 6, F, f)
DVAGLVPCKDSPAFQKRAAAAVNTTADPASGQKRFERYSQALCGEDGLPHLVVDGRLSRA
GDFLIPSVLFLYIAGWIGWVGRAYLIAVRNSGEANEKEIIIDVPLAIKCMLTGFAWPLAA
LKELASGELTAKDNEITVSPR

Sequence of entity 7 (7, I, i), FASTA

>6TRD_7 Photosystem I reaction center subunit VIII (chains 7, I, i)
MMGSYAASFLPWIFIPVVCWLMPTVVMGLLFLYIEGEA

Sequence of entity 8 (8, J, j), FASTA

>6TRD_8 Photosystem I reaction center subunit IX (chains 8, J, j)
MKHFLTYLSTAPVLAAIWMTITAGILIEFNRFYPDLLFHPL

Sequence of entity 9 (9, K, k), FASTA

>6TRD_9 Photosystem I reaction center subunit PsaK (chains 9, K, k)
MVLATLPDTTWTPSVGLVVILCNLFAIALGRYAIQSRGKGPGLPIALPALFEGFGLPELL
ATTSFGHLLAAGVVSGLQYAGAL

Sequence of entity 10 (0, L, l), FASTA

>6TRD_10 Photosystem I reaction center subunit XI (chains 0, L, l)
MAEELVKPYNGDPFVGHLSTPISDSGLVKTFIGNLPAYRQGLSPILRGLEVGMAHGYFLI
GPWVKLGPLRDSDVANLGGLISGIALILVATACLAAYGLVSFQKGGSSSDPLKTSEGWSQ
FTAGFFVGAMGSAFVAFFLLENFLVVDGIMTGLFN

Sequence of entity 11 (M, m, y), FASTA

>6TRD_11 Photosystem I reaction center subunit XII (chains M, m, y)
MALTDTQVYVALVIALLPAVLAFRLSTELYK

Sequence of entity 12 (X, x, z), FASTA

>6TRD_12 Photosystem I 4.8K protein (chains X, x, z)
MATKSAKPTYAFRTFWAVLLLAINFLVAAYYFGILK

Ligands and cofactors

ID	Name	Formula	Copies
PQN	Phylloquinone	C31 H46 O2	6
BCR	Beta-carotene	C40 H56	72
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	15
LMG	1,2-distearoyl-monogalactosyl-diglyceride	C45 H86 O10	3
CA	Calcium ion	Ca	6
SF4	Iron/sulfur cluster	Fe4 S4	9
CLA	Chlorophyll a	C55 H72 Mg N4 O5	288
CL0	Chlorophyll a isomer	C55 H72 Mg N4 O5	3

Primary citation

Current limits of structural biology: The transient interaction between cytochrome c6 and photosystem I. Koelsch, A., Radon, C., Golub, M. et al. Curr Opin Struct Biol (2020) 2:171-179. DOI 10.1016/j.crstbi.2020.08.003

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
7FIX 1.97 Å, Cryo-EM structure of cyanobacterial photosystem I in the presence of ferredoxin and…
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…
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

Browse structure collections

About this viewer

MolViewer shows 6TRD 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.