7DKZ: Lhca1

Structure of plant photosystem I-light harvesting complex I supercomplex. Determined by X-ray diffraction at 2.39 Å resolution. Released 31 Mar 2021.

Method: X-ray diffraction
Resolution: 2.39 Å
Organism: Pisum sativum
Chains: 16
Atoms: 36,093
Mol. weight: 543.37 kDa
Ligands: CLA, CHL, LUT, XAT
Released: 31 Mar 2021

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

Secondary structure: helices and β-sheets

7DKZ contains 175 α-helices and 73 β-strands across 16 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: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
α-helix	62-64	3
α-helix	66-95	30
α-helix	103-105	3
β-strand	116-117	2	1
β-strand	120-121	2	1
α-helix	127-146	20
α-helix	151-155	5
α-helix	159-161	3
α-helix	170-200	31
α-helix	206-215	10
α-helix	223-226	4

Chain 2: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	86-117	32
α-helix	139-162	24
β-strand	169	1	2
β-strand	177	1	2
α-helix	188-191	4
α-helix	201-231	31
α-helix	236-245	10

Chain 3: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	54	1	3
β-strand	72	1	3
β-strand	84	1	4
β-strand	87	1	4
α-helix	89-109	21
α-helix	112-119	8
α-helix	130-132	3
α-helix	148-171	24
α-helix	184-187	4
α-helix	199-202	4
α-helix	211-242	32
α-helix	246-255	10

Chain 4: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	85-118	34
α-helix	138-161	24
β-strand	168	1	5
β-strand	176	1	5
α-helix	177-178	2
α-helix	187-189	3
α-helix	198-225	28
α-helix	229-238	10

Chain A: 48 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	6
α-helix	42-45	4
β-strand	50	1	7
α-helix	52-59	8
α-helix	64-67	4
α-helix	71-102	32
α-helix	106-111	6
α-helix	117-118	2
β-strand	119-121	3	8
α-helix	129-132	4
β-strand	134-137	4	9
β-strand	140-142	3	9
β-strand	143-144	2	8
α-helix	145	1
α-helix	149-155	7
α-helix	161-183	23
α-helix	184-188	5
β-strand	189-191	3	6
α-helix	192	1
α-helix	193-197	5
α-helix	199-204	6
α-helix	205-212	8
α-helix	213-221	9
α-helix	222-226	5
α-helix	227-235	9
α-helix	239-241	3
α-helix	243-244	2
α-helix	247-250	4
α-helix	252-258	7
α-helix	260-264	5
α-helix	267-270	4
α-helix	274-277	4
β-strand	287	1	10
β-strand	294	1	10
α-helix	296-313	18
β-strand	317	1	11
β-strand	325	1	11
α-helix	327-332	6
α-helix	346-349	4
α-helix	354-378	25
α-helix	389-420	32
α-helix	430-436	7
α-helix	439-455	17
α-helix	458-469	12
α-helix	473-475	3
β-strand	477	1	12
β-strand	482	1	12
α-helix	487-497	11
β-strand	521-523	3	13
β-strand	526-529	4	13
α-helix	536-561	26
α-helix	572-575	4
α-helix	594-619	26
α-helix	620-624	5
β-strand	626-627	2	13
β-strand	635-636	2	13
α-helix	642-645	4
α-helix	649-651	3
α-helix	652-658	7
α-helix	659-660	2
α-helix	662-665	4
α-helix	673-694	22
α-helix	697-713	17
β-strand	721	1	7
α-helix	724-726	3
α-helix	727-757	31

Chain B: 47 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
β-strand	17	1	14
α-helix	19-27	9
α-helix	31-33	3
α-helix	39-71	33
α-helix	74-79	6
α-helix	85-86	2
β-strand	87-90	4	15
α-helix	98-103	6
β-strand	113-115	3	15
α-helix	116	1
α-helix	120-126	7
α-helix	132-155	24
α-helix	159-161	3
α-helix	162-164	3
α-helix	165-168	4
α-helix	171-177	7
α-helix	178-185	8
α-helix	186-193	8
α-helix	194-198	5
α-helix	199-202	4
α-helix	223-227	5
α-helix	230-234	5
α-helix	237-239	3
β-strand	261-262	2	16
β-strand	267-268	2	16
α-helix	270-287	18
β-strand	291	1	17
β-strand	299	1	17
α-helix	301-307	7
α-helix	322-327	6
α-helix	330-354	25
α-helix	365-392	28
α-helix	393-397	5
α-helix	407-413	7
α-helix	415-445	31
α-helix	449-451	3
β-strand	455	1	18
α-helix	458-466	9
α-helix	477-479	3
α-helix	484-489	6
α-helix	494-501	8
α-helix	514-539	26
α-helix	550-553	4
α-helix	563-565	3
α-helix	572-602	31
α-helix	607-612	6
α-helix	616-618	3
α-helix	619-625	7
α-helix	626-627	2
α-helix	631-633	3
β-strand	635-636	2	19
β-strand	639-640	2	19
α-helix	644-665	22
α-helix	668-683	16
β-strand	696	1	14
α-helix	699-701	3
α-helix	702-730	29

Chain C: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	20
α-helix	16-20	5
β-strand	27-30	4	21
β-strand	38-41	4	21
α-helix	45-47	3
α-helix	53-57	5
β-strand	65-68	4	20

Chain D: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	78-81	4
β-strand	82	1	22
β-strand	90	1	23
α-helix	92-96	5
β-strand	99-106	8	24
β-strand	110-113	4	22
β-strand	119-122	4	22
α-helix	123	1
β-strand	124-131	8	24
α-helix	134-143	10
α-helix	144-148	5
β-strand	152-157	6	24
β-strand	163-167	5	24
α-helix	181-183	3
β-strand	186-187	2	20
α-helix	191-193	3
α-helix	194-196	3
α-helix	197-200	4

8 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
Lhca1	1	protein	195	Pisum sativum
Chlorophyll a-b binding protein, chloroplastic	2	protein	269	Pisum sativum	Q41038 (AlphaFold model)
Chlorophyll a-b binding protein 3, chloroplastic	3	protein	275	Pisum sativum	Q32904 (AlphaFold model)
Chlorophyll a-b binding protein P4, chloroplastic	4	protein	198	Pisum sativum	Q9SQL2 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A1	A	protein	758	Pisum sativum	P05310 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A2	B	protein	734	Pisum sativum	A0A0F6NGI2
Photosystem I iron-sulfur center	C	protein	81	Pisum sativum	P10793
PsaD	D	protein	143	Pisum sativum	E1C9K8
PsaE	E	protein	66	Pisum sativum	E1C9K6
Psi-F	F	protein	154	Pisum sativum	A0A0M3KL12
PsaG	G	protein	97	Pisum sativum
PsaH	H	protein	88	Pisum sativum	A0A0M3KL10

4 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>7DKZ_1 Lhca1 (chains 1)
ADWMPGQPRPSYLDGSAPGDFGFDPLRLGEVPENLERFKESELIHCRWAMLAVPGILVPE
ALGLGNWVKAQEWAALPGGQATYLGNPVPWGTLPTILVIEFLSIAFVEHQRSMEKDPEKK
KYPGGAFDPLGYSKDPKKFHEYKIKEVKNGRLALLAFVGICVQQSAYPGTGPLENLATHL
ADPWHNTIGNVLIPA

Sequence of entity 2 (2), FASTA

>7DKZ_2 Chlorophyll a-b binding protein, chloroplastic (chains 2)
MASACASSAIAAVAISTPSSQKNGSPSGTSKAFLGRKLKVNSSTASPSRVRSTSTVCTVA
EPDRPLWFPGSTPPPWLDGSLPGDFGFDPLGLGSDPESLRWNVQAELVHSRWAMLGAAGI
FIPEFLTKLGILNTPSWYTAGEQEYFTDTTTLFIVELVFIGWAEGRRWADILNPGCVNTD
PIFPNNKLTGTDVGYPGGLWFDPLGWGSASPQKLKELRTKEIKNGRLAMLAVMGAWFQHI
YTGTGPIDNLFAHLADPGHATIFAAFTPK

Sequence of entity 3 (3), FASTA

>7DKZ_3 Chlorophyll a-b binding protein 3, chloroplastic (chains 3)
MATQALVSSSSLTFAAEAVRQSFRARSLPSSVGCSRKGLVRAAATPPVKQGGVDRPLWFA
SKQSLSYLDGSLPGDYGFDPLGLSDPEGTGGFIEPRWLAYGEVINGRFAMLGAVGAIAPE
YLGKVGLIPQETALAWFQTGVIPPAGTYNYWADNYTLFVLEMALMGFAEHRRFQDWAKPG
SMGKQYFLGLEKGFGGSGNPAYPGGPFFNPLGFGKDEKSLKELKLKEVKNGRLAMLAILG
YFIQGLVTGVGPYQNLLDHVADPVNNNVLTSLKFH

Sequence of entity 4 (4), FASTA

>7DKZ_4 Chlorophyll a-b binding protein P4, chloroplastic (chains 4)
KKGEWLPGLASPGYLTGSLPGDNGFDPLGLAEDPENLKWFVQAELVNGRWAMLGVAGMLL
PEVFTSIGIINVPKWYDAGKEEYFASSSTLFVIEFILFHYVEIRRWQDIKNPGSVNQDPI
FKQYSLPAGEVGYPGGIFNPLNFAPTLEAKEKEIANGRLAMLAFLGFIIQHNVTGKGPFD
NLLQHISDPWHNTIVQTL

Sequence of entity 5 (A), FASTA

>7DKZ_5 Photosystem I P700 chlorophyll a apoprotein A1 (chains A)
MIIRSPEPKVQILADPEVKILVDRDPIKTSFEQWAKPGHFSRTIAKGPDTTTWIWNLHAD
AHDFDSHTSDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLNDPTHIRPSA
QVVWPIVGQEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAALMLF
AGWFHYHKAAPKLVWFQDVESMLNHHLAGLLGLGSLSWAGHQIHVSLPINQFLNAGVDPK
EIPLPHEFILNRDLLAQLYPSFAEGATPFFTLNWSKYADFLTFRGGLDPLTGGLWLTDIA
HHHLAIAILFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSI
NLAMLGSLTIIVAHHMYAMPPYPYLATDYGTQLSLFTHHMWIGGFLIVGAAAHAAIFMVR
DYDPTTRYNDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDT
AIQLQPVFAQWIQNTHALAPGTTAPGATTSTSLTWGGGDLVSVGGKVALLPIPLGTADFL
VHHIHAFTIHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFL
GLFWMYNAISVVIFHFSWKMQSDVWGSINDQGVVTHITGGNFAQSSITINGWLRDFLWAQ
ASQVIQSYGSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPAT
QPRALSIVQGRAVGVTHYLLGGIATTWAFFLARIIAVG

Sequence of entity 6 (B), FASTA

>7DKZ_6 Photosystem I P700 chlorophyll a apoprotein A2 (chains B)
MALRFPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEGRLYQNIFASHFGQLAIIFLW
TSGNLFHVAWQGNFEAWVQDPLHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGV
YQWWYTIGLRTNEDLYTGAIFLLFLSFISLLAGWLHLQPKWKPSVSWFKNAESRLNHHLS
GLFGVSSLAWAGHLVHVAIPGSRGEYVRWNNFLSVLPHPQGLGPLFTGQWNLYAQNPDSS
NHLFSTSQGAGTAILTLLGGFHPQTQSLWLTDMAHHHLAIAILFLIGGHMYRTNFGIGHS
IKYILEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAF
IAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNPEQNADNVLARMLEHKEAIIS
HLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSS
TNSPALNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALD
ARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHIT
LWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMFLFGHLVWATG
FMFLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVALSIVQARLVGLVHFSVGYIFT
YAAFLIASTSGKFG

Sequence of entity 7 (C), FASTA

>7DKZ_7 Photosystem I iron-sulfur center (chains C)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY

Sequence of entity 8 (D), FASTA

>7DKZ_8 PsaD (chains D)
GFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPN
LLKLARKEQCLALGTRLRSKYKIKYQFYRVFPSGEVQYLHPKDGVYPEKVNPGRQGVGVN
FRSIGKNVSPIEVKFTGKQPYDL

Sequence of entity 9 (E), FASTA

>7DKZ_9 PsaE (chains E)
PPIGPKRGAKVKILRQESYWYKGTGSVVAVDQDPNTRYPVVVRFNKVNYANVSTNNYALD
EVEEVK

Sequence of entity 10 (F), FASTA

>7DKZ_10 PSI-F (chains F)
DIAGLTPCKDSKQFAKREKQSIKKLESSLKLYAPDSAPALAINATIEKTKRRFDNYGKQG
LLCGADGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDDKKPTQKEII
IDVPLATRLVFRGFSWPIAAYRELLNGELVAKDV

Sequence of entity 11 (G), FASTA

>7DKZ_11 PsaG (chains G)
LNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDTRAKEYVSLLKS
NDPVGFNIVDVLAWGSIGHIVAYYILATSSNGYDPKF

Sequence of entity 12 (H), FASTA

>7DKZ_12 PsaH (chains H)
VYFDLEDLGNTTGQWDLYGSDAPSPYNSLQSKFFETFAAPFTKRGLLLKFLILGGGSTLA
YFSATASGDILPIKKGPQLPPQLGPRLG

Ligands and cofactors

ID	Name	Formula	Copies
CLA	Chlorophyll a	C55 H72 Mg N4 O5	140
CHL	Chlorophyll B	C55 H70 Mg N4 O6	12
LUT	(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol	C40 H56 O2	4
XAT	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-…	C40 H56 O4	4
BCR	Beta-carotene	C40 H56	26
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	7
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	2
LMG	1,2-distearoyl-monogalactosyl-diglyceride	C45 H86 O10	5
HTG	heptyl 1-thio-beta-D-glucopyranoside	C13 H26 O5 S	8
DGD	Digalactosyl diacyl glycerol (DGDG)	C51 H96 O15	2
PQN	Phylloquinone	C31 H46 O2	2
SF4	Iron/sulfur cluster	Fe4 S4	3

Primary citation

Structure of plant photosystem I-light harvesting complex I supercomplex at 2.4 angstrom resolution. Wang, J., Yu, L.J., Wang, W. et al. J Integr Plant Biol (2021) 63:1367-1381. DOI 10.1111/jipb.13095 · PubMed

Other PDB entries of the same protein (UniProt Q41038 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YAC 2.5 Å, Plant PSI-ferredoxin supercomplex
5L8R 2.6 Å, The structure of plant photosystem I super-complex at 2.6 angstrom resolution.
6YEZ 2.7 Å, Plant PSI-ferredoxin-plastocyanin supercomplex
6ZOO 2.74 Å, Photosystem I reduced Plastocyanin Complex
4XK8 2.8 Å, Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution
4Y28 2.8 Å, The structure of plant photosystem I super-complex at 2.8 angstrom resolution.
4RKU 3.0 Å, Crystal structure of plant Photosystem I at 3 Angstrom resolution
6ZXS 3.0 Å, Cold grown Pea Photosystem I
2WSC 3.3 Å, Improved Model of Plant Photosystem I
3LW5 3.3 Å, Improved model of plant photosystem I
2O01 3.4 Å, The Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution
2WSF 3.48 Å, Improved Model of Plant Photosystem I

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