4XK8: Plant photosystem I-LHCI super-complex

Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution. Determined by X-ray diffraction at 2.8 Å resolution. Released 10 Jun 2015.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Pisum sativum
Chains: 32
Atoms: 71,157
Mol. weight: 1046.38 kDa
Ligands: LHG, XAT, LUT, CHL
Released: 10 Jun 2015

Explore 4XK8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XK8 contains 357 α-helices and 146 β-strands across 32 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: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
α-helix	62-64	3
α-helix	66-95	30
β-strand	116-117	2	34
β-strand	120-121	2	34
α-helix	122	1
α-helix	127-146	20
α-helix	159-161	3
α-helix	170-200	31
α-helix	206-215	10
α-helix	223-226	4

Chains 2 and 7: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	62-64	3
α-helix	86-117	32
α-helix	127-129	3
α-helix	139-162	24
β-strand	169	1	35
β-strand	177	1	35
α-helix	188-191	4
α-helix	201-231	31
α-helix	236-245	10
α-helix	253-256	4

Chain 3: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	56-61	6
β-strand	84	1	36
β-strand	87	1	36
α-helix	89-109	21
α-helix	112-119	8
α-helix	124-126	3
α-helix	137-139	3
α-helix	148-171	24
α-helix	199-202	4
α-helix	211-242	32
α-helix	246-255	10

Chains 4 and 9: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	60-63	4
α-helix	85-117	33
α-helix	126-128	3
α-helix	138-161	24
β-strand	168	1	37
β-strand	176	1	37
β-strand	181	1	38
β-strand	184	1	38
α-helix	187-189	3
α-helix	198-225	28
α-helix	229-238	10
α-helix	245-248	4

Chain 6: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-44	4
α-helix	62-64	3
α-helix	66-86	21
α-helix	88-95	8
β-strand	116-117	2	19
β-strand	120-121	2	19
α-helix	122	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 8: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	54	1	25
α-helix	56-61	6
β-strand	72	1	25
β-strand	84	1	26
β-strand	87	1	26
α-helix	89-109	21
α-helix	112-119	8
α-helix	124-126	3
α-helix	137-139	3
α-helix	148-171	24
α-helix	185-187	3
α-helix	199-202	4
α-helix	211-242	32
α-helix	246-255	10

Chain a: 46 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	39
α-helix	44-46	3
β-strand	50	1	40
α-helix	52-59	8
α-helix	71-102	32
α-helix	106-111	6
β-strand	119-121	3	41
α-helix	129-132	4
β-strand	134-137	4	42
β-strand	140-142	3	42
β-strand	143-144	2	41
α-helix	145	1
α-helix	149-155	7
α-helix	161-183	23
α-helix	184-188	5
β-strand	189-191	3	39
α-helix	192	1
α-helix	193-196	4
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	274-279	6
β-strand	288	1	43
β-strand	293	1	43
α-helix	296-313	18
β-strand	317	1	44
β-strand	325	1	44
α-helix	327-333	7
α-helix	346-349	4
α-helix	354-378	25
α-helix	389-420	32
β-strand	423	1	45
β-strand	427	1	45
α-helix	430-437	8
α-helix	439-469	31
α-helix	473-475	3
α-helix	487-498	12
β-strand	521-523	3	46
β-strand	526-529	4	46
α-helix	536-561	26
α-helix	572-575	4
α-helix	594-619	26
α-helix	620-624	5
β-strand	627-628	2	46
α-helix	630-632	3
β-strand	634-635	2	46
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	40
α-helix	724-726	3
α-helix	727-757	31

Chain A: 47 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	1
α-helix	44-46	3
β-strand	50	1	2
α-helix	52-59	8
α-helix	64-66	3
α-helix	71-102	32
α-helix	106-111	6
β-strand	119-121	3	3
α-helix	129-132	4
β-strand	134-137	4	4
β-strand	140-142	3	4
β-strand	143-144	2	3
α-helix	145	1
α-helix	149-155	7
α-helix	161-183	23
α-helix	184-188	5
β-strand	189-191	3	1
α-helix	192	1
α-helix	193-196	4
α-helix	199-205	7
α-helix	206-212	7
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	288	1	5
β-strand	293	1	5
α-helix	296-313	18
β-strand	317	1	6
β-strand	325	1	6
α-helix	327-333	7
α-helix	346-349	4
α-helix	354-378	25
α-helix	389-420	32
α-helix	430-437	8
α-helix	439-469	31
α-helix	473-475	3
β-strand	477	1	7
β-strand	482	1	7
α-helix	487-498	12
β-strand	521-523	3	8
β-strand	526-529	4	8
α-helix	536-561	26
α-helix	572-575	4
α-helix	594-619	26
α-helix	620-624	5
β-strand	627-628	2	8
α-helix	630-632	3
β-strand	634-635	2	8
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	2
α-helix	724-726	3
α-helix	727-757	31

19 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	A, a	protein	742	Pisum sativum	P05310 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A2	B, b	protein	733	Pisum sativum	P05311 (AlphaFold model)
Photosystem I iron-sulfur center	C, c	protein	80	Pisum sativum	P10793 (AlphaFold model)
Uncharacterized protein	D, d	protein	141	Pisum sativum	A5Z2K3 (AlphaFold model)
Putative uncharacterized protein	E, e	protein	64	Pisum sativum	E1C9K6
Photosystem I reaction center subunit III, chloroplastic	F, f	protein	151	Pisum sativum	P12355
Photosystem I reaction center subunit V, chloroplastic	G, g	protein	95	Pisum sativum	P12357
Putative uncharacterized protein	H, h	protein	90	Pisum sativum	C6T221
Photosystem I reaction center subunit VIII	I, i	protein	30	Pisum sativum	P17227
Photosystem I reaction center subunit IX	J, j	protein	39	Pisum sativum	A4GGC6
Photosystem I reaction center subunit X psaK	K, k	protein	84	Pisum sativum	E1C9L3
Putative uncharacterized protein	L, l	protein	153	Pisum sativum	E1C9L1

4 more molecules are not listed.

Sequence of entity 1 (A, a), FASTA

>4XK8_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains A, a)
EVKILVDRDPIKTSFEQWAKPGHFSRTIAKGPDTTTWIWNLHADAHDFDSHTSDLEEISR
KVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLNDPTHIKPSAQVVWPIVGQEILNGDV
GGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAGLMLFAGWFHYHKAAPKLAWF
QDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPKEIPLPHEFILNRDLLA
QLYPSFAEGATPFFTLNWSKYADFLTFRGGLDPLTGGLWLTDIAHHHLAIAILFLIAGHM
YRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSINLAMLGSLTIVVAQHM
YSMPPYPYLATDYATQLSLFTHHMWIGGFLIVGAAAHAAIFMVRDYDPTTRYNDLLDRVL
RHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVFAQWIQNTH
ALAPGTTAPGATASTSLTWGGGDLVAVGGKVALLPIPLGTADFLVHHIHAFTIHVTVLIL
LKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNSISVVIFHF
SWKMQSDVWGTINDQGVVTHITAGNFAQSSITINGWLRDFLWAQASQVIQSYGSSLSAYG
LFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSIVQGRAVGVT
HYLLGGIATTWAFFLARIIAVG

Sequence of entity 2 (B, b), FASTA

>4XK8_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains B, b)
ALRFPRFSQGIAQDPTTRRIWFGIATAHDFESHDDITEGRLYQNIFASHFGQLAIIFLWT
SGNLFHVAWQGNFEAWVQDPFHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNNAYSGVY
QWWYTIGLRTNEDLYTGAIFLLFLSFISLLAGWLHLQPKWKPSVSWFKNAESRLNHHLSG
LFGVSSLAWAGHLVHVAIPGSRGEYVRWNNFLDVLPHPQGLGPLLTGQWNLYAQNPSSSN
HLFGTTQGAGTAILTILGGFHPQTQSLWLTDMAHHHLAIAFLFLIGGHMYRTNFGIGHSI
KYILEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAFI
AQDFTTQAALYTHHQYIAGFIMTGAFAHGPIFFIRDYNPEQNADNVLARMLEHKEAIISH
LSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTTYGFDVLLSST
NGPALNAGRNIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDA
RGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHITL
WRGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMFLFGHLVWATGF
MFLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVALSIVQARLVGLVHFSVGYIFTY
AAFLIASTSGKFG

Sequence of entity 3 (C, c), FASTA

>4XK8_3 Photosystem I iron-sulfur center (chains C, c)
SHSVKIYDTCIGCTQCVRACPTDVLEMIPWGGCKAKQIASAPRTEDCVGCKRCESACPTD
FLSVRVYLWHETTRSMGLAY

Sequence of entity 4 (D, d), FASTA

>4XK8_4 Uncharacterized protein (chains D, d)
TPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAIMREGPNLL
KLARKEQCLALGTRLRSKYKIKYQFYRVFPNGEVQYLHPKDGVYPEKVNAGRQGVGQNFR
SIGKNVSPIEVKFTGKQPYDL

Sequence of entity 5 (E, e), FASTA

>4XK8_5 Putative uncharacterized protein (chains E, e)
IGPKRGAKVKILRKESYWYKGTGSVVAVDQDPNTRYPVVVRFNKVNYANVSTNNYALDEI
QEVE

Sequence of entity 6 (F, f), FASTA

>4XK8_6 Photosystem I reaction center subunit III, chloroplastic (chains F, f)
DISGLTPCKESKQFAKREKQALKKLQASLKLYADDSAPALAIKATMEKTKKRFDNYGKYG
LLCGSDGLPHLIVSGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAIRDEKKPTQKEII
IDVPLASRLLFRGFSWPVAAYRELLNGELVD

Sequence of entity 7 (G, g), FASTA

>4XK8_7 Photosystem I reaction center subunit V, chloroplastic (chains G, g)
ELSPSLVISLSTGLSLFLGRFVFFNFQRENVAKQVPEQNGLTHFEAGDTRAKEYVSLLKS
NDPVGFNIVDVLAWGSIGHIVAYYILATTSNGYDP

Sequence of entity 8 (H, h), FASTA

>4XK8_8 Putative uncharacterized protein (chains H, h)
SVYFDLEDLGNTTGQWDSYGSDAPSPYNPLQSKLFETFAAPFTKRGLLLKFLILGGGSTL
AYLSATASGDILPITRGPQQPPKLGPRGKI

Sequence of entity 9 (I, i), FASTA

>4XK8_9 Photosystem I reaction center subunit VIII (chains I, i)
INLPSLFVPLVGLLFPAVAMASLFLHVEKR

Sequence of entity 10 (J, j), FASTA

>4XK8_10 Photosystem I reaction center subunit IX (chains J, j)
MRDLKTYLSVAPVVSTLWFGALAGLLIEINRFFPDALIF

Sequence of entity 11 (K, k), FASTA

>4XK8_11 Photosystem I reaction center subunit X psaK (chains K, k)
DFIGSPTNLIMVTSTSLMLFAGRFGLAPSANRKATAGLKLEVRDSGLQTGDPAGFTLADT
LACGVVGHIIGVGVVLGLKNIGAL

Sequence of entity 12 (L, l), FASTA

>4XK8_12 Putative uncharacterized protein (chains L, l)
YQVIQPINGDPFIGSLETPVTSSPLIAWYLSNLPAYRTAVSPLLRGIEVGLAHGYLLVGP
FVKAGPLRNTEIAGQAGSLAAGGLVVILSLCLTIYGISSFNEGAPSTAPSLTLTGRKKEP
DQLQTADGWAKFTGGFFFGGISGVIWAYFLLYV

Ligands and cofactors

ID	Name	Formula	Copies
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	11
XAT	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-…	C40 H56 O4	8
LUT	(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol	C40 H56 O2	10
CHL	Chlorophyll B	C55 H70 Mg N4 O6	24
LMG	1,2-distearoyl-monogalactosyl-diglyceride	C45 H86 O10	5
DGD	Digalactosyl diacyl glycerol (DGDG)	C51 H96 O15	2
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	1
HTG	heptyl 1-thio-beta-D-glucopyranoside	C13 H26 O5 S	6
SF4	Iron/sulfur cluster	Fe4 S4	6
BCR	Beta-carotene	C40 H56	52
PQN	Phylloquinone	C31 H46 O2	4
CLA	Chlorophyll a	C55 H72 Mg N4 O5	285

Primary citation

Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex. Qin, X., Suga, M., Kuang, T. et al. Science (2015) 348:989-995. DOI 10.1126/science.aab0214 · PubMed

Other PDB entries of the same protein (UniProt P05310 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7DKZ 2.39 Å, Structure of plant photosystem I-light harvesting complex I supercomplex
5L8R 2.6 Å, The structure of plant photosystem I super-complex at 2.6 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
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
2WSE 3.49 Å, Improved Model of Plant Photosystem I

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