7WG5: Photosystem I P700 chlorophyll a apoprotein A1

Name: PDB 7WG5: Cyclic electron transport supercomplex NDH-PSI from Arabidopsis
Published: 2022-03-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: electron transport

Cyclic electron transport supercomplex NDH-PSI from Arabidopsis. Determined by electron microscopy at 3.89 Å resolution. Released 16 Mar 2022.

Method: Electron microscopy
Resolution: 3.89 Å
Organism: Arabidopsis thaliana
Chains: 58
Atoms: 112,687
Mol. weight: 1963.89 kDa
Ligands: FES, SQD, XAT, CHL
Released: 16 Mar 2022

Explore 7WG5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7WG5 contains 553 α-helices and 311 β-strands across 58 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 a: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	117-118	2	55
α-helix	126-130	5
α-helix	133-142	10
β-strand	147-148	2	55
β-strand	151-152	2	56
α-helix	157-161	5
β-strand	166	1	55
β-strand	170-171	2	56
α-helix	174-176	3
α-helix	181-194	14
β-strand	198	1	55
α-helix	210-215	6
β-strand	220	1	55
β-strand	222	1	57
β-strand	225	1	58
α-helix	235-237	3
β-strand	240	1	57
β-strand	243	1	58
α-helix	249-252	4
α-helix	258-263	6
α-helix	285-296	12
β-strand	306	1	59
β-strand	307	1	60
α-helix	316-318	3
α-helix	332-340	9
β-strand	346	1	59
β-strand	348-350	3	61
α-helix	354-362	9
β-strand	369-371	3	61
α-helix	375-384	10
β-strand	388	1	60
α-helix	394-400	7
α-helix	401-403	3
β-strand	406	1	60
β-strand	409	1	62
α-helix	413-419	7
α-helix	423-426	4
β-strand	432	1	62
α-helix	445-453	9

Chain A: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	27-58	32
α-helix	70-83	14
α-helix	95-110	16
α-helix	111-113	3
α-helix	130-139	10
α-helix	141-151	11
α-helix	155-170	16
α-helix	172-186	15
α-helix	191-197	7
α-helix	207-210	4
α-helix	212-225	14
α-helix	251-271	21
α-helix	272-276	5
α-helix	298-324	27
α-helix	331-334	4
α-helix	335-340	6
α-helix	341-355	15

Chain A1: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	53-55	3
α-helix	77-106	30
α-helix	114-120	7
β-strand	127-128	2	52
β-strand	131-132	2	52
α-helix	133	1
α-helix	139-157	19
α-helix	170-172	3
α-helix	174-176	3
α-helix	181-211	31
α-helix	217-226	10
α-helix	234-237	4

Chain A3: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	62-64	3
β-strand	88	1	53
β-strand	91	1	53
α-helix	95-114	20
α-helix	116-119	4
β-strand	140	1	54
β-strand	144	1	54
α-helix	152-175	24
α-helix	188-190	3
α-helix	215-246	32
α-helix	250-258	9

Chain A4: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	62-64	3
α-helix	82-84	3
α-helix	86-108	23
α-helix	112-118	7
α-helix	141-162	22
α-helix	164-166	3
α-helix	181-182	2
α-helix	188-190	3
α-helix	199-224	26
α-helix	230-239	10
α-helix	241-243	3
α-helix	246-249	4

Chain A6: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	73-75	3
α-helix	97-130	34
α-helix	138-140	3
α-helix	148-150	3
α-helix	152-173	22
β-strand	184	1	70
β-strand	187	1	70
α-helix	189-191	3
β-strand	193	1	71
β-strand	196	1	71
α-helix	199-202	4
α-helix	215-239	25
α-helix	247-256	10

Chain AA: 43 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	1
α-helix	24-27	4
β-strand	42	1	2
α-helix	44-51	8
α-helix	56-59	4
α-helix	63-94	32
α-helix	98-103	6
β-strand	111-113	3	3
α-helix	121-124	4
β-strand	126-127	2	4
β-strand	133-134	2	4
β-strand	135-136	2	3
α-helix	141-147	7
α-helix	153-175	23
α-helix	176-180	5
β-strand	181-183	3	1
α-helix	185-188	4
α-helix	192-196	5
α-helix	197-204	8
α-helix	205-213	9
α-helix	214-218	5
α-helix	219-227	9
α-helix	237-242	6
α-helix	244-250	7
α-helix	253-256	4
α-helix	259-262	4
α-helix	266-269	4
β-strand	279	1	5
β-strand	286	1	5
α-helix	288-305	18
β-strand	309	1	6
β-strand	317	1	6
α-helix	319-323	5
α-helix	338-342	5
α-helix	346-370	25
α-helix	381-411	31
α-helix	422-429	8
α-helix	431-445	15
α-helix	446-451	6
α-helix	452-461	10
α-helix	465-467	3
β-strand	469	1	7
β-strand	474	1	7
α-helix	479-494	16
α-helix	522-525	4
α-helix	528-553	26
α-helix	564-567	4
α-helix	586-615	30
β-strand	618-620	3	8
β-strand	626-628	3	8
α-helix	634-637	4
α-helix	641-643	3
α-helix	644-650	7
α-helix	651-652	2
α-helix	665-686	22
α-helix	689-704	16
β-strand	713	1	2
α-helix	716-718	3
α-helix	719-749	31

Chain AB: 42 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	10
α-helix	19-26	8
α-helix	27-29	3
α-helix	31-33	3
α-helix	39-71	33
α-helix	74-77	4
α-helix	81-83	3
β-strand	89-90	2	11
α-helix	98-103	6
β-strand	113-114	2	11
α-helix	120-126	7
α-helix	132-155	24
α-helix	165-168	4
α-helix	173-177	5
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	242-243	2
β-strand	261	1	12
β-strand	268	1	12
α-helix	270-288	19
β-strand	291	1	13
β-strand	299	1	13
α-helix	301-305	5
α-helix	324-327	4
α-helix	330-352	23
α-helix	365-392	28
α-helix	393-397	5
α-helix	409-413	5
α-helix	415-445	31
α-helix	449-451	3
β-strand	454-455	2	14
α-helix	458-465	8
α-helix	485-488	4
α-helix	494-501	8
α-helix	514-539	26
α-helix	550-553	4
α-helix	572-603	32
α-helix	606-612	7
α-helix	616-619	4
α-helix	620-625	6
α-helix	626-627	2
α-helix	629-632	4
β-strand	635-636	2	15
β-strand	639-640	2	15
α-helix	644-665	22
α-helix	672-684	13
β-strand	696	1	10
α-helix	698-701	4
α-helix	702-731	30

48 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	AA, BA	protein	750	Arabidopsis thaliana	P56766 (AlphaFold model)
Photosystem I P700 chlorophyll a apoprotein A2	AB, BB	protein	734	Arabidopsis thaliana	P56767 (AlphaFold model)
Photosystem I iron-sulfur center	AC, BC	protein	81	Arabidopsis thaliana	P62090 (AlphaFold model)
Photosystem I reaction center subunit II-2, chloroplastic	AD, BD	protein	204	Arabidopsis thaliana	Q9SA56 (AlphaFold model)
Photosystem I reaction center subunit IV A, chloroplastic	AE, BE	protein	143	Arabidopsis thaliana	Q9S831
Photosystem I reaction center subunit III, chloroplastic	AF, BF	protein	221	Arabidopsis thaliana	Q9SHE8
Photosystem I reaction center subunit V, chloroplastic	AG, BG	protein	160	Arabidopsis thaliana	Q9S7N7
Photosystem I reaction center subunit VI-2, chloroplastic	AH, BH	protein	145	Arabidopsis thaliana	Q9SUI6
Photosystem I reaction center subunit VIII	AI, BI	protein	37	Arabidopsis thaliana	P56768
Photosystem I reaction center subunit IX	AJ, BJ	protein	44	Arabidopsis thaliana	P56769
Photosystem I reaction center subunit psaK, chloroplastic	AK, BK	protein	130	Arabidopsis thaliana	Q9SUI5
Photosystem I reaction center subunit XI, chloroplastic	AL, BL	protein	219	Arabidopsis thaliana	Q9SUI4

32 more molecules are not listed.

Sequence of entity 1 (AA, BA), FASTA

>7WG5_1 Photosystem I P700 chlorophyll a apoprotein A1 (chains AA, BA)
MIIRSPEPEVKILVDRDPIKTSFEEWAKPGHFSRTIAKGPDTTTWIWNLHADAHDFDSHT
SDLEEISRKVFSAHFGQLSIIFLWLSGMYFHGARFSNYEAWLSDPTHIGPSAQVVWPIVG
QEILNGDVGGGFRGIQITSGFFQIWRASGITSELQLYCTAIGALVFAALMLFAGWFHYHK
AAPKLAWFQDVESMLNHHLAGLLGLGSLSWAGHQVHVSLPINQFLNAGVDPKEIPLPHEF
ILNRDLLAQLYPSFAEGATPFFTLNWSKYSEFLTFRGGLDPVTGGLWLTDIAHHHLAIAI
LFLIAGHMYRTNWGIGHGIKDILEAHKGPFTGQGHKGLYEILTTSWHAQLSLNLAMLGSL
TIIVAHHMYSMPPYPYLATDYATQLSLFTHHMWIGGFLIVGAAAHAAIFMVRDYDPTNRY
NDLLDRVLRHRDAIISHLNWVCIFLGFHSFGLYIHNDTMSALGRPQDMFSDTAIQLQPVF
AQWIQNTHALAPGVTAPGETASTSLTWGGGELVAVGGKVALLPIPLGTADFLVHHIHAFT
IHVTVLILLKGVLFARSSRLIPDKANLGFRFPCDGPGRGGTCQVSAWDHVFLGLFWMYNA
ISVVIFHFSWKMQSDVWGSISDQGVVTHITGGNFAQSSITINGWLRDFLWAQASQVIQSY
GSSLSAYGLFFLGAHFVWAFSLMFLFSGRGYWQELIESIVWAHNKLKVAPATQPRALSII
QGRAVGVTHYLLGGIATTWAFFLARIIAVG

Sequence of entity 2 (AB, BB), FASTA

>7WG5_2 Photosystem I P700 chlorophyll a apoprotein A2 (chains AB, BB)
MALRFPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEERLYQNIFASHFGQLAIIFLW
TSGNLFHVAWQGNFETWVQDPLHVRPIAHAIWDPHFGQPAVEAFTRGGALGPVNIAYSGV
YQWWYTIGLRTNEDLYTGALFLLFLSALSLIGGWLHLQPKWKPRVSWFKNAESRLNHHLS
GLFGVSSLAWTGHLVHVAIPASRGEYVRWNNFLNVLPHPQGLGPLFTGQWNLYAQNPDSS
SHLFGTSQGSGTAILTLLGGFHPQTQSLWLTDMAHHHLAIAILFLIAGHMYRTNFGIGHS
IKDLLEAHIPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQHMYSLPAYAF
IAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNPEQNEDNVLARMLDHKEAIIS
HLSWASLFLGFHTLGLYVHNDVMLAFGTPEKQILIEPIFAQWIQSAHGKTSYGFDVLLSS
TSGPAFNAGRSIWLPGWLNAINENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALD
ARGSKLMPDKKDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHIT
LWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMFLFGHLVWATG
FMFLISWRGYWQELIETLAWAHERTPLANLIRWKDKPVALSIVQARLVGLAHFSVGYIFT
YAAFLIASTSGKFG

Sequence of entity 3 (AC, BC), FASTA

>7WG5_3 Photosystem I iron-sulfur center (chains AC, BC)
MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRTEDCVGCKRCESACPT
DFLSVRVYLWHETTRSMGLAY

Sequence of entity 4 (AD, BD), FASTA

>7WG5_4 Photosystem I reaction center subunit II-2, chloroplastic (chains AD, BD)
MATQAAGIFSPAITTTTSAVKKLHLFSSSHRPKSLSFTKTAIRAEKTESSSAAPAVKEAP
VGFTPPQLDPNTPSPIFAGSTGGLLRKAQVEEFYVITWNSPKEQIFEMPTGGAAIMREGP
NLLKLARKEQCLALGTRLRSKYKITYQFYRVFPNGEVQYLHPKDGVYPEKANPGREGVGL
NMRSIGKNVSPIEVKFTGKQSYDL

Sequence of entity 5 (AE, BE), FASTA

>7WG5_5 Photosystem I reaction center subunit IV A, chloroplastic (chains AE, BE)
MAMTTASTVFVLPANVTSVAGASSSRSSVSFLPMRNAGSRLVVRAAEDPAPASSSSKDSP
AAAAAPDGATATKPKPPPIGPKRGSKVKILRRESYWFKNVGSVVAVDQDPKTRYPVVVRF
AKVNYANISTNNYALDEVEEVAA

Sequence of entity 6 (AF, BF), FASTA

>7WG5_6 Photosystem I reaction center subunit III, chloroplastic (chains AF, BF)
MSLTIPANLVLNPRSNKSLTQSVPKSSARFVCSDDKSSSSTPQSMKAFSAAVALSSILLS
APMPAVADISGLTPCKDSKQFAKREKQQIKKLESSLKLYAPESAPALALNAQIEKTKRRF
DNYGKYGLLCGSDGLPHLIVNGDQRHWGEFITPGILFLYIAGWIGWVGRSYLIAISGEKK
PAMKEIIIDVPLASRIIFRGFIWPVAAYREFLNGDLIAKDV

Sequence of entity 7 (AG, BG), FASTA

>7WG5_7 Photosystem I reaction center subunit V, chloroplastic (chains AG, BG)
MATSASALLSPTTFSTAISHKNPNSISFHGLRPLRLGGSSSALPKLSTTGRKSSSAVVRA
ELSPSIVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGKTHFEAGDDRAKEYVSLLK
SNDPIGFNIVDVLAWGSIGHIVAYYILATSSNGYDPSFFG

Sequence of entity 8 (AH, BH), FASTA

>7WG5_8 Photosystem I reaction center subunit VI-2, chloroplastic (chains AH, BH)
MASFATIAAVQPSAAVKGLGGSSLAGAKLFIKPSRQSFKTKSTRAGAVVAKYGDKSVYFD
LEDLGNTTGQWDVYGSDAPSPYNPLQSKFFETFAAPFTKRGLLLKFLILGGGSLLTYVSA
NSTGDVLPIKRGPQEPPKLGPRGKL

Sequence of entity 9 (AI, BI), FASTA

>7WG5_9 Photosystem I reaction center subunit VIII (chains AI, BI)
MTTFNNLPSIFVPLVGLVFPAIAMASLFLHIQKNKIF

Sequence of entity 10 (AJ, BJ), FASTA

>7WG5_10 Photosystem I reaction center subunit IX (chains AJ, BJ)
MRDLKTYLSVAPVLSTLWFGSLAGLLIEINRLFPDALTFPFFSF

Sequence of entity 11 (AK, BK), FASTA

>7WG5_11 Photosystem I reaction center subunit psaK, chloroplastic (chains AK, BK)
MASTMMTTLPQFNGLRATKISAAPVQGLASVQPMRRKGNGALGAKCDFIGSSTNLIMVTS
TTLMLFAGRFGLAPSANRKATAGLRLEARDSGLQTGDPAGFTLADTLACGTVGHIIGVGV
VLGLKNIGAI

Sequence of entity 12 (AL, BL), FASTA

>7WG5_12 Photosystem I reaction center subunit XI, chloroplastic (chains AL, BL)
MAASASPMASQLRSSFSSASLSQRLAVPKGISGAPFGVSPTKRVSSFTVRAVKSDKTTFQ
VVQPINGDPFIGSLETPVTSSPLIAWYLSNLPGYRTAVNPLLRGVEVGLAHGFFLVGPFV
KAGPLRNTAYAGSAGSLAAAGLVVILSMCLTIYGISSFKEGEPSIAPSLTLTGRKKQPDQ
LQTADGWAKFTGGFFFGGISGVTWAYFLLYVLDLPYFVK

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	1
SQD	1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol	C41 H78 O12 S	2
XAT	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-…	C40 H56 O4	8
CHL	Chlorophyll B	C55 H70 Mg N4 O6	22
LMG	1,2-distearoyl-monogalactosyl-diglyceride	C45 H86 O10	4
LUT	(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol	C40 H56 O2	9
DGD	Digalactosyl diacyl glycerol (DGDG)	C51 H96 O15	2
LMU	Dodecyl-alpha-D-maltoside	C24 H46 O11	8
SF4	Iron/sulfur cluster	Fe4 S4	9
BCR	Beta-carotene	C40 H56	51
LHG	1,2-dipalmitoyl-phosphatidyl-glycerole	C38 H75 O10 P	19
PQN	Phylloquinone	C31 H46 O2	4
CLA	Chlorophyll a	C55 H72 Mg N4 O5	284

Primary citation

Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana. Su, X., Cao, D., Pan, X. et al. Mol Plant (2022) 15:454-467. DOI 10.1016/j.molp.2022.01.020 · PubMed

Other PDB entries of the same protein (UniProt P56766 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9WLS 2.18 Å, PSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method
8J6Z 2.79 Å, Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)
8J7A 3.06 Å, Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 1 (PSI-ST1)
8J7B 3.22 Å, Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 2 (PSI-ST2)
7WFD 3.25 Å, Left PSI in the cyclic electron transport supercomplex NDH-PSI from Arabidopsis
7WFE 3.25 Å, Right PSI in the cyclic electron transfer supercomplex NDH-PSI from Arabidopsis

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