7ZYV: Cytochrome b6

Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.13 A resolution. Determined by electron microscopy at 2.13 Å resolution. Released 25 Jan 2023.

Method: Electron microscopy
Resolution: 2.13 Å
Organism: Spinacia oleracea
Chains: 18
Atoms: 16,452
Mol. weight: 290.62 kDa
Ligands: BCR, FES, SQD, PL9
Released: 25 Jan 2023

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

Secondary structure: helices and β-sheets

7ZYV contains 86 α-helices and 99 β-strands across 18 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 A and I: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	15-21	7
β-strand	25-26	2	1
α-helix	32-35	4
α-helix	36-54	19
α-helix	65-74	10
α-helix	79-106	28
α-helix	115-136	22
β-strand	141	1	2
α-helix	142-151	10
α-helix	154-157	4
α-helix	162-170	9
α-helix	177-185	9
α-helix	186-190	5
α-helix	191-209	19

Chains B and J: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	3
α-helix	12-18	7
β-strand	28	1	3
β-strand	29-30	2	1
α-helix	40-57	18
β-strand	65	1	2
α-helix	79-81	3
α-helix	82-88	7
α-helix	94-109	16
α-helix	111-114	4
α-helix	123-125	3
α-helix	127-146	20
α-helix	151-153	3

Chain C: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	13	1	4
β-strand	19	1	4
α-helix	20-23	4
β-strand	28	1	5
β-strand	32-34	3	6
β-strand	38-39	2	5
β-strand	44-50	7	6
β-strand	59-60	2	7
β-strand	66-67	2	7
β-strand	70-76	7	5
β-strand	82-83	2	6
α-helix	84-85	2
α-helix	86-88	3
α-helix	91-97	7
β-strand	103-106	4	5
β-strand	109-119	11	5
β-strand	125-131	7	6
α-helix	135-137	3
β-strand	145-154	10	5
β-strand	159	1	8
β-strand	165	1	8
β-strand	172	1	9
β-strand	177-178	2	10
β-strand	179-184	6	11
β-strand	190-194	5	11
β-strand	204-207	4	11
β-strand	213	1	12
β-strand	220-221	2	10
β-strand	226	1	9
β-strand	228	1	12
β-strand	235-245	11	5
α-helix	248-282	35

Chain D: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	12-40	29
α-helix	43-44	2
β-strand	53-54	2	13
β-strand	56	1	13
α-helix	61	1
β-strand	62	1	13
α-helix	63	1
α-helix	65-70	6
β-strand	77-81	5	13
α-helix	83-85	3
β-strand	87-91	5	13
β-strand	92	1	14
β-strand	98	1	14
β-strand	101-104	4	13
β-strand	106	1	15
α-helix	112	1
β-strand	113	1	15
α-helix	114-115	2
β-strand	116-117	2	16
β-strand	122-124	3	16
β-strand	131-132	2	16
β-strand	138-140	3	16
α-helix	146-148	3
β-strand	149-155	7	13
β-strand	158-163	6	13

Chains E and M: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-27	26

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-34	33

Chains G and O: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-31	28

Chains H and P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23

4 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
Cytochrome b6	A, I	protein	215	Spinacia oleracea	P00165 (AlphaFold model)
Cytochrome b6-f complex subunit 4	B, J	protein	160	Spinacia oleracea	P00166 (AlphaFold model)
Cytochrome f	C, K	protein	320	Spinacia oleracea	P16013 (AlphaFold model)
Cytochrome b6-f complex iron-sulfur subunit, chloroplastic	D, L	protein	230	Spinacia oleracea	P08980 (AlphaFold model)
Cytochrome b6-f complex subunit 6	E, M	protein	31	Spinacia oleracea	Q9M3L0
Cytochrome b6-f complex subunit 7	F, N	protein	131	Spinacia oleracea	A0A9R0IV89
Cytochrome b6-f complex subunit 5	G, O	protein	37	Spinacia oleracea	P69461
Cytochrome b6-f complex subunit 8	H, P	protein	29	Spinacia oleracea	P61045
Thylakoid soluble phosphoprotein	Q, R	protein	103	Spinacia oleracea	Q8GT36

Sequence of entity 1 (A, I), FASTA

>7ZYV_1 Cytochrome b6 (chains A, I)
MSKVYDWFEERLEIQAIADDITSKYVPPHVNIFYCLGGITLTCFLVQVATGFAMTFYYRP
TVTDAFASVQYIMTEVNFGWLIRSVHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWVT
GVVLGVLTASFGVTGYSLPWDQIGYWAVKIVTGVPDAIPVIGSPLVELLRGSASVGQSTL
TRFYSLHTFVLPLLTAVFMLMHFLMIRKQGISGPL

Sequence of entity 2 (B, J), FASTA

>7ZYV_2 Cytochrome b6-f complex subunit 4 (chains B, J)
MGVTKKPDLNDPVLRAKLAKGMGHNYYGEPAWPNDLLYIFPVVILGTIACNVGLAVLEPS
MIGEPADPFATPLEILPEWYFFPVFQILRTVPNKLLGVLLMASVPAGLLTVPFLENVNKF
QNPFRRPVATTVFLVGTVVALWLGIGATLPIDKSLTLGLF

Sequence of entity 3 (C, K), FASTA

>7ZYV_3 Cytochrome f (chains C, K)
MQTINTFSWIKEQITRSISISLILYIITRSSIANAYPIFAQQGYENPREATGRIVCANCH
LANKPVDIEVPQAVLPDTVFEAVVRIPYDMQLKQVLANGKKGGLNVGAVLILPEGFELAP
PDRISPEMKEKMGNLSFQSYRPNKQNILVIGPVPGQKYSEITFPILAPDPATKKDVHFLK
YPIYVGGNRGRGQIYPDGSKSNNTVYNSTATGIVKKIVRKEKGGYEINIADASDGREVVD
IIPRGPELLVSEGESIKLDQPLTSNPNVGGFGQGDAEVVLQDPLRIQGLLFFFASVILAQ
IFLVLKKKQFEKVQLSEMNF

Sequence of entity 4 (D, L), FASTA

>7ZYV_4 Cytochrome b6-f complex iron-sulfur subunit, chloroplastic (chains D, L)
MASFTLSSATPSQLCSSKNGMFAPSLALAKAGRVNVLISKERIRGMKLTCQATSIPADNV
PDMQKRETLNLLLLGALSLPTGYMLLPYASFFVPPGGGAGTGGTIAKDALGNDVIAAEWL
KTHAPGDRTLTQGLKGDPTYLVVESDKTLATFGINAVCTHLGCVVPFNAAENKFICPCHG
SQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETDFRTGEAPWWSA

Sequence of entity 5 (E, M), FASTA

>7ZYV_5 Cytochrome b6-f complex subunit 6 (chains E, M)
MFTLTSYFGFLLAALTITSALFIGLNKIRLI

Sequence of entity 6 (F, N), FASTA

>7ZYV_6 Cytochrome b6-f complex subunit 7 (chains F, N)
MATAAASTTLSSAAVPAISGSRGQRKMNKVVYMSGVNSYGGLKANNAVLGLGQAVCTEQC
FANVVSSLRSTATKKGRSGGGGGAGGGALTSTCNAAAEIFRIAAVMNGLTLVGVAIGFVL
LRIEATVEEAE

Sequence of entity 7 (G, O), FASTA

>7ZYV_7 Cytochrome b6-f complex subunit 5 (chains G, O)
MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL

Sequence of entity 8 (H, P), FASTA

>7ZYV_8 Cytochrome b6-f complex subunit 8 (chains H, P)
MDIVSLAWAALMVVFTFSLSLVVWGRSGL

Sequence of entity 9 (Q, R), FASTA

>7ZYV_9 Thylakoid soluble phosphoprotein (chains Q, R)
MSSLPFVFGAAASSRVVTAAAAKGTAETKQEKSFVDWLLGKITKEDQFYETDPILRGGDV
KSSGSTSGKKGGTTSGKKGTVSIPSKKKNGNGGVFGGLFAKKD

Ligands and cofactors

ID	Name	Formula	Copies
BCR	Beta-carotene	C40 H56	2
FES	FE2/S2 (inorganic) cluster	Fe2 S2	2
SQD	1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol	C41 H78 O12 S	2
PL9	2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-he…	C53 H80 O2	6
UMQ	Undecyl-maltoside	C23 H44 O11	10
CLA	Chlorophyll a	C55 H72 Mg N4 O5	2
HEC	Heme C	C34 H36 Fe N4 O4	4
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4

Primary citation

High-resolution cryo-EM structures of plant cytochrome b 6 f at work. Sarewicz, M., Szwalec, M., Pintscher, S. et al. Sci Adv (2023) 9:eadd9688-eadd9688. DOI 10.1126/sciadv.add9688 · PubMed

Other PDB entries of the same protein (UniProt P00165 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9ES7 1.94 Å, Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at…
9ES8 2.24 Å, Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at…
9ES9 2.33 Å, Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound…
7QRM 2.7 Å, Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex…
9TGG 3.18 Å, Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin
6RQF 3.58 Å, 3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia…

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