4H13: Cytochrome b6

Crystal Structure of the Cytochrome b6f Complex from Mastigocladus laminosus with TDS. Determined by X-ray diffraction at 3.07 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 3.07 Å
Organism: Mastigocladus laminosus
Chains: 8
Atoms: 8,127
Mol. weight: 117.21 kDa
Ligands: CD, HEM, OPC, MYS
Released: 13 Feb 2013

Explore 4H13 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4H13 contains 41 α-helices and 46 β-strands across 8 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: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
α-helix	14-21	8
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	112-114	3
α-helix	115-136	22
β-strand	141	1	2
α-helix	142-153	12
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

Chain B: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	3
α-helix	12-20	9
β-strand	28	1	3
β-strand	29-30	2	1
α-helix	40-57	18
β-strand	61	1	4
α-helix	64	1
β-strand	65	1	2
α-helix	66	1
α-helix	71-72	2
α-helix	79-81	3
α-helix	82-88	7
α-helix	94-114	21
α-helix	115-117	3
α-helix	127-148	22

Chain C: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	21-24	4
β-strand	29	1	4
β-strand	33-35	3	5
β-strand	39-40	2	4
β-strand	45-51	7	5
β-strand	60	1	6
β-strand	68	1	6
β-strand	71-77	7	4
α-helix	78-79	2
β-strand	83-84	2	5
α-helix	85-86	2
α-helix	92-98	7
β-strand	104-105	2	4
β-strand	113-120	8	4
β-strand	126-132	7	5
β-strand	145-155	11	4
β-strand	160	1	7
β-strand	166	1	7
β-strand	183	1	8
β-strand	187	1	9
β-strand	193	1	9
β-strand	196-198	3	8
β-strand	208-210	3	8
β-strand	239-249	11	4
α-helix	252-287	36

Chain D: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	14-42	29
α-helix	44-46	3
β-strand	55	1	10
β-strand	57	1	11
α-helix	67-72	6
β-strand	78-79	2	12
β-strand	82	1	11
α-helix	84-86	3
β-strand	88	1	11
β-strand	89-90	2	13
β-strand	91-92	2	12
β-strand	93	1	14
α-helix	94	1
β-strand	99	1	14
β-strand	102	1	10
β-strand	104-105	2	13
β-strand	107	1	15
α-helix	113	1
β-strand	114	1	15
α-helix	115-116	2
β-strand	117-118	2	16
β-strand	123-125	3	16
β-strand	132-133	2	16
β-strand	139	1	16
β-strand	151-154	4	10
β-strand	161-164	4	10

Chain E: 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	3-30	28

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-29	26

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytochrome b6	A	protein	215	Mastigocladus laminosus	P83791 (AlphaFold model)
Cytochrome b6-f complex subunit 4	B	protein	160	Mastigocladus laminosus	P83792 (AlphaFold model)
Apocytochrome f	C	protein	289	Mastigocladus laminosus	P83793 (AlphaFold model)
Cytochrome b6-f complex iron-sulfur subunit	D	protein	179	Mastigocladus laminosus	P83794 (AlphaFold model)
Cytochrome b6-f complex subunit 6	E	protein	32	Mastigocladus laminosus	P83795
Cytochrome b6-f complex subunit 7	F	protein	35	Mastigocladus laminosus	P83796
Cytochrome b6-f complex subunit 5	G	protein	37	Mastigocladus laminosus	P83797
Cytochrome b6-f complex subunit 8	H	protein	29	Mastigocladus laminosus	P83798

Sequence of entity 1 (A), FASTA

>4H13_1 Cytochrome b6 (chains A)
MANVYDWFQERLEIQALADDVTSKYVPPHVNIFYCLGGITLTCFLIQFATGFAMTFYYKP
TVTEAYASVQYIMNEVSFGWLIRSIHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWIS
GVILAVITVSFGVTGYSLPWDQVGYWAVKIVSGVPEAIPVVGVLISDLLRGGSSVGQATL
TRYYSAHTFVLPWLIAVFMLLHFLMIRKQGISGPL

Sequence of entity 2 (B), FASTA

>4H13_2 Cytochrome b6-f complex subunit 4 (chains B)
MATLKKPDLSDPKLRAKLAKGMGHNYYGEPAWPNDLLYVFPVVIMGTFACIVALSVLDPA
MVGEPADPFATPLEILPEWYLYPVFQILRSVPNKLLGVLLMASVPLGLILVPFIENVNKF
QNPFRRPVATTIFLFGTLVTIWLGIGATFPLDKTLTLGLF

Sequence of entity 3 (C), FASTA

>4H13_3 Apocytochrome f (chains C)
YPFWAQQTYPPTPREPTGRIVCANCHLAAKPAEVEVPQSVLPDTVFKAVVKIPYDTKLQQ
VAADGSKVGLNVGAVLMLPEGFKIAPEERIPEELKKEVGDVYFQPYKEGQDNVLLVGPLP
GEQYQEIVFPVLSPNPTTDKNIHFGKYAIHLGANRGRGQIYPTGEKSNNNVFTASATGTI
TKIAKEEDEYGNVKYQVSIQTDSGKTVVDTIPAGPELIVSEGQAVKAGEALTNNPNVGGF
GQDDTEIVLQDPNRVKWMIAFICLVMLAQLMLILKKKQVEKVQAAEMNF

Sequence of entity 4 (D), FASTA

>4H13_4 Cytochrome b6-f complex iron-sulfur subunit (chains D)
MAQFTESMDVPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPSGGAVGGGTTAKDKL
GNNVKVSKFLESHNAGDRVLVQGLKGDPTYIVVESKEAIRDYGINAVCTHLGCVVPWNAA
ENKFKCPCHGSQYDETGKVIRGPAPLSLALCHATVQDDNIVLTPWTETDFRTGEKPWWV

Sequence of entity 5 (E), FASTA

>4H13_5 Cytochrome b6-f complex subunit 6 (chains E)
MILGAVFYIVFIALFFGIAVGIIFAIKSIKLI

Sequence of entity 6 (F), FASTA

>4H13_6 Cytochrome b6-f complex subunit 7 (chains F)
MTEEMLYAALLSFGLIFVGWGLGVLLLKIQGAEKE

Sequence of entity 7 (G), FASTA

>4H13_7 Cytochrome b6-f complex subunit 5 (chains G)
MVEPLLDGLVLGLVFATLGGLFYAAYQQYKRPNELGG

Sequence of entity 8 (H), FASTA

>4H13_8 Cytochrome b6-f complex subunit 8 (chains H)
MEIDVLGWVALLVVFTWSIAMVVWGRNGL

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	1
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4
OPC	(7R,17E)-4-hydroxy-N,N,N,7-tetramethyl-7-[(8E)-octadec-8-enoyloxy]-10-oxo-3,5,9…	C45 H87 N O8 P	2
MYS	Pentadecane	C15 H32	1
8K6	Octadecane	C18 H38	1
UMQ	Undecyl-maltoside	C23 H44 O11	2
TDS	8-hydroxy-5,7-dimethoxy-3-methyl-2-tridecyl-4H-chromen-4-one	C25 H38 O5	2
CLA	Chlorophyll a	C55 H72 Mg N4 O5	1
7PH	(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate	C29 H57 O8 P	1
SQD	1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol	C41 H78 O12 S	1
FES	FE2/S2 (inorganic) cluster	Fe2 S2	1
OCT	N-octane	C8 H18	1
BCR	Beta-carotene	C40 H56	1

Primary citation

Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex. Hasan, S.S., Yamashita, E., Baniulis, D. et al. Proc Natl Acad Sci U S A (2013) 110:4297-4302. DOI 10.1073/pnas.1222248110 · PubMed

Other PDB entries of the same protein (UniProt P83791 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4I7Z 2.8 Å, Crystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein…
1VF5 3.0 Å, Crystal Structure of Cytochrome b6f Complex from M.laminosus
2E74 3.0 Å, Crystal Structure of the Cytochrome b6f Complex from M.laminosus
4PV1 3.0 Å, Cytochrome B6F structure from M. laminosus with the quinone analog inhibitor stigmatellin
4H0L 3.25 Å, Cytochrome b6f Complex Crystal Structure from Mastigocladus laminosus with n-Side…
2E76 3.41 Å, Crystal Structure of the Cytochrome b6f Complex with tridecyl-stigmatellin (TDS) from…
2E75 3.55 Å, Crystal Structure of the Cytochrome b6f Complex with 2-nonyl-4-hydroxyquinoline N-oxide…
2D2C 3.8 Å, Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. Laminosus

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