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9tgg

Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin

Method: ELECTRON MICROSCOPY D_max: 147.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tgg
deposition_date	2025-12-01
title	Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin
keywords	;b6f complex, photosynthesis, membrane protein, electron transport, proton transport, quinone catalysis, plastocyanin, OXIDOREDUCTASE ;; OXIDOREDUCTASE
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	46.11 Å
rg_electron	44.64 Å
i0	644614000.00
molecular_weight	237190.0 kDa
excluded_volume	308050 Å³
envelope_volume	429740 Å³
shell_volume	79142 Å³
envelope_diameter	155.5 Å
shell_rg	50.21 Å
envelope_rg	44.58 Å
shape_rg	44.62 Å
total_rg	45.00 Å
total_atoms	16731
n_residues	2001
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	147.2 Å
rg_real	46.01 Å
rg_real_error	1.17 Å
i0_real	6.4460e+08
i0_real_error	1.1730e+07
rg_reciprocal	46.11 Å
i0_reciprocal	644700000.0000
total_estimate	0.6636
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	56.3 Å
skewness	0.240
kurtosis	-0.471
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	67930000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 0.021; Positv: 1.000; Valcen: 0.991; Smooth: 0.750

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4. Crystallography & Experiment

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5. Entities & Polymer Info (18)

Entity 1 polymer

description	Cytochrome b6
formula_weight	24186.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,I
atom_count	16731

MSKVYDWFEERLEIQAIADDITSKYVPPHVNIFYCLGGITLTCFLVQVATGFAMTFYYRPTVTDAFASVQYIMTEVNFGWLIRSVHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWVTGVVLGVLTASFGVTGYSLPWDQIGYWAVKIVTGVPDAIPVIGSPLVELLRGSASVGQSTLTRFYSLHTFVLPLLTAVFMLMHFLMIRKQGISGPL

Entity 2 polymer

description	Cytochrome b6-f complex subunit 4
formula_weight	17456.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,J

MGVTKKPDLNDPVLRAKLAKGMGHNYYGEPAWPNDLLYIFPVVILGTIACNVGLAVLEPSMIGEPADPFATPLEILPEWYFFPVFQILRTVPNKLLGVLLMASVPAGLLTVPFLENVNKFQNPFRRPVATTVFLVGTVVALWLGIGATLPIDKSLTLGLF

Entity 3 polymer

description	Cytochrome f
formula_weight	31357.0 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,K

YPIFAQQGYENPREATGRIVCANCHLANKPVDIEVPQAVLPDTVFEAVVRIPYDMQLKQVLANGKKGGLNVGAVLILPEGFELAPPDRISPEMKEKMGNLSFQSYRPNKQNILVIGPVPGQKYSEITFPILAPDPATKKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNSTATGIVKKIVRKEKGGYEINIADASDGREVVDIIPRGPELLVSEGESIKLDQPLTSNPNVGGFGQGDAEVVLQDPLRIQGLLFFFASVILAQIFLVLKKKQFEKVQLSEMNF

Entity 4 polymer

description	Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
formula_weight	18956.5 kDa
ec_number	7.1.1.6
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,L

ATSIPADNVPDMQKRETLNLLLLGALSLPTGYMLLPYASFFVPPGGGAGTGGTIAKDALGNDVIAAEWLKTHAPGDRTLTQGLKGDPTYLVVESDKTLATFGINAVCTHLGCVVPFNAAENKFICPCHGSQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETDFRTGEAPWWSA

Entity 5 polymer

description	Cytochrome b6-f complex subunit 6
formula_weight	3452.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,M

MFTLTSYFGFLLAALTITSALFIGLNKIRLI

Entity 6 polymer

description	Cytochrome b6-f complex subunit 7
formula_weight	3774.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,N

NAAAEIFRIAAVMNGLTLVGVAIGFVLLRIEATVEE

Entity 7 polymer

description	Cytochrome b6-f complex subunit 5
formula_weight	4172.0 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,O

MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL

Entity 8 polymer

description	Cytochrome b6-f complex subunit 8
formula_weight	3170.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,P

MDIVSLAWAALMVVFTFSLSLVVWGRSGL

Entity 9 polymer

description	Plastocyanin, chloroplastic
formula_weight	10420.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Q

VEVLLGGGDGSLAFLPGDFSVASGEEIVFKNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGETYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN

Entity 10 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	4

Entity 11 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	4

Entity 12 non-polymer

description	UNDECYL-MALTOSIDE
formula_weight	496.6 kDa
src_method	syn
entity_count	6

Entity 13 non-polymer

description	;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ;
formula_weight	749.2 kDa
src_method	syn
entity_count	7

Entity 14 non-polymer

description	CHLOROPHYLL A
formula_weight	893.5 kDa
src_method	syn
entity_count	2

Entity 15 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	2

Entity 16 non-polymer

description	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
formula_weight	795.1 kDa
src_method	syn
entity_count	2

Entity 17 non-polymer

description	BETA-CAROTENE
formula_weight	536.9 kDa
src_method	syn
entity_count	2

Entity 18 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.180 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.18 Å
resolution_method	—
num_particles	87892

fit	/app/data/saxs_computation/tg/9tgg/9tgg.fit
pddf	/app/data/pr_computation/tg/9tgg/9tgg.pr.out
profile	/app/data/saxs_computation/tg/9tgg/9tgg.dat

Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (18)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 polymer

Polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 non-polymer

Entity 15 non-polymer

Entity 16 non-polymer

Entity 17 non-polymer

Entity 18 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)