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9qdm

CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II WITH THE INHIBITOR BIXAFEN

Method: ELECTRON MICROSCOPY D_max: 114.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdm
deposition_date	2025-03-06
title	CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II WITH THE INHIBITOR BIXAFEN
keywords	COMPLEX II, MEMBRANE PROTEIN, OXIDOREDUCTASE, OXIDOREDUCTASE INHIBITOR COMPLEX, BIXAFEN; 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	32.67 Å
rg_electron	32.86 Å
i0	419110000.00
molecular_weight	109490.0 kDa
excluded_volume	105310 Å³
envelope_volume	176670 Å³
shell_volume	45214 Å³
envelope_diameter	121.9 Å
shell_rg	39.15 Å
envelope_rg	33.56 Å
shape_rg	32.97 Å
total_rg	33.00 Å
total_atoms	8225
n_residues	1038
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	114.1 Å
rg_real	32.94 Å
rg_real_error	1.04 Å
i0_real	4.1910e+08
i0_real_error	8.0530e+06
rg_reciprocal	32.82 Å
i0_reciprocal	419100000.0000
total_estimate	0.6002
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	35.6 Å
skewness	0.633
kurtosis	0.116
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	69580000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.683; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 0.919; Smooth: 0.684

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

Entity 1 polymer

description	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
formula_weight	70404.5 kDa
ec_number	1.3.5.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8258

MLSLKKSALSKLTLLRNTRTFTSSALVRQTQGSVNGSASRSADGKYHIIDHEYDCVVIGAGGAGLRAAFGLAEAGYKTACISKLFPTRSHTVAAQGGINAALGNMHKDNWKWHMYDTVKGSDWLGDQDSIHYMTREAPKSIIELEHYGVPFSRTENGKIYQRAFGGQTKEYGKGAQAYRTCAVADRTGHALLHTLYGQALRHDTHFFIEYFALDLLTHNGEVVGVIAYNQEDGTIHRFRAHKTIIATGGYGRAYFSCTSAHTCTGDGNAMVSRAGFPLQDLEFVQFHPSGIYGSGCLITEGARGEGGFLVNSEGERFMERYAPTAKDLACRDVVSRAITMEIREGRGVGKKKDHMYLQLSHLPPEVLKERLPGISETAAIFAGVDVTKEPIPIIPTVHYNMGGIPTKWNGEALTIDEETGEDKVIPGLMACGEAACVSVHGANRLGANSLLDLVVFGRAVAHTVADTLQPGLPHKPLPSDLGKESIANLDKLRNANGSRSTAEIRMNMKQTMQKDVSVFRTQSSLDEGVRNITAVEKTFDDVKTTDRSMIWNSDLVETLELQNLLTCASQTAVSAANRKESRGAHAREDYPNRDDEHWMKHTLSWQKDVAAPVTLKYRRVIDHTLDEKECPSVPPTVRAY

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Saccharomyces cerevisiae

Entity 2 polymer

description	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
formula_weight	30347.4 kDa
ec_number	1.3.5.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MLNVLLRRKAFCLVTKKGMATATTAAATHTPRLKTFKVYRWNPDEPSAKPHLQSYQVDLNDCGPMVLDALLKIKDEQDSTLTFRRSCREGICGSCAMNIGGRNTLACICKIDQNESKQLKIYPLPHMFIVKDLVPDLTNFYQQYKSIQPYLQRSSFPKDGTEVLQSIEDRKKLDGLYECILCACCSTSCPSYWWNQEQYLGPAVLMQAYRWLIDSRDQATKTRKAMLNNSMSLYRCHTIMNCTRTCPKGLNPGLAIAEIKKSLAFA

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Saccharomyces cerevisiae

Entity 3 polymer

description	Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
formula_weight	22167.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MSAMMVKLGLNKPALLLKPSAFSRAAALSSSRRLLFNTARTNFLSTSPLKNVASEMNTKAAIAEEQILNKQRARRPISPHLTIYQPQLTWYLSSFHRISLVLMGLGFYLFTILFGVSGLLGLGLTTEKVSNWYHQKFSKITEWSIKGSFAYLFAIHYGGAIRHLIWDTAKELTLKGVYRTGYALIGFTAVLGTYLLTL

Source

organism	Saccharomyces cerevisiae W303
ncbi_taxonomy_id	580240
host_organism	Saccharomyces cerevisiae W303

Entity 4 polymer

description	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
formula_weight	22081.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MMLPRSMKFMTGRRIFHTATVRAFQSTAKKSLTIPFLPVLPQKPGGVRGTPNDAYVPPPENKLEGSYHWYMEKIFALSVVPLATTAMLTTGPLSTAADSFFSVMLLGYCYMEFNSCITDYISERVYGVWHKYAMYMLGLGSAVSLFGIYKLETENDGVVGLVKSLWDSSEKDNSQKIEAKKGARGSHHHHHHHHHH

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Saccharomyces cerevisiae

Entity 5 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	FE3-S4 CLUSTER
formula_weight	295.8 kDa
src_method	syn
entity_count	1

Entity 10 non-polymer

description	bixafen
formula_weight	414.2 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

description	1,2-Distearoyl-sn-glycerophosphoethanolamine
formula_weight	748.1 kDa
src_method	syn
entity_count	1

Entity 12 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	27

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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	triclinic

resolution	3.00 Å
resolution_method	—
num_particles	146416

fit	/app/data/saxs_computation/qd/9qdm/9qdm.fit
pddf	/app/data/pr_computation/qd/9qdm/9qdm.pr.out
profile	/app/data/saxs_computation/qd/9qdm/9qdm.dat

CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II WITH THE INHIBITOR BIXAFEN

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

EM 3D

5. Entities & Polymer Info (12)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)