9qdl

CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial × 1 （P21801） Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial × 1 （P33421） Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial × 1 （P37298） FLAVIN-ADENINE DINUCLEOTIDE × 1 POTASSIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 Ubiquinone-6 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 hexacosanoic acid × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDHA_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–640； UniProt 1–640

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

Saccharomyces cerevisiae

UniProt P21801

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （Q00711） Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial × 1 （P33421） Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial × 1 （P37298） FLAVIN-ADENINE DINUCLEOTIDE × 1 POTASSIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 Ubiquinone-6 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 hexacosanoic acid × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDHB_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–266； UniProt 1–266

Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial

Saccharomyces cerevisiae W303

UniProt P33421

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （Q00711） Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial × 1 （P21801） Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial × 1 （P37298） FLAVIN-ADENINE DINUCLEOTIDE × 1 POTASSIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 Ubiquinone-6 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 hexacosanoic acid × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDH3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–198； UniProt 1–198

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

Saccharomyces cerevisiae

UniProt P37298

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （Q00711） Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial × 1 （P21801） Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial × 1 （P33421） FLAVIN-ADENINE DINUCLEOTIDE × 1 POTASSIUM ION × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 Ubiquinone-6 × 1 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 hexacosanoic acid × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHSD_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–181； UniProt 1–181

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9qdl
Deposition date deposition_date	2025-03-06
Structure title title	CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II
Keywords keywords	COMPLEX II, MEMBRANE PROTEIN, OXIDOREDUCTASE, UBIQUINONE-1; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9qdl__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9qdl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qdl__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.44 Å
Rg (electron density)	32.82 Å
Total Rg	32.95 Å
Atom count	8107
Residues	1016
Excluded volume	144520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qdl__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Molecular weight formula_weight	70404.5 kDa
EC 编号 ec_number	1.3.5.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8131

MLSLKKSALSKLTLLRNTRTFTSSALVRQTQGSVNGSASRSADGKYHIIDHEYDCVVIGAGGAGLRAAFGLAEAGYKTACISKLFPTRSHTVAAQGGINAALGNMHKDNWKWHMYDTVKGSDWLGDQDSIHYMTREAPKSIIELEHYGVPFSRTENGKIYQRAFGGQTKEYGKGAQAYRTCAVADRTGHALLHTLYGQALRHDTHFFIEYFALDLLTHNGEVVGVIAYNQEDGTIHRFRAHKTIIATGGYGRAYFSCTSAHTCTGDGNAMVSRAGFPLQDLEFVQFHPSGIYGSGCLITEGARGEGGFLVNSEGERFMERYAPTAKDLACRDVVSRAITMEIREGRGVGKKKDHMYLQLSHLPPEVLKERLPGISETAAIFAGVDVTKEPIPIIPTVHYNMGGIPTKWNGEALTIDEETGEDKVIPGLMACGEAACVSVHGANRLGANSLLDLVVFGRAVAHTVADTLQPGLPHKPLPSDLGKESIANLDKLRNANGSRSTAEIRMNMKQTMQKDVSVFRTQSSLDEGVRNITAVEKTFDDVKTTDRSMIWNSDLVETLELQNLLTCASQTAVSAANRKESRGAHAREDYPNRDDEHWMKHTLSWQKDVAAPVTLKYRRVIDHTLDEKECPSVPPTVRAY

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
Molecular weight formula_weight	30347.4 kDa
EC 编号 ec_number	1.3.5.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MLNVLLRRKAFCLVTKKGMATATTAAATHTPRLKTFKVYRWNPDEPSAKPHLQSYQVDLNDCGPMVLDALLKIKDEQDSTLTFRRSCREGICGSCAMNIGGRNTLACICKIDQNESKQLKIYPLPHMFIVKDLVPDLTNFYQQYKSIQPYLQRSSFPKDGTEVLQSIEDRKKLDGLYECILCACCSTSCPSYWWNQEQYLGPAVLMQAYRWLIDSRDQATKTRKAMLNNSMSLYRCHTIMNCTRTCPKGLNPGLAIAEIKKSLAFA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 polymer

Description description	Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial
Molecular weight formula_weight	22167.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSAMMVKLGLNKPALLLKPSAFSRAAALSSSRRLLFNTARTNFLSTSPLKNVASEMNTKAAIAEEQILNKQRARRPISPHLTIYQPQLTWYLSSFHRISLVLMGLGFYLFTILFGVSGLLGLGLTTEKVSNWYHQKFSKITEWSIKGSFAYLFAIHYGGAIRHLIWDTAKELTLKGVYRTGYALIGFTAVLGTYLLTL

Source Source

Source organism organism	Saccharomyces cerevisiae W303
NCBI taxonomy ID ncbi_taxonomy_id	580240
Host organism host_organism	Saccharomyces cerevisiae W303

Entity 4 Entity 4 polymer

Description description	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
Molecular weight formula_weight	22081.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MMLPRSMKFMTGRRIFHTATVRAFQSTAKKSLTIPFLPVLPQKPGGVRGTPNDAYVPPPENKLEGSYHWYMEKIFALSVVPLATTAMLTTGPLSTAADSFFSVMLLGYCYMEFNSCITDYISERVYGVWHKYAMYMLGLGSAVSLFGIYKLETENDGVVGLVKSLWDSSEKDNSQKIEAKKGARGSHHHHHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 5 Entity 5 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	Ubiquinone-6
Molecular weight formula_weight	590.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	1,2-Distearoyl-sn-glycerophosphoethanolamine
Molecular weight formula_weight	748.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	hexacosanoic acid
Molecular weight formula_weight	396.7 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.15 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	149808

CRYO-EM STRUCTURE OF THE YEAST RESPIRATORY COMPLEX II

1. Protein Identity and Related Structures Protein Identity & Related Structures

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Succinate dehydrogenase [ubiquinone] cytochrome b subunit, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9qdl__assembly_1__model_1

9qdl__assembly_1__model_1 | I(q)

9qdl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

7. Citations (1)