9lig

Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in Y19315-bound state

Method: ELECTRON MICROSCOPY

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

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

OrganismNot specified

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） Sdh3p × 1 （C7GVH5） Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial × 1 （P37298） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 3-[bis(fluoranyl)methyl]-~{N}-cyclopropyl-~{N}-[2-(2,4-dichlorophenyl)prop-2-enyl]-5-fluoranyl-1-methyl-pyrazole-4-carboxamide × 1 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1	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 1–592； UniProt 45–636

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

OrganismNot specified

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） Sdh3p × 1 （C7GVH5） Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial × 1 （P37298） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 3-[bis(fluoranyl)methyl]-~{N}-cyclopropyl-~{N}-[2-(2,4-dichlorophenyl)prop-2-enyl]-5-fluoranyl-1-methyl-pyrazole-4-carboxamide × 1 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1	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 1–235； UniProt 30–264

Sdh3p

OrganismNot specified

UniProt C7GVH5

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 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 3-[bis(fluoranyl)methyl]-~{N}-cyclopropyl-~{N}-[2-(2,4-dichlorophenyl)prop-2-enyl]-5-fluoranyl-1-methyl-pyrazole-4-carboxamide × 1 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C7GVH5_YEAS2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–143； UniProt 56–198

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

OrganismNot specified

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） Sdh3p × 1 （C7GVH5） FLAVIN-ADENINE DINUCLEOTIDE × 1 FE2/S2 (INORGANIC) CLUSTER × 1 IRON/SULFUR CLUSTER × 1 FE3-S4 CLUSTER × 1 3-[bis(fluoranyl)methyl]-~{N}-cyclopropyl-~{N}-[2-(2,4-dichlorophenyl)prop-2-enyl]-5-fluoranyl-1-methyl-pyrazole-4-carboxamide × 1 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1	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 1–131； UniProt 37–167

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	9lig
Deposition date deposition_date	2025-01-14
Structure title title	Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in Y19315-bound state
Keywords keywords	Complex, mitochondria, ELECTRON TRANSPORT, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

9lig__assembly_1__model_1

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

Download this curve (.dat)

9lig__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9lig__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.68 Å
Rg (electron density)	34.00 Å
Total Rg	34.19 Å
Atom count	8773
Residues	1101
Excluded volume	156390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9lig__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 (10)

Entity 1 Entity 1 polymer

Description description	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Molecular weight formula_weight	65208.5 kDa
EC 编号 ec_number	1.3.5.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8773

KYHIIDHEYDCVVIGAGGAGLRAAFGLAEAGYKTACISKLFPTRSHTVAAQGGINAALGNMHKDNWKWHMYDTVKGSDWLGDQDSIHYMTREAPKSIIELEHYGVPFSRTENGKIYQRAFGGQTKEYGKGAQAYRTCAVADRTGHALLHTLYGQALRHDTHFFIEYFALDLLTHNGEVVGVIAYNQEDGTIHRFRAHKTIIATGGYGRAYFSCTSAHTCTGDGNAMVSRAGFPLQDLEFVQFHPSGIYGSGCLITEGARGEGGFLVNSEGERFMERYAPTAKDLACRDVVSRAITMEIREGRGVGKKKDHMYLQLSHLPPEVLKERLPGISETAAIFAGVDVTKEPIPIIPTVHYNMGGIPTKWNGEALTIDEETGEDKVIPGLMACGEAACVSVHGANRLGANSLLDLVVFGRAVAHTVADTLQPGLPHKPLPSDLGKESIANLDKLRNANGSRSTAEIRMNMKQTMQKDVSVFRTQSSLDEGVRNITAVEKTFDDVKTTDRSMIWNSDLVETLELQNLLTCASQTAVSAANRKESRGAHAREDYPNRDDEHWMKHTLSWQKDVAAPVTLKYRRVIDHTLDEKECPSVPPT

Entity 2 Entity 2 polymer

Description description	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
Molecular weight formula_weight	26946.2 kDa
EC 编号 ec_number	1.3.5.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TPRLKTFKVYRWNPDEPSAKPHLQSYQVDLNDCGPMVLDALLKIKDEQDSTLTFRRSCREGICGSCAMNIGGRNTLACICKIDQNESKQLKIYPLPHMFIVKDLVPDLTNFYQQYKSIQPYLQRSSFPKDGTEVLQSIEDRKKLDGLYECILCACCSTSCPSYWWNQEQYLGPAVLMQAYRWLIDSRDQATKTRKAMLNNSMSLYRCHTIMNCTRTCPKGLNPGLAIAEIKKSLA

Entity 3 Entity 3 polymer

Description description	Sdh3p
Molecular weight formula_weight	16267.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MNTKAAIAEEQILNKQRARRPISPHLTIYQPQLTWYLSSFHRISLVLMGLGFYLFTILFGVSGLLGLGLTTEKVSNWYHQKFSKITEWSIKGSFAYLFAIHYGGAIRHLIWDTAKELTLKGVYRTGYALIGFTAVLGTYLLTL

Entity 4 Entity 4 polymer

Description description	Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
Molecular weight formula_weight	14441.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

LPVLPQKPGGVRGTPNDAYVPPPENKLEGSYHWYMEKIFALSVVPLATTAMLTTGPLSTAADSFFSVMLLGYCYMEFNSCITDYISGRVYGVWHKYAMYMLGLGSAVSLFGIYKLETENDGVVGLVKSLWD

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

Entity 7 Entity 7 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 8 Entity 8 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 9 Entity 9 non-polymer

Description description	3-[bis(fluoranyl)methyl]-~{N}-cyclopropyl-~{N}-[2-(2,4-dichlorophenyl)prop-2-enyl]-5-fluoranyl-1-methyl-pyrazole-4-carboxamide
Molecular weight formula_weight	418.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Molecular weight formula_weight	744.0 kDa
Source method src_method	syn
Copy count entity_count	1

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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	—

Resolution resolution	3.06 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	121864

Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in Y19315-bound state

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

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Sdh3p

State in the Current Structure

Other States of the Same Protein in the Database

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9lig__assembly_1__model_1

9lig__assembly_1__model_1 | I(q)

9lig__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

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

7. Citations (1)

Cryo-EM structure of Saccharomyces cerevisiae Mitochondrial Respiratory Complex II in Y19315-bound state

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

Sdh3p

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

9lig__assembly_1__model_1

9lig__assembly_1__model_1 | I(q)

9lig__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

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

7. Citations (1)