8dyd

Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate

Method: X-RAY DIFFRACTION

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

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Succinate dehydrogenase assembly factor 2, mitochondrial × 1 （Q9NX18） Succinate dehydrogenase assembly factor 4, mitochondrial × 1 （Q5VUM1） FLAVIN-ADENINE DINUCLEOTIDE × 1 TETRAETHYLENE GLYCOL × 2 POTASSIUM ION × 1 CHLORIDE ION × 1 1,2-ETHANEDIOL × 30 DI(HYDROXYETHYL)ETHER × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDHA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–632； UniProt 44–664

Succinate dehydrogenase assembly factor 2, mitochondrial

Homo sapiens

UniProt Q9NX18

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （P31040） Succinate dehydrogenase assembly factor 4, mitochondrial × 1 （Q5VUM1） FLAVIN-ADENINE DINUCLEOTIDE × 1 TETRAETHYLENE GLYCOL × 2 POTASSIUM ION × 1 CHLORIDE ION × 1 1,2-ETHANEDIOL × 30 DI(HYDROXYETHYL)ETHER × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDHF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–137； UniProt 30–166

Succinate dehydrogenase assembly factor 4, mitochondrial

Homo sapiens

UniProt Q5VUM1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （P31040） Succinate dehydrogenase assembly factor 2, mitochondrial × 1 （Q9NX18） FLAVIN-ADENINE DINUCLEOTIDE × 1 TETRAETHYLENE GLYCOL × 2 POTASSIUM ION × 1 CHLORIDE ION × 1 1,2-ETHANEDIOL × 30 DI(HYDROXYETHYL)ETHER × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SDHF4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 24–98； UniProt 34–108

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	8dyd
Deposition date deposition_date	2022-08-04
Structure title title	Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate
Keywords keywords	SDHA, FLAVOPROTEIN, SDHAF2, SDHAF4, ASSEMBLY INTERMEDIATE, RESPIRATORY COMPLEX, OXIDOREDUCTASE, ELECTRON TRANSPORT; FLAVOPROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

8dyd__assembly_1__model_1

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

Download this curve (.dat)

8dyd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8dyd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.84 Å
Rg (electron density)	24.84 Å
Total Rg	25.68 Å
Atom count	11818
Residues	767
Excluded volume	109270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8dyd__assembly_1__model_1`	trimeric （3）	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	69416.4 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	A
Atom count atom_count	12592

MRGSHHHHHHGSAKVSDSISAQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEEDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPAAVVELENYGMPFSRTEDGKIYQRAFGGQSLKFGKGGQAHRCCCVADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGSIHRIRAKNTVVATGGYGRTYFSCTSAHTSTGDGTAMITRAGLPCQDLEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTLEIREGRGCGPEKDHVYLQLHHLPPEQLATRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMGGIPTNYKGQVLRHVNGQDQIVPGLYACGEAACASVHGANRLGANSLLDLVVFGRACALSIEESCRPGDKVPPIKPNAGEESVMNLDKLRFADGSIRTSELRLSMQKSMQNHAAVFRVGSVLQEGCGKISKLYGDLKHLKTFDRGMVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKVRIDEYDYSKPIQGQQKKPFEEHWRKHTLSYVDVGTGKVTLEYRPVIDKTLNEADCATVPPAIRSY

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	Succinate dehydrogenase assembly factor 2, mitochondrial
Molecular weight formula_weight	16592.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SFRRFYRGDSPTDSQKDMIEIPLPPWQERTDESIETKRARLLYESRKRGMLENCILLSLFAKEHLQHMTEKQLNLYDRLINEPSNDWDIYYWATEAKPAPEIFENEVMALLRDFAKNKNKEQRLRAPDLEYLFEKPR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli K-12

Entity 3 Entity 3 polymer

Description description	Succinate dehydrogenase assembly factor 4, mitochondrial
Molecular weight formula_weight	11227.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MRSHHHHHHENLYFQGIDPFTGSSSSQGGKSELVKQSLKKPKLPEGRFDAPEDSHLEKEPLEKFPDDVNPVTKEKGGPRGPEPTRYGDWERKGRCIDF

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 4 Entity 4 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 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	30

Entity 9 Entity 9 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	519

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Unit-cell length a length_a	66.048 Å
Unit-cell length b length_b	103.206 Å
Unit-cell length c length_c	126.237 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.520 Å
Low-resolution limit resolution_low	35.490 Å
R factor r_factor	0.1581
R_work r_work	0.1567
R_free r_free	0.1842

Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate

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 assembly factor 2, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Succinate dehydrogenase assembly factor 4, 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

8dyd__assembly_1__model_1

8dyd__assembly_1__model_1 | I(q)

8dyd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

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 non-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 water

7. Citations (1)

Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate

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 assembly factor 2, 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 assembly factor 4, 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

8dyd__assembly_1__model_1

8dyd__assembly_1__model_1 | I(q)

8dyd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

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 non-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 water

7. Citations (1)