6vax

Crystal structure of human SDHA-SDHAF2 assembly intermediate

Method: X-RAY DIFFRACTION

▼

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 2	Succinate dehydrogenase assembly factor 2, mitochondrial × 1 （Q9NX18） FLAVIN-ADENINE DINUCLEOTIDE × 1 OXALOACETATE ION × 1 MALONATE ION × 1 GLYCEROL × 1 POTASSIUM ION × 1 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Succinate dehydrogenase assembly factor 2, mitochondrial × 1 （Q9NX18） FLAVIN-ADENINE DINUCLEOTIDE × 1 OXALOACETATE ION × 1 GLYCEROL × 1 POTASSIUM ION × 1 1,2-ETHANEDIOL × 5 water × 2	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 Author chain C； 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 2	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （P31040） FLAVIN-ADENINE DINUCLEOTIDE × 1 OXALOACETATE ION × 1 MALONATE ION × 1 GLYCEROL × 1 POTASSIUM ION × 1 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial × 1 （P31040） FLAVIN-ADENINE DINUCLEOTIDE × 1 OXALOACETATE ION × 1 GLYCEROL × 1 POTASSIUM ION × 1 1,2-ETHANEDIOL × 5 water × 2	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 1–166； UniProt 1–166 Author chain D； PDBConstruct 1–166； UniProt 1–166

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6vax
Deposition date deposition_date	2019-12-18
Structure title title	Crystal structure of human SDHA-SDHAF2 assembly intermediate
Keywords keywords	SDHA, FLAVOPROTEIN, SDHAF2, ASSEMBLY INTERMEDIATE, RESPIRATORY COMPLEX, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6vax__assembly_1__model_1

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

Download this curve (.dat)

6vax__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6vax__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.58 Å
Rg (electron density)	24.58 Å
Total Rg	25.38 Å
Atom count	5708
Residues	724
Excluded volume	100670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6vax__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6vax__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	11494

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	19626.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MAVSTVFSTSSLMLALSRHSLLSPLLSVTSFRRFYRGDSPTDSQKDMIEIPLPPWQERTDESIETKRARLLYESRKRGMLENCILLSLFAKEHLQHMTEKQLNLYDRLINEPSNDWDIYYWATEAKPAPEIFENEVMALLRDFAKNKNKEQRLRAPDLEYLFEKPR

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 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	OXALOACETATE ION
Molecular weight formula_weight	131.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	9

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

▶

Unit-cell length a length_a	210.558 Å
Unit-cell length b length_b	68.782 Å
Unit-cell length c length_c	126.578 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	45.050 Å
R factor r_factor	0.2015
R_work r_work	0.1991
R_free r_free	0.2489

Crystal structure of human SDHA-SDHAF2 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6vax__assembly_1__model_1

6vax__assembly_1__model_1 | I(q)

6vax__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

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 water

7. Citations (1)

Crystal structure of human SDHA-SDHAF2 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6vax__assembly_1__model_1

6vax__assembly_1__model_1 | I(q)

6vax__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

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 water

7. Citations (1)