8ca4

Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 2 N-domain).

Method: ELECTRON MICROSCOPY Dmax: 125.9 Å Quality: GOOD

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

NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

OrganismNot specified

UniProt Q9D6J6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 1–248 Not recorded NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial × 1 (Q91YT0) NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial × 1 (Q91VD9) NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 × 1 (Q9CQ75) NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial × 1 (Q8BK30) FES FE2/S2 (INORGANIC) CLUSTER × 2 SF4 IRON/SULFUR CLUSTER × 3 FMN FLAVIN MONONUCLEOTIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.14;pH was corrected at room temperature ~22 C cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.25 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

47 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NDUV2_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain E; PDBConstruct 1–248; UniProt 1–248

NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

OrganismNot specified

UniProt Q91YT0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 1–464 Not recorded NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial × 1 (Q9D6J6) NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial × 1 (Q91VD9) NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 × 1 (Q9CQ75) NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial × 1 (Q8BK30) FES FE2/S2 (INORGANIC) CLUSTER × 2 SF4 IRON/SULFUR CLUSTER × 3 FMN FLAVIN MONONUCLEOTIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.14;pH was corrected at room temperature ~22 C cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.25 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

47 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NDUV1_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain F; PDBConstruct 1–464; UniProt 1–464

NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

OrganismNot specified

UniProt Q91VD9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 1–727 Not recorded NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial × 1 (Q9D6J6) NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial × 1 (Q91YT0) NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 × 1 (Q9CQ75) NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial × 1 (Q8BK30) FES FE2/S2 (INORGANIC) CLUSTER × 2 SF4 IRON/SULFUR CLUSTER × 3 FMN FLAVIN MONONUCLEOTIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.14;pH was corrected at room temperature ~22 C cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.25 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

47 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NDUS1_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain G; PDBConstruct 1–727; UniProt 1–727

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

OrganismNot specified

UniProt Q9CQ75

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain S; UniProt 1–99 Not recorded NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial × 1 (Q9D6J6) NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial × 1 (Q91YT0) NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial × 1 (Q91VD9) NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial × 1 (Q8BK30) FES FE2/S2 (INORGANIC) CLUSTER × 2 SF4 IRON/SULFUR CLUSTER × 3 FMN FLAVIN MONONUCLEOTIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.14;pH was corrected at room temperature ~22 C cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.25 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

47 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NDUA2_MOUSE
Isoform
PDB entities 4
Chains and sequence ranges Author chain S; PDBConstruct 1–99; UniProt 1–99

NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

OrganismNot specified

UniProt Q8BK30

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain s; UniProt 1–104 Not recorded NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial × 1 (Q9D6J6) NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial × 1 (Q91YT0) NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial × 1 (Q91VD9) NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 × 1 (Q9CQ75) FES FE2/S2 (INORGANIC) CLUSTER × 2 SF4 IRON/SULFUR CLUSTER × 3 FMN FLAVIN MONONUCLEOTIDE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.14;pH was corrected at room temperature ~22 C cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.25 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

47 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NDUV3_MOUSE
Isoform
PDB entities 5
Chains and sequence ranges Author chain s; PDBConstruct 1–104; UniProt 1–104

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.

SAXS scattering curve SAXS Profile

SAXS profile for 8ca4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ca4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ca4
Deposition date deposition_date2023-01-24
Structure title titleCryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 2 N-domain).
Keywords keywordsNADH ubiquinone oxidoreductase, Complex I, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.45
Radius of gyration Rg (electron density) rg_electron38.51
Forward intensity I(0) i0396578000.00
Molecular weight molecular_weight159360.0 kDa
Excluded volume excluded_volume198050 ų
Envelope volume envelope_volume246790 ų
Hydration-shell volume shell_volume53710 ų
Envelope diameter envelope_diameter129.2
Shell Rg shell_rg43.88
Envelope Rg envelope_rg38.40
Shape Rg shape_rg38.62
Total Rg total_rg38.47
Total atoms total_atoms11113
Residues n_residues1439
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax125.9
Rg (real space) rg_real38.67
Rg uncertainty (real space) rg_real_error1.15
I(0) (real space) i0_real3.9660e+08
I(0) uncertainty (real space) i0_real_error7.5870e+06
Rg (reciprocal space) rg_reciprocal38.54
I(0) (reciprocal space) i0_reciprocal396500000.0000
Solution quality estimate total_estimate0.8448
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.9
Skewness Skewness skewness0.468
Kurtosis Kurtosis kurtosis-0.405
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha83200000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.458

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)