9jxv

human translocase of the outer mitochondrial membrane (TOM complex)

Method: ELECTRON MICROSCOPY Dmax: 118.5 Å Quality: GOOD

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

Mitochondrial import receptor subunit TOM40 homolog

Homo sapiens

UniProt O96008

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 1–361 Chain B; UniProt 1–361 Not recorded Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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.

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOM40_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–361; UniProt 1–361 Author chain B; PDBConstruct 1–361; UniProt 1–361

Mitochondrial import receptor subunit TOM22 homolog

Homo sapiens

UniProt Q9NS69

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain C; UniProt 1–142 Chain D; UniProt 1–142 Not recorded Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOM22_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–142; UniProt 1–142 Author chain D; PDBConstruct 1–142; UniProt 1–142

Mitochondrial import receptor subunit TOM6 homolog

Homo sapiens

UniProt Q96B49

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain E; UniProt 1–74 Chain F; UniProt 1–74 Not recorded Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOM6_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–74; UniProt 1–74 Author chain F; PDBConstruct 1–74; UniProt 1–74

Mitochondrial import receptor subunit TOM7 homolog

Homo sapiens

UniProt Q9P0U1

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain G; UniProt 1–55 Chain H; UniProt 1–55 Not recorded Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOM7_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain G; PDBConstruct 1–55; UniProt 1–55 Author chain H; PDBConstruct 1–55; UniProt 1–55

Mitochondrial import receptor subunit TOM5 homolog

Homo sapiens

UniProt Q8N4H5

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 × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain I; UniProt 1–51 Chain J; UniProt 1–51 Not recorded Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.8 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.89 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.

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOM5_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain I; PDBConstruct 1–51; UniProt 1–51 Author chain J; PDBConstruct 1–51; UniProt 1–51

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 9jxv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9jxv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9jxv
Deposition date deposition_date2024-10-12
Structure title titlehuman translocase of the outer mitochondrial membrane (TOM complex)
Keywords keywordscomplex, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier36.74
Radius of gyration Rg (electron density) rg_electron36.41
Forward intensity I(0) i0159444000.00
Molecular weight molecular_weight104860.0 kDa
Excluded volume excluded_volume133120 ų
Envelope volume envelope_volume203580 ų
Hydration-shell volume shell_volume47722 ų
Envelope diameter envelope_diameter130.5
Shell Rg shell_rg41.79
Envelope Rg envelope_rg35.69
Shape Rg shape_rg36.39
Total Rg total_rg36.94
Total atoms total_atoms7390
Residues n_residues934
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 dmax118.5
Rg (real space) rg_real36.70
Rg uncertainty (real space) rg_real_error0.77
I(0) (real space) i0_real1.5940e+08
I(0) uncertainty (real space) i0_real_error2.4680e+06
Rg (reciprocal space) rg_reciprocal36.73
I(0) (reciprocal space) i0_reciprocal159400000.0000
Solution quality estimate total_estimate0.8921
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.4
Skewness Skewness skewness0.295
Kurtosis Kurtosis kurtosis-0.437
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14890000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.935

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)