9eii

Import stalled PINK1 TOM complex, symmetry expanded

Method: ELECTRON MICROSCOPY Dmax: 164.8 Å Quality: GOOD

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

Serine/threonine-protein kinase PINK1, mitochondrial

Homo sapiens

UniProt Q9BXM7

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 × 13 PDB declaration: 13-meric(13) Consistent with protein copy count Chain B; UniProt 1–581 Not recorded Mitochondrial import receptor subunit TOM20 homolog × 1 (Q15388) Voltage-dependent anion-selective channel protein 2 × 1 (P45880) Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;Blot force 10 for 2 s. Resolution 2.75 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.

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PINK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–581; UniProt 1–581

Mitochondrial import receptor subunit TOM20 homolog

OrganismNot specified

UniProt Q15388

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 × 13 PDB declaration: 13-meric(13) Consistent with protein copy count Chain D; UniProt 1–145 Not recorded Serine/threonine-protein kinase PINK1, mitochondrial × 1 (Q9BXM7) Voltage-dependent anion-selective channel protein 2 × 1 (P45880) Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;Blot force 10 for 2 s. Resolution 2.75 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 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOM20_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–145; UniProt 1–145

Voltage-dependent anion-selective channel protein 2

OrganismNot specified

UniProt P45880

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 × 13 PDB declaration: 13-meric(13) Consistent with protein copy count Chain F; UniProt 1–294 Not recorded Serine/threonine-protein kinase PINK1, mitochondrial × 1 (Q9BXM7) Mitochondrial import receptor subunit TOM20 homolog × 1 (Q15388) Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;Blot force 10 for 2 s. Resolution 2.75 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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VDAC2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain F; PDBConstruct 1–294; UniProt 1–294

Mitochondrial import receptor subunit TOM40 homolog

OrganismNot specified

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 × 13 PDB declaration: 13-meric(13) Consistent with protein copy count Chain I; UniProt 1–361 Chain J; UniProt 1–361 Not recorded Serine/threonine-protein kinase PINK1, mitochondrial × 1 (Q9BXM7) Mitochondrial import receptor subunit TOM20 homolog × 1 (Q15388) Voltage-dependent anion-selective channel protein 2 × 1 (P45880) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;Blot force 10 for 2 s. Resolution 2.75 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 4
Chains and sequence ranges Author chain I; PDBConstruct 1–361; UniProt 1–361 Author chain J; PDBConstruct 1–361; UniProt 1–361

Mitochondrial import receptor subunit TOM5 homolog

OrganismNot specified

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 × 13 PDB declaration: 13-meric(13) Consistent with protein copy count Chain L; UniProt 1–51 Chain Z; UniProt 1–51 Not recorded Serine/threonine-protein kinase PINK1, mitochondrial × 1 (Q9BXM7) Mitochondrial import receptor subunit TOM20 homolog × 1 (Q15388) Voltage-dependent anion-selective channel protein 2 × 1 (P45880) Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;Blot force 10 for 2 s. Resolution 2.75 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 L; PDBConstruct 1–51; UniProt 1–51 Author chain Z; PDBConstruct 1–51; UniProt 1–51

Mitochondrial import receptor subunit TOM7 homolog

OrganismNot specified

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 × 13 PDB declaration: 13-meric(13) Consistent with protein copy count Chain N; UniProt 1–55 Chain X; UniProt 1–55 Not recorded Serine/threonine-protein kinase PINK1, mitochondrial × 1 (Q9BXM7) Mitochondrial import receptor subunit TOM20 homolog × 1 (Q15388) Voltage-dependent anion-selective channel protein 2 × 1 (P45880) Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;Blot force 10 for 2 s. Resolution 2.75 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 6
Chains and sequence ranges Author chain N; PDBConstruct 1–55; UniProt 1–55 Author chain X; PDBConstruct 1–55; UniProt 1–55

Mitochondrial import receptor subunit TOM6 homolog

OrganismNot specified

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 × 13 PDB declaration: 13-meric(13) Consistent with protein copy count Chain P; UniProt 1–74 Chain V; UniProt 1–74 Not recorded Serine/threonine-protein kinase PINK1, mitochondrial × 1 (Q9BXM7) Mitochondrial import receptor subunit TOM20 homolog × 1 (Q15388) Voltage-dependent anion-selective channel protein 2 × 1 (P45880) Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM22 homolog × 2 (Q9NS69) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;Blot force 10 for 2 s. Resolution 2.75 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 7
Chains and sequence ranges Author chain P; PDBConstruct 1–74; UniProt 1–74 Author chain V; PDBConstruct 1–74; UniProt 1–74

Mitochondrial import receptor subunit TOM22 homolog

OrganismNot specified

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 × 13 PDB declaration: 13-meric(13) Consistent with protein copy count Chain R; UniProt 1–142 Chain T; UniProt 1–142 Not recorded Serine/threonine-protein kinase PINK1, mitochondrial × 1 (Q9BXM7) Mitochondrial import receptor subunit TOM20 homolog × 1 (Q15388) Voltage-dependent anion-selective channel protein 2 × 1 (P45880) Mitochondrial import receptor subunit TOM40 homolog × 2 (O96008) Mitochondrial import receptor subunit TOM5 homolog × 2 (Q8N4H5) Mitochondrial import receptor subunit TOM7 homolog × 2 (Q9P0U1) Mitochondrial import receptor subunit TOM6 homolog × 2 (Q96B49) PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE;Blot force 10 for 2 s. Resolution 2.75 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 8
Chains and sequence ranges Author chain R; PDBConstruct 1–142; UniProt 1–142 Author chain T; PDBConstruct 1–142; UniProt 1–142

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 9eii

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9eii
Deposition date deposition_date2024-11-26
Structure title titleImport stalled PINK1 TOM complex, symmetry expanded
Keywords keywordsPINK1, TOM complex, VDAC, TRANSLOCASE; TRANSLOCASE
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier47.80
Radius of gyration Rg (electron density) rg_electron47.52
Forward intensity I(0) i0563951000.00
Molecular weight molecular_weight205460.0 kDa
Excluded volume excluded_volume261730 ų
Envelope volume envelope_volume416240 ų
Hydration-shell volume shell_volume74017 ų
Envelope diameter envelope_diameter167.4
Shell Rg shell_rg50.56
Envelope Rg envelope_rg46.85
Shape Rg shape_rg47.55
Total Rg total_rg47.55
Total atoms total_atoms14448
Residues n_residues1789
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 dmax164.8
Rg (real space) rg_real47.89
Rg uncertainty (real space) rg_real_error1.83
I(0) (real space) i0_real5.6400e+08
I(0) uncertainty (real space) i0_real_error1.0180e+07
Rg (reciprocal space) rg_reciprocal47.80
I(0) (reciprocal space) i0_reciprocal563900000.0000
Solution quality estimate total_estimate0.8091
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary54.9
Skewness Skewness skewness0.374
Kurtosis Kurtosis kurtosis-0.322
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha90930000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)