SAXSdb — 7vc9

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

Mitochondrial import receptor subunit TOM20 homolog

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain M； UniProt 1–145 Chain N； UniProt 1–145	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 13.00 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.

Other PDB	Difference from Current Entry 7VC9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4APO AIP TPR domain in complex with human Tomm20 peptide Deposited 2012-04-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 140–145（6 aa） Fragment：RESIDUES 140-145	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions PEG 3350, AMMONIUM SULFATE, BIS-TRIS PH 5.5	Resolution 1.90 Å R-free 0.234
4APO AIP TPR domain in complex with human Tomm20 peptide Deposited 2012-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 140–145（6 aa） Fragment：RESIDUES 140-145	Not recorded	12P DODECAETHYLENE GLYCOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions PEG 3350, AMMONIUM SULFATE, BIS-TRIS PH 5.5	Resolution 1.90 Å R-free 0.234
8UY3 Fem1B with FNIP1 and Tom20 fragment Deposited 2023-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 62–127（66 aa） Fragment：residues 62-127	Not recorded	ZN ZINC ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10 mg/mL protein complex in 50 mM HEPES pH 7.5, 500 mM NaCl, 1 mM TCEP were mixed in a 2:1 ratio with the reservoir solution containing 30% PEG 3350, 0.2M Ammonium Citrate pH 7	Resolution 3.20 Å R-free 0.264
8UY3 Fem1B with FNIP1 and Tom20 fragment Deposited 2023-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 62–127（66 aa） Fragment：residues 62-127	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10 mg/mL protein complex in 50 mM HEPES pH 7.5, 500 mM NaCl, 1 mM TCEP were mixed in a 2:1 ratio with the reservoir solution containing 30% PEG 3350, 0.2M Ammonium Citrate pH 7	Resolution 3.20 Å R-free 0.264
8UY3 Fem1B with FNIP1 and Tom20 fragment Deposited 2023-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 62–127（66 aa） Fragment：residues 62-127	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；10 mg/mL protein complex in 50 mM HEPES pH 7.5, 500 mM NaCl, 1 mM TCEP were mixed in a 2:1 ratio with the reservoir solution containing 30% PEG 3350, 0.2M Ammonium Citrate pH 7	Resolution 3.20 Å R-free 0.264
8XVA Human TOM complex with whole Tom20 Deposited 2024-01-14	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric	Chain K 1–145（145 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.92 Å
9EIH Import stalled PINK1 TOM complex Deposited 2024-11-26	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 26 PDB declaration: 26-meric	Chain C 1–145（145 aa） Chain D 1–145（145 aa）	Not recorded	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 17	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9EII Import stalled PINK1 TOM complex, symmetry expanded Deposited 2024-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric	Chain D 1–145（145 aa）	Not recorded	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
9EIJ Import stalled PINK1 TOM complex, extended TOM20 helix class Deposited 2024-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric	Chain D 1–145（145 aa）	Not recorded	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 3.30 Å
9J79 Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer) Deposited 2024-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-meric	Chain B 25–145（121 aa） Chain C 25–145（121 aa） Chain G 25–145（121 aa） Chain S 25–145（121 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.08 Å
9J7A local refinement of FEM1B bound with TOM20 (dimer) Deposited 2024-08-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 25–145（121 aa） Chain C 25–145（121 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.13 Å
9J7B local refinement of FEM1B bound with TOM20(tetramer) Deposited 2024-08-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric	Chain B 25–145（121 aa） Chain C 25–145（121 aa） Chain G 25–145（121 aa） Chain Q 25–145（121 aa） Chain S 25–145（121 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.12 Å
9JCE local refinement of FEM1B bound with TOM20 Deposited 2024-08-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 25–145（121 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.59 Å

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	1
Chains and sequence ranges	Author chain M； PDBConstruct 1–145； UniProt 1–145 Author chain N； PDBConstruct 1–145； UniProt 1–145

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	7vc9
Deposition date deposition_date	2021-09-02
Structure title title	Tom20 subunits
Keywords keywords	Tom20, Cryo-EM, TRANSLOCASE; TRANSLOCASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	29.95 Å
Radius of gyration Rg (electron density) rg_electron	29.37 Å
Forward intensity I(0) i0	6749530.00
Molecular weight molecular_weight	20089.0 kDa
Excluded volume excluded_volume	25475 Å³
Envelope volume envelope_volume	47663 Å³
Hydration-shell volume shell_volume	14509 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	34.99 Å
Envelope Rg envelope_rg	26.63 Å
Shape Rg shape_rg	29.40 Å
Total Rg total_rg	30.10 Å
Total atoms total_atoms	2850
Residues n_residues	182
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	83.1 Å
Rg (real space) rg_real	30.08 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	6.7500e+06
I(0) uncertainty (real space) i0_real_error	9.2040e+04
Rg (reciprocal space) rg_reciprocal	30.03 Å
I(0) (reciprocal space) i0_reciprocal	6749000.0000
Solution quality estimate total_estimate	0.7328
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.103
Kurtosis Kurtosis kurtosis	-1.145
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	302600.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.675; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.386; Smooth: 0.110

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	13.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	347600

Description description	Mitochondrial import receptor subunit TOM20 homolog
Molecular weight formula_weight	16319.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N
Atom count atom_count	2850

Tom20 subunits

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

Mitochondrial import receptor subunit TOM20 homolog

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

fit	/app/data/saxs_computation/vc/7vc9/7vc9.fit
pddf	/app/data/pr_computation/vc/7vc9/7vc9.pr.out
profile	/app/data/saxs_computation/vc/7vc9/7vc9.dat