SAXSdb — 4apo

▼

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

AH RECEPTOR-INTERACTING PROTEIN

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 166–330	Fragment：TETRATRICOPEPTIDE REPEAT DOMAIN, RESIDUES 172-313 Mutation：YES	MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG × 1 （Q15388）	X-RAY DIFFRACTION X-ray crystallization conditions：PEG 3350, AMMONIUM SULFATE, BIS-TRIS PH 5.5	Resolution 1.90 Å R-free 0.234
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 166–330	Fragment：TETRATRICOPEPTIDE REPEAT DOMAIN, RESIDUES 172-313 Mutation：YES	MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG × 1 （Q15388） 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

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 4APO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LKN Solution structure of the PPIase domain of human aryl-hydrocarbon receptor-interacting protein (AIP) Deposited 2011-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–166（165 aa） Fragment：PPIase FKBP-type domain containing residues 1-166	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition 2 mM AIP, 10 mM sodium phosphate, 5 mM DTT, 0.05 mM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 2 mM [U-15N] AIP, 10 mM sodium phosphate, 5 mM DTT, 0.05 mM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 2 mM [U-13C; U-15N] AIP, 10 mM sodium phosphate, 5 mM DTT, 0.05 mM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
4AIF AIP TPR domain in complex with human Hsp90 peptide Deposited 2012-02-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 172–315（144 aa） Fragment：TETRATRICOPEPTIDE DOMAIN, RESIDUES 172-315	Mutation：YES	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 1 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5, 1% PEG 3350	Resolution 2.01 Å R-free 0.236
4AIF AIP TPR domain in complex with human Hsp90 peptide Deposited 2012-02-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 172–315（144 aa） Fragment：TETRATRICOPEPTIDE DOMAIN, RESIDUES 172-315	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 1 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5, 1% PEG 3350	Resolution 2.01 Å R-free 0.236
7ZUB Cryo-EM structure of the indirubin-bound Hsp90-XAP2-AHR complex Deposited 2022-05-12	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 × 4 PDB declaration: tetrameric	Chain C 1–330（330 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MOO MOLYBDATE ION × 2 JY6 (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
8QMO Cryo-EM structure of the benzo[a]pyrene-bound Hsp90-XAP2-AHR complex Deposited 2023-09-24	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 × 4 PDB declaration: tetrameric	Chain C 1–330（330 aa）	Not recorded	MOO MOLYBDATE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 W62 benzo[a]pyrene × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å

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

View Construct and Data Evidence

UniProt name	AIP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–165； UniProt 166–330 Author chain B； PDBConstruct 1–165； UniProt 166–330

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 140–145	Fragment：RESIDUES 140-145	AH RECEPTOR-INTERACTING PROTEIN × 1 （O00170）	X-RAY DIFFRACTION X-ray crystallization conditions：PEG 3350, AMMONIUM SULFATE, BIS-TRIS PH 5.5	Resolution 1.90 Å R-free 0.234
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 140–145	Fragment：RESIDUES 140-145	AH RECEPTOR-INTERACTING PROTEIN × 1 （O00170） 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

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 4APO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7VC9 Tom20 subunits Deposited 2021-09-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain M 1–145（145 aa） Chain N 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 13.00 Å
8UY3 Fem1B with FNIP1 and Tom20 fragment Deposited 2023-11-12	Different construct Different oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different experimental method Different experimental conditions 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 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 × 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 mutation/modification Different oligomeric state Different experimental method 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 method 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 oligomeric state Different experimental method 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 12 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 1–6； UniProt 140–145 Author chain E； PDBConstruct 1–6； UniProt 140–145

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4apo
Deposition date deposition_date	2012-04-04
Structure title title	AIP TPR domain in complex with human Tomm20 peptide
Keywords keywords	SIGNALING PROTEIN-PEPTIDE COMPLEX, ARYL HYDROCARBON RECEPTOR; SIGNALING PROTEIN/PEPTIDE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.25 Å
Radius of gyration Rg (electron density) rg_electron	21.18 Å
Forward intensity I(0) i0	21507300.00
Molecular weight molecular_weight	35013.0 kDa
Excluded volume excluded_volume	43722 Å³
Envelope volume envelope_volume	53557 Å³
Hydration-shell volume shell_volume	21450 Å³
Envelope diameter envelope_diameter	73.9 Å
Shell Rg shell_rg	27.37 Å
Envelope Rg envelope_rg	21.51 Å
Shape Rg shape_rg	21.18 Å
Total Rg total_rg	22.00 Å
Total atoms total_atoms	2464
Residues n_residues	308
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

▼

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

Maximum dimension Dmax dmax	71.1 Å
Rg (real space) rg_real	22.19 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	2.1510e+07
I(0) uncertainty (real space) i0_real_error	2.7270e+05
Rg (reciprocal space) rg_reciprocal	22.21 Å
I(0) (reciprocal space) i0_reciprocal	21510000.0000
Solution quality estimate total_estimate	0.7074
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.1 Å
Skewness Skewness skewness	0.267
Kurtosis Kurtosis kurtosis	-0.268
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2847000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 0.189; Positv: 1.000; Valcen: 0.999; Smooth: 0.955

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	AH RECEPTOR-INTERACTING PROTEIN
Molecular weight formula_weight	18973.6 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2997

DPWAMTAEEKAKAVPLIHQEGNRLYREGHVKEAAAKYYDAIACLKNLQMKEQPGSPEWIQLDQQITPLLLNYCQCKLVVEEYYEVLDHCSSILNKYDDNVKAYFKRGKAHAAVWNAQEAQADFAKVLELDPALAPVVSRELQALEARIRQKDEEDKARFRGIFSH

来源 Source

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	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 HOMOLOG
Molecular weight formula_weight	676.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

AEDDVE

Entity 3 Entity 3 non-polymer

Description description	DODECAETHYLENE GLYCOL
Molecular weight formula_weight	546.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	478

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4apoA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	4apoB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	60.200 Å
Unit-cell length b length_b	106.820 Å
Unit-cell length c length_c	68.470 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.85 °
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	—

Resolution resolution	1.895 Å
Low-resolution limit resolution_low	28.454 Å
R factor r_factor	0.1836
R_work r_work	0.1809
R_free r_free	0.2344

fit	/app/data/saxs_computation/ap/4apo/4apo.fit
pddf	/app/data/pr_computation/ap/4apo/4apo.pr.out
profile	/app/data/saxs_computation/ap/4apo/4apo.dat

AIP TPR domain in complex with human Tomm20 peptide

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

AH RECEPTOR-INTERACTING PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)