SAXSdb — 9c9i

▼

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

WD repeat domain phosphoinositide-interacting protein 3

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 12–344	Not recorded	Hamartin × 1 （Q92574）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.	Resolution 3.18 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 12–344	Not recorded	Hamartin × 1 （Q92574）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.	Resolution 3.18 Å R-free 0.255
3	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 12–344	Not recorded	Hamartin × 2 （Q92574）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.	Resolution 3.18 Å R-free 0.255
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 12–344	Not recorded	Hamartin × 1 （Q92574）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.	Resolution 3.18 Å R-free 0.255

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 9C9I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6IYY Crystal structure of human WIPI3,loop deletion mutant Deposited 2018-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–344（337 aa）	Mutation：DELETION OF RESIDUES 75-80 and 264-281	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；289 K；1.6M Ammonium Sulfate, 0.1M Tris-HCl	Resolution 1.80 Å R-free 0.204
6KLR Crystal structure of human WIPI3 in complex with the WIR-peptide from ATG2A Deposited 2019-07-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 8–344（337 aa） Chain B 8–344（337 aa）	Mutation：Deletion of 75-80 and Deletion of 264-280 Mutation：Deletion of 75-80 and Deletion of 264-280	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M Tirs-HCl, pH 8.5, 20% (v/v) Ethanol	Resolution 2.21 Å R-free 0.255
8ZQG Crystal structure of WIPI3 in complex with ATG16L1 Deposited 2024-06-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 8–344（337 aa） Chain B 8–344（337 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；289 K；0.02 M Citric acid, 0.08 M BIS-TRIS propane (pH 8.8); 16% w/v Polyethylene glycol 3350	Resolution 2.77 Å R-free 0.233
9CE3 Structure of the TSC:WIPI3 lysosomal recruitment complex Deposited 2024-06-26	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain F 12–344（333 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES (pH 7.6), 250 mM NaCl, 2 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

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

View Construct and Data Evidence

UniProt name	WIPI3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–316； UniProt 12–344 Author chain C； PDBConstruct 8–316； UniProt 12–344 Author chain E； PDBConstruct 8–316； UniProt 12–344 Author chain G； PDBConstruct 8–316； UniProt 12–344

Hamartin

Homo sapiens

UniProt Q92574

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 B； UniProt 648–681	Not recorded	WD repeat domain phosphoinositide-interacting protein 3 × 1 （Q5MNZ6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.	Resolution 3.18 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 648–681	Not recorded	WD repeat domain phosphoinositide-interacting protein 3 × 1 （Q5MNZ6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.	Resolution 3.18 Å R-free 0.255
3	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 648–681 Chain X； UniProt 648–681	Not recorded	WD repeat domain phosphoinositide-interacting protein 3 × 1 （Q5MNZ6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.	Resolution 3.18 Å R-free 0.255
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 648–681	Not recorded	WD repeat domain phosphoinositide-interacting protein 3 × 1 （Q5MNZ6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.	Resolution 3.18 Å R-free 0.255

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 9C9I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Z6Y Structure of the TBC1D7-TSC1 complex Deposited 2015-04-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 938–993（56 aa） Fragment：UNP RESIDUES 938-993 Chain F 938–993（56 aa） Fragment：UNP RESIDUES 938-993	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；8% PEG 6000, 4% 2-methyl-2,4-pentanediol (MPD), 0.1M HEPES, pH7.5	Resolution 2.81 Å R-free 0.255
4Z6Y Structure of the TBC1D7-TSC1 complex Deposited 2015-04-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 938–993（56 aa） Fragment：UNP RESIDUES 938-993 Chain H 938–993（56 aa） Fragment：UNP RESIDUES 938-993	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；8% PEG 6000, 4% 2-methyl-2,4-pentanediol (MPD), 0.1M HEPES, pH7.5	Resolution 2.81 Å R-free 0.255
5EJC Crystal structural of the TSC1-TBC1D7 complex Deposited 2015-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 939–992（54 aa） Fragment：UNP residues 939-992 Chain F 939–992（54 aa） Fragment：UNP residues 939-992	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200 mM NaCl, 20mM CaCl2 and 15% PEG-3350	Resolution 3.10 Å R-free 0.239
5EJC Crystal structural of the TSC1-TBC1D7 complex Deposited 2015-11-01	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 939–992（54 aa） Fragment：UNP residues 939-992 Chain D 939–992（54 aa） Fragment：UNP residues 939-992	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200 mM NaCl, 20mM CaCl2 and 15% PEG-3350	Resolution 3.10 Å R-free 0.239
7DL2 Cryo-EM structure of human TSC complex Deposited 2020-11-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–1164（1164 aa） Chain D 1–1164（1164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
9CE3 Structure of the TSC:WIPI3 lysosomal recruitment complex Deposited 2024-06-26	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 1–1164（1164 aa） Chain D 1–1164（1164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES (pH 7.6), 250 mM NaCl, 2 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TSC1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–34； UniProt 648–681 Author chain D； PDBConstruct 1–34； UniProt 648–681 Author chain F； PDBConstruct 1–34； UniProt 648–681 Author chain H； PDBConstruct 1–34； UniProt 648–681 Author chain X； PDBConstruct 1–34； UniProt 648–681

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	9c9i
Deposition date deposition_date	2024-06-14
最后修订 last_revision	2024-12-04
Structure title title	Structure of the TSC1:WIPI3 complex
Keywords keywords	TSC, Tuberous sclerosis complex, TSC1, TSC2, TBC1D7, WIPI3, end-some, MTOR, cell growth, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	35.98 Å
Radius of gyration Rg (electron density) rg_electron	35.65 Å
Forward intensity I(0) i0	311734000.00
Molecular weight molecular_weight	143900.0 kDa
Excluded volume excluded_volume	180490 Å³
Envelope volume envelope_volume	231070 Å³
Hydration-shell volume shell_volume	53662 Å³
Envelope diameter envelope_diameter	121.9 Å
Shell Rg shell_rg	42.26 Å
Envelope Rg envelope_rg	35.41 Å
Shape Rg shape_rg	35.65 Å
Total Rg total_rg	36.11 Å
Total atoms total_atoms	10118
Residues n_residues	1304
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	113.3 Å
Rg (real space) rg_real	35.83 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	3.1170e+08
I(0) uncertainty (real space) i0_real_error	5.1210e+06
Rg (reciprocal space) rg_reciprocal	35.93 Å
I(0) (reciprocal space) i0_reciprocal	311800000.0000
Solution quality estimate total_estimate	0.9040
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.9 Å
Skewness Skewness skewness	0.155
Kurtosis Kurtosis kurtosis	-0.553
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	127000000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.938

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	WD repeat domain phosphoinositide-interacting protein 3
Molecular weight formula_weight	35222.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	10118

MHHHHHHGLLYAGFNQDHGCFACGMENGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRCNYLALVGGGKKKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPHQLHVFETCYNPKGLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSCIALNLQGTRIATASEKGTLIRIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAEDPKSKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGSYYKFLFNPKGECIRDVYAQFLEMTDDKL

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Hamartin
Molecular weight formula_weight	3490.0 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,B,D,F,H

XXXXXXXXXXXAHSKELNKLPLPSKSVDWTHFGG

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	Spodoptera frugiperda

▶

8. Citations (1)

▶

Unit-cell length a length_a	94.241 Å
Unit-cell length b length_b	94.241 Å
Unit-cell length c length_c	199.386 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	20

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	3.180 Å
Low-resolution limit resolution_low	47.120 Å
R factor r_factor	0.2005
R_work r_work	0.1976
R_free r_free	0.2554

fit	/app/data/saxs_computation/c9/9c9i/9c9i.fit
pddf	/app/data/pr_computation/c9/9c9i/9c9i.pr.out
profile	/app/data/saxs_computation/c9/9c9i/9c9i.dat

Structure of the TSC1:WIPI3 complex

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

WD repeat domain phosphoinositide-interacting protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Hamartin

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)