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6klr

Crystal structure of human WIPI3 in complex with the WIR-peptide from ATG2A

Method: X-RAY DIFFRACTION Dmax: 63.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

chimera ATG2A and WIPI3

Homo sapiens

UniProt Q2TAZ0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1374–1404 Chain B； UniProt 1374–1404 Mutation：Deletion of 75-80 and Deletion of 264-280 No other associated polymer 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

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 6KLR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8KBX Cryo-EM structure of human ATG2A-WIPI4 complex Deposited 2023-08-04 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 B 1–1938（1938 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
8KBY Cryo-EM structure of ATG2A Deposited 2023-08-04 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 B 1–1938（1938 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
8KC3 Cryo-EM structure of human C-terminally bound ATG9A-ATG2A-WIPI4 complex Deposited 2023-08-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–1938（1938 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
8Y1L Cryo-EM structure of human N-terminally bound ATG9A-ATG2A-WIPI4 complex Deposited 2024-01-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–1938（1938 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.05 Å

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

View Construct and Data Evidence
UniProt name ATG2A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–35； UniProt 1374–1404 Author chain B； PDBConstruct 5–35； UniProt 1374–1404

chimera ATG2A and WIPI3

Homo sapiens

UniProt Q5MNZ6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 8–344 Chain B； UniProt 8–344 Mutation：Deletion of 75-80 and Deletion of 264-280 No other associated polymer 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

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 6KLR 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
8ZQG Crystal structure of WIPI3 in complex with ATG16L1 Deposited 2024-06-02 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
9C9I Structure of the TSC1:WIPI3 complex Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 12–344（333 aa）
Not recorded No recorded non-water small molecule 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
9C9I Structure of the TSC1:WIPI3 complex Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 12–344（333 aa）
Not recorded No recorded non-water small molecule 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
9C9I Structure of the TSC1:WIPI3 complex Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 12–344（333 aa）
Not recorded No recorded non-water small molecule 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
9C9I Structure of the TSC1:WIPI3 complex Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 12–344（333 aa）
Not recorded No recorded non-water small molecule 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
9CE3 Structure of the TSC:WIPI3 lysosomal recruitment complex Deposited 2024-06-26 Different construct Different mutation/modification 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 7 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 38–350； UniProt 8–344 Author chain B； PDBConstruct 38–350； UniProt 8–344

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 6klr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6klr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6klr
Deposition date deposition_date2019-07-30
Structure title titleCrystal structure of human WIPI3 in complex with the WIR-peptide from ATG2A
Keywords keywordsMEMBRANE BOUND PROTEIN, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.18 Å
Radius of gyration Rg (electron density) rg_electron19.13 Å
Forward intensity I(0) i020645300.00
Molecular weight molecular_weight34857.0 kDa
Excluded volume excluded_volume43697 ų
Envelope volume envelope_volume50915 ų
Hydration-shell volume shell_volume21719 ų
Envelope diameter envelope_diameter65.5 Å
Shell Rg shell_rg26.08 Å
Envelope Rg envelope_rg19.24 Å
Shape Rg shape_rg19.15 Å
Total Rg total_rg20.00 Å
Total atoms total_atoms2451
Residues n_residues319
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax63.1 Å
Rg (real space) rg_real20.05 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real2.0650e+07
I(0) uncertainty (real space) i0_real_error2.0930e+05
Rg (reciprocal space) rg_reciprocal20.08 Å
I(0) (reciprocal space) i0_reciprocal20650000.0000
Solution quality estimate total_estimate0.8965
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.1 Å
Skewness Skewness skewness0.133
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5763000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)