SAXSdb — 8zqg

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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 8–344 Chain B； UniProt 8–344	Not recorded	Autophagy-related protein 16-1 × 2 （Q676U5）	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

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 8ZQG	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 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
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 5–323； UniProt 8–344 Author chain B； PDBConstruct 5–323； UniProt 8–344

Autophagy-related protein 16-1

Homo sapiens

UniProt Q676U5

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 124–188 Chain D； UniProt 124–188	Not recorded	WD repeat domain phosphoinositide-interacting protein 3 × 2 （Q5MNZ6）	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

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 8ZQG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4GDK Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 Deposited 2012-07-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 11–43（33 aa） Chain F 11–43（33 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M Hepes pH7.5, 0.2 M lithium citrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.236
4GDL Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1 Deposited 2012-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 11–43（33 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M BICINE pH9.0, 0.2 M sodium phosphate dibasic, 18% PEG 3350, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.88 Å R-free 0.254
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 11–43（33 aa） Fragment：UNP residues 11-43	Not recorded	SO4 SULFATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 11–43（33 aa） Fragment：UNP residues 11-43	Not recorded	SO4 SULFATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 11–43（33 aa） Fragment：UNP residues 11-43	Not recorded	SO4 SULFATE ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4NAW Crystal Structure of Human ATG12~ATG5-ATG16N in complex with a fragment of ATG3 Deposited 2013-10-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain O 11–43（33 aa） Fragment：UNP residues 11-43	Not recorded	SO4 SULFATE ION × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PROTEIN - 10 MG/ML in 0.01M HEPES pH 7.0, 0.15 M NaCl, 0.001 M DTT, RESERVOIR - 0.1M MES pH6.0-6.75, 0.2 M ammonium sulfate, 10-16% PEG 5000 MME, vapor diffusion, sitting drop, temperature 293K	Resolution 2.19 Å R-free 0.215
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10	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 B 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, MgCl2, KCl, Tris-HCl	Resolution 2.70 Å R-free 0.274
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10	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 D 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, MgCl2, KCl, Tris-HCl	Resolution 2.70 Å R-free 0.274
4TQ0 Crystal structure of human ATG5-ATG16N69 Deposited 2014-06-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 400, MgCl2, KCl, Tris-HCl	Resolution 2.70 Å R-free 0.274
5D7G Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms Deposited 2015-08-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–69（69 aa） Fragment：UNP residues 1-69 Chain D 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Micro crystal: 37.5 mM MES, pH 5.2 to pH 5.8, 0.2 M sodium tartrate, and 11 to 13% polyethylene glycol 3350; Micor seeding condition:40 mM MES, pH 5.5, 0.2M sodium tartrate, 8.5% PEG3350, 10 mM DTT	Resolution 3.00 Å R-free 0.244
5D7G Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms Deposited 2015-08-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–69（69 aa） Fragment：UNP residues 1-69 Chain H 1–69（69 aa） Fragment：UNP residues 1-69	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Micro crystal: 37.5 mM MES, pH 5.2 to pH 5.8, 0.2 M sodium tartrate, and 11 to 13% polyethylene glycol 3350; Micor seeding condition:40 mM MES, pH 5.5, 0.2M sodium tartrate, 8.5% PEG3350, 10 mM DTT	Resolution 3.00 Å R-free 0.244
5NPV Structure of human ATG5-ATG16L1(ATG5BD) complex (I4) Deposited 2017-04-19	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 B 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.76；293 K；0.1 M MES pH 5.76, 0.378 M KCl, 21.7 % PEG 3350	Resolution 3.10 Å R-free 0.278
5NPV Structure of human ATG5-ATG16L1(ATG5BD) complex (I4) Deposited 2017-04-19	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 D 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.76；293 K；0.1 M MES pH 5.76, 0.378 M KCl, 21.7 % PEG 3350	Resolution 3.10 Å R-free 0.278
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	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 B 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	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 D 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NPW Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) Deposited 2017-04-19	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 H 11–307（297 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M KCl and 18 % PEG 3350	Resolution 3.10 Å R-free 0.264
5NUV Structure of the WD40-domain of human ATG16L1 Deposited 2017-05-02	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 303–607（305 aa）	Mutation：E354A/K355A/Y607P	BU3 (R,R)-2,3-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；303 K；1.61 M (NH4)2SO4, 0.09 M NaCl, 0.1 M MES pH 6.3	Resolution 1.55 Å R-free 0.197
7W36 Crystal structure of human Atg5 complexed with a stapled peptide Deposited 2021-11-25	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 B 13–33（21 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.2M MgCl2, 0.1M Tris-HCl pH8.5	Resolution 3.00 Å R-free 0.287
7XFR Crystal structure of WIPI2b in complex with the second site of ATG16L1 Deposited 2022-04-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 124–188（65 aa） Chain D 124–188（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M MES monohydrate(pH 6.5), 12% w/v Polyethylene glycol 20000	Resolution 1.76 Å R-free 0.193
9H2Q Stabilized complex of Chlamydia trachomatic efector CT622 in complex with human WD40 domain of ATG16L1 Deposited 2024-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 303–607（305 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.80 Å
9J54 Crystal structure of FIP200 Claw in complex with ATG16L1 Deposited 2024-08-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 235–247（13 aa） Chain D 235–247（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；10% v/v 2-Propanol, 0.1 M BICINE (pH 8.5), 30% w/v Polyethylene glycol 1500	Resolution 1.61 Å R-free 0.216
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 235–247（13 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000	Resolution 1.76 Å R-free 0.215
9JF2 Crystal structure of GABARAPL1 in complex with ATG16L1 Deposited 2024-09-03	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 235–247（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate (pH 6.5), 40% v/v MPD, 5% w/v PEG 8000	Resolution 1.76 Å R-free 0.215

13 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A16L1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–69； UniProt 124–188 Author chain D； PDBConstruct 5–69； UniProt 124–188

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	8zqg
Deposition date deposition_date	2024-06-02
Structure title title	Crystal structure of WIPI3 in complex with ATG16L1
Keywords keywords	WIPI3, ATG16L1, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	32.74 Å
Radius of gyration Rg (electron density) rg_electron	32.33 Å
Forward intensity I(0) i0	102184000.00
Molecular weight molecular_weight	80046.0 kDa
Excluded volume excluded_volume	100010 Å³
Envelope volume envelope_volume	127530 Å³
Hydration-shell volume shell_volume	34131 Å³
Envelope diameter envelope_diameter	110.9 Å
Shell Rg shell_rg	37.72 Å
Envelope Rg envelope_rg	31.95 Å
Shape Rg shape_rg	32.38 Å
Total Rg total_rg	32.62 Å
Total atoms total_atoms	5617
Residues n_residues	725
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	106.4 Å
Rg (real space) rg_real	32.86 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	1.0220e+08
I(0) uncertainty (real space) i0_real_error	1.5440e+06
Rg (reciprocal space) rg_reciprocal	32.81 Å
I(0) (reciprocal space) i0_reciprocal	102200000.0000
Solution quality estimate total_estimate	0.8798
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.0 Å
Skewness Skewness skewness	0.347
Kurtosis Kurtosis kurtosis	-0.633
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17470000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.891

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	WD repeat domain phosphoinositide-interacting protein 3
Molecular weight formula_weight	35664.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	5631

GPGSPHGNGLLYAGFNQDHGCFACGMENGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRCNYLALVGGGKKPKYPPNKVMIWDDLKKKTVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPHQLHVFETCYNPKGLCVLCPNSNNSLLAFPGTHTGHVQLVDLASTEKPPVDIPAHEGVLSCIALNLQGTRIATASEKGTLIRIFDTSSGHLIQELRRGSQAANIYCINFNQDASLICVSSDHGTVHIFAAEDPKSKWSFSKFQVPSGSPCICAFGTEPNAVIAICADGSYYKFLFNPKGECIRDVYAQFLEMTDDKL

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	Autophagy-related protein 16-1
Molecular weight formula_weight	7815.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPGSMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKLRKTTEENQ

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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8. Citations (1)

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Unit-cell length a length_a	182.663 Å
Unit-cell length b length_b	182.663 Å
Unit-cell length c length_c	54.340 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	hexagonal

Resolution resolution	2.770 Å
Low-resolution limit resolution_low	43.870 Å
R factor r_factor	0.1920
R_work r_work	0.1899
R_free r_free	0.2326

fit	/app/data/saxs_computation/zq/8zqg/8zqg.fit
pddf	/app/data/pr_computation/zq/8zqg/8zqg.pr.out
profile	/app/data/saxs_computation/zq/8zqg/8zqg.dat

Crystal structure of WIPI3 in complex with ATG16L1

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

Autophagy-related protein 16-1

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)