SAXSdb — 5xv1

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

Autophagy-related protein 13

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 1–190	Fragment：UNP residues 1-190	Autophagy-related protein 101 × 1 （Q9BSB4）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.51 Å R-free 0.251
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–190	Fragment：UNP residues 1-190	Autophagy-related protein 101 × 1 （Q9BSB4）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.51 Å R-free 0.251

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 5XV1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WAN Crystal structure of Atg13 LIR-fused human LC3A_2-121 Deposited 2013-05-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 436–447（12 aa） Fragment：UNP RESIDUES 436-447, 2-121 Chain B 436–447（12 aa） Fragment：UNP RESIDUES 436-447, 2-121	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；12% MPD, 0.1M Sodium chloride, 0.1M Sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.77 Å R-free 0.227
3WAO Crystal structure of Atg13 LIR-fused human LC3B_2-119 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 436–447（12 aa） Fragment：RESIDUES 436-447, RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium citrate tribasic dihydrate 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.294
3WAO Crystal structure of Atg13 LIR-fused human LC3B_2-119 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 436–447（12 aa） Fragment：RESIDUES 436-447, RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium citrate tribasic dihydrate 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.294
3WAO Crystal structure of Atg13 LIR-fused human LC3B_2-119 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 436–447（12 aa） Fragment：RESIDUES 436-447, RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium citrate tribasic dihydrate 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.294
3WAO Crystal structure of Atg13 LIR-fused human LC3B_2-119 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 436–447（12 aa） Fragment：RESIDUES 436-447, RESIDUES 2-119	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium citrate tribasic dihydrate 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.294
3WAP Crystal structure of Atg13 LIR-fused human LC3C_8-125 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 436–447（12 aa） Fragment：UNP RESIDUES 436-447, 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.273
3WAP Crystal structure of Atg13 LIR-fused human LC3C_8-125 Deposited 2013-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 436–447（12 aa） Fragment：UNP RESIDUES 436-447, 8-125	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1M Sodium acetate trihydrate, 8% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.10 Å R-free 0.273
5C50 Crystal structure of the complex of human Atg101-Atg13 HORMA domain Deposited 2015-06-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 12–200（189 aa） Fragment：UNP residues 12-200	Not recorded	BEN BENZAMIDINE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；19% PEG 3350, 0.5 M benzamidine, and 0.2 M lithium citrate	Resolution 1.63 Å R-free 0.195
5XUY Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.275
5XUY Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.275
5XV3 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.57 Å R-free 0.283
5XV3 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.57 Å R-free 0.283
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV6 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa） Fragment：UNP residues 1-190	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.46 Å R-free 0.271
6HYN Structure of ATG13 LIR motif bound to GABARAP Deposited 2018-10-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 441–454（14 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M NaCl, 10% PEG 8000, 0.1M Na K phosphate 6.2	Resolution 1.14 Å R-free 0.185
8DO8 Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer Deposited 2022-07-12	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 D 1–197（197 aa）	Not recorded	GOL GLYCEROL × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 12% PEG8000	Resolution 2.41 Å R-free 0.251
8DO8 Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer Deposited 2022-07-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–197（197 aa）	Not recorded	GOL GLYCEROL × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 12% PEG8000	Resolution 2.41 Å R-free 0.251
8SOI Structure of human ULK1 complex core (2:1:1 stoichiometry) Deposited 2023-04-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 346–401（56 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8SQZ Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture Deposited 2023-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 363–517（155 aa） Chain F 363–517（155 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.85 Å
8SRM Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 334–401（68 aa） Chain F 334–401（68 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.46 Å

13 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATG13_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–190； UniProt 1–190 Author chain C； PDBConstruct 1–190； UniProt 1–190

Autophagy-related protein 101

Homo sapiens

UniProt Q9BSB4

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 1–218	Mutation：K40A/K41A/E42A	Autophagy-related protein 13 × 1 （O75143）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.51 Å R-free 0.251
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–218	Mutation：K40A/K41A/E42A	Autophagy-related protein 13 × 1 （O75143）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.51 Å R-free 0.251

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 5XV1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WZG Structure of human ATG101 Deposited 2014-11-19	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 1–218（218 aa）	Not recorded	BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG3350, MES, NACL, BME	Resolution 1.90 Å R-free 0.220
5C50 Crystal structure of the complex of human Atg101-Atg13 HORMA domain Deposited 2015-06-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–198（198 aa） Fragment：UNP residues 1-198	Not recorded	BEN BENZAMIDINE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；19% PEG 3350, 0.5 M benzamidine, and 0.2 M lithium citrate	Resolution 1.63 Å R-free 0.195
5XUY Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.275
5XUY Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.275
5XV3 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.57 Å R-free 0.283
5XV3 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–218（218 aa）	Mutation：K40A/K41A/E42A	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.57 Å R-free 0.283
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV4 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.95 Å R-free 0.313
5XV6 Crystal structure of ATG101-ATG13HORMA Deposited 2017-06-26	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–218（218 aa）	Mutation：K40A/K41A/E42A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350	Resolution 2.46 Å R-free 0.271
8DO8 Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer Deposited 2022-07-12	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 1–198（198 aa） Chain F 1–198（198 aa）	Not recorded	GOL GLYCEROL × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 12% PEG8000	Resolution 2.41 Å R-free 0.251
8DO8 Crystal structure ATG9 HDIR in complex with the ATG13:ATG101 HORMA dimer Deposited 2022-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–198（198 aa） Chain E 1–198（198 aa）	Not recorded	GOL GLYCEROL × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M HEPES pH 7.5, 0.2 M NaCl, 12% PEG8000	Resolution 2.41 Å R-free 0.251

7 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ATGA1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–218； UniProt 1–218 Author chain D； PDBConstruct 1–218； UniProt 1–218

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	5xv1
Deposition date deposition_date	2017-06-26
Structure title title	Crystal structure of ATG101-ATG13HORMA
Keywords keywords	AUTOPHAGY, ATG101, ATG13, HORMA, 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	34.86 Å
Radius of gyration Rg (electron density) rg_electron	34.33 Å
Forward intensity I(0) i0	115883000.00
Molecular weight molecular_weight	86276.0 kDa
Excluded volume excluded_volume	108150 Å³
Envelope volume envelope_volume	144300 Å³
Hydration-shell volume shell_volume	36015 Å³
Envelope diameter envelope_diameter	131.6 Å
Shell Rg shell_rg	39.07 Å
Envelope Rg envelope_rg	34.99 Å
Shape Rg shape_rg	34.31 Å
Total Rg total_rg	34.79 Å
Total atoms total_atoms	6063
Residues n_residues	793
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	121.5 Å
Rg (real space) rg_real	35.07 Å
Rg uncertainty (real space) rg_real_error	1.29 Å
I(0) (real space) i0_real	1.1590e+08
I(0) uncertainty (real space) i0_real_error	1.9200e+06
Rg (reciprocal space) rg_reciprocal	34.94 Å
I(0) (reciprocal space) i0_reciprocal	115900000.0000
Solution quality estimate total_estimate	0.8404
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.478
Kurtosis Kurtosis kurtosis	-0.361
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	28710000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.858

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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	Autophagy-related protein 13
Molecular weight formula_weight	21319.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6095

METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSSPTGSDWFNLAIKDIPEVTHEAKKALAGQLPAVGRSMCVEISLKTSEGDSMELEIWCLEMNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQLSGLGEGFQTVRVGTVGTPVGTITLSCAYR

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 101
Molecular weight formula_weight	24862.4 kDa
Mutation mutation	K40A/K41A/E42A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MNCRSEVLEVSVEGRQVEEAMLAVLHTVLLHRSTGKFHYAAAGTYSIGTVGTQDVDCDFIDFTYVRVSSEELDRALRKVVGEFKDALRNSGGDGLGQMSLEFYQKKKSRWPFSDECIPWEVWTVKVHVVALATEQERQICREKVGEKLCEKIINIVEVMNRHEYLPKMPTQSEVDNVFDTGLRDVQPYLYKISFQITDALGTSVTTTMRRLIKDTLAL

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	32

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5xv1A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	5xv1C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

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8. Citations (1)

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Unit-cell length a length_a	88.483 Å
Unit-cell length b length_b	125.505 Å
Unit-cell length c length_c	101.038 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.66 °
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	2.508 Å
Low-resolution limit resolution_low	32.984 Å
R factor r_factor	0.2128
R_work r_work	0.2105
R_free r_free	0.2512

fit	/app/data/saxs_computation/xv/5xv1/5xv1.fit
pddf	/app/data/pr_computation/xv/5xv1/5xv1.pr.out
profile	/app/data/saxs_computation/xv/5xv1/5xv1.dat

Crystal structure of ATG101-ATG13HORMA

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

Autophagy-related protein 13

State in the Current Structure

Other States of the Same Protein in the Database

Autophagy-related protein 101

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

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)