4ddp

crystal structure of Beclin 1 evolutionarily conserved domain(ECD)

Method: X-RAY DIFFRACTION D_max: 66.7 Å Quality: REASONABLE

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

Beclin-1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 241–450	Fragment：UNP residues 241-450	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；30% PEG 3350, 0.3M NaCl, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.55 Å R-free 0.203

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 4DDP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
13BV Cryo-EM structure of human PI3KC3-C1 complex Deposited 2026-04-28	Different construct 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 D 1–450（450 aa）	Not recorded	MYR MYRISTIC ACID × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.77 Å
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05	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 107–135（29 aa） Fragment：Beclin 1	Mutation：BH3 domain (residues 107-135)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05	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 107–135（29 aa） Fragment：Beclin 1	Mutation：BH3 domain (residues 107-135)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05	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 107–135（29 aa） Fragment：Beclin 1	Mutation：BH3 domain (residues 107-135)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05	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 107–135（29 aa） Fragment：Beclin 1	Mutation：BH3 domain (residues 107-135)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 107–135（29 aa） Fragment：Beclin 1 Chain D 107–135（29 aa） Fragment：Beclin 1 Chain F 107–135（29 aa） Fragment：Beclin 1 Chain H 107–135（29 aa） Fragment：Beclin 1	Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 107–135（29 aa） Fragment：Beclin 1 Chain H 107–135（29 aa） Fragment：Beclin 1	Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
2P1L Structure of the Bcl-XL:Beclin 1 complex Deposited 2007-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 107–135（29 aa） Fragment：Beclin 1 Chain D 107–135（29 aa） Fragment：Beclin 1	Mutation：BH3 domain (residues 107-135) Mutation：BH3 domain (residues 107-135)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
2PON Solution structure of the Bcl-xL/Beclin-1 complex Deposited 2007-04-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–23（23 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50mM potassium phosphate；Pressure 1 NMR sample composition 1.5mM unlabelled Bcl-xL/Beclin-1 complex in 99.9% D2O; 50mM potassium phosphate \| 99.9% D2O NMR sample composition 1.5mM uniformly 15N labelled Bcl-xL/Beclin-1 complex in 90% H2O/10% D2O; 50mM potassium phosphate \| 90% H2O/10% D2O NMR sample composition 1.5mM uniformly 15N/13C labelled Bcl-xL/Beclin-1 complex in 99.9% D2O; 50mM potassium phosphate \| 99.9% D2O NMR sample composition 1.5mM 80% deuterated, uniformly 15N/13C labelled Bcl-xL/Beclin-1 complex in 90% H2O/10% D2O; 50mM potassium phosphate \| 90% H2O/10% D2O NMR sample composition 1.5mM 100% deuterated, uniformly 15N labelled Bcl-xL/Beclin-1 complex in 90% H2O/10% D2O; 50mM potassium phosphate \| 90% H2O/10% D2O	Resolution not provided
3DVU Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain Deposited 2008-07-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 105–130（26 aa） Fragment：BH3 domain, residues 105-130	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；20% PEG 3350, 0.1M sodium acetate, pH 4.5, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.261
3DVU Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain Deposited 2008-07-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 105–130（26 aa） Fragment：BH3 domain, residues 105-130	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；20% PEG 3350, 0.1M sodium acetate, pH 4.5, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.261
4MI8 Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide Deposited 2013-08-30	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 C 107–130（24 aa） Fragment：UNP residues 107-130	Mutation：G120E, D121A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.224
4MI8 Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide Deposited 2013-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 107–130（24 aa） Fragment：UNP residues 107-130	Mutation：G120E, D121A	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.224
4MI8 Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide Deposited 2013-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 107–130（24 aa） Fragment：UNP residues 107-130 Chain D 107–130（24 aa） Fragment：UNP residues 107-130	Mutation：G120E, D121A Mutation：G120E, D121A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.224
5EFM Beclin 1 Flexible-helical Domian (FHD) (141-171) Deposited 2015-10-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 141–171（31 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.6；293 K；250mM potassium sodium tartrate tetrahydrate, 2.2 M ammonium sulfate, 100mM sodium citrate tribasic dihydrate (pH 5.6)	Resolution 1.95 Å R-free 0.216
5HHE Human Beclin 1 coiled-coil domain Deposited 2016-01-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 175–265（91 aa） Fragment：UNP entries 175-265	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；39% 2-methyl-2, 4-pentadiol, 9% PEG400 and 100 mM Tris buffer, pH 7.5.	Resolution 1.46 Å R-free 0.208
5HHE Human Beclin 1 coiled-coil domain Deposited 2016-01-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 175–265（91 aa） Fragment：UNP entries 175-265	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；39% 2-methyl-2, 4-pentadiol, 9% PEG400 and 100 mM Tris buffer, pH 7.5.	Resolution 1.46 Å R-free 0.208
5VAU Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 105–130（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M Bis-tris chloride, pH 5.5, ).2M ammonium acetate, 25% PEG 3350	Resolution 1.75 Å R-free 0.215
5VAU Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 105–130（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M Bis-tris chloride, pH 5.5, ).2M ammonium acetate, 25% PEG 3350	Resolution 1.75 Å R-free 0.215
5VAU Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 105–130（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M Bis-tris chloride, pH 5.5, ).2M ammonium acetate, 25% PEG 3350	Resolution 1.75 Å R-free 0.215
5VAU Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 105–130（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M Bis-tris chloride, pH 5.5, ).2M ammonium acetate, 25% PEG 3350	Resolution 1.75 Å R-free 0.215
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28	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 E 105–130（26 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；pH 4.5；293 K；bis-tris chloride, pH 4.5, 0.2M ammonium acetate, 25% PEG 3350	Resolution 2.00 Å R-free 0.243
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28	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 F 105–130（26 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；pH 4.5；293 K；bis-tris chloride, pH 4.5, 0.2M ammonium acetate, 25% PEG 3350	Resolution 2.00 Å R-free 0.243
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28	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 G 105–130（26 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；pH 4.5；293 K；bis-tris chloride, pH 4.5, 0.2M ammonium acetate, 25% PEG 3350	Resolution 2.00 Å R-free 0.243
5VAX Bcl-2 complex with Beclin 1 BH3 domain Deposited 2017-03-28	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 105–130（26 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；pH 4.5；293 K；bis-tris chloride, pH 4.5, 0.2M ammonium acetate, 25% PEG 3350	Resolution 2.00 Å R-free 0.243
5VAY Bcl-2 complex with Beclin 1 T108D BH3 domain Deposited 2017-03-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 105–130（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350	Resolution 1.80 Å R-free 0.228
5VAY Bcl-2 complex with Beclin 1 T108D BH3 domain Deposited 2017-03-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 105–130（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350	Resolution 1.80 Å R-free 0.228
5VAY Bcl-2 complex with Beclin 1 T108D BH3 domain Deposited 2017-03-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 105–130（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350	Resolution 1.80 Å R-free 0.228
5VAY Bcl-2 complex with Beclin 1 T108D BH3 domain Deposited 2017-03-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 105–130（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350	Resolution 1.80 Å R-free 0.228
6DCN Bcl-xL complex with Beclin 1 BH3 domain T108pThr Deposited 2018-05-07	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 C 105–130（26 aa） Chain D 105–130（26 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；2M NaCl, 10% glycerol	Resolution 2.44 Å R-free 0.229
6DCN Bcl-xL complex with Beclin 1 BH3 domain T108pThr Deposited 2018-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 105–130（26 aa） Chain D 105–130（26 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；2M NaCl, 10% glycerol	Resolution 2.44 Å R-free 0.229
6DCO Bcl-xL complex with Beclin 1 BH3 domain T108D Deposited 2018-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 105–130（26 aa） Chain D 105–130（26 aa）	Mutation：T108D Mutation：T108D	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Tris pH 7.0, 0.2M MgCl2, 2.5M NaCl	Resolution 2.20 Å R-free 0.231
6HOI Structure of Beclin1 LIR motif bound to GABARAPL1 Deposited 2018-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 93–102（10 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000	Resolution 1.14 Å R-free 0.166
6HOI Structure of Beclin1 LIR motif bound to GABARAPL1 Deposited 2018-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 93–102（10 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000	Resolution 1.14 Å R-free 0.166
6HOJ Structure of Beclin1 LIR motif bound to GABARAP Deposited 2018-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 93–105（13 aa） Chain B 93–105（13 aa） Chain C 93–105（13 aa）	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG 4000, 50 mM Bicine pH 8.8	Resolution 1.51 Å R-free 0.211
6HOK Structure of Beclin1 LIR (S96E) motif bound to GABARAP Deposited 2018-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 93–105（13 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6 M ammonium sulfate, 100 mM TRIS pH 8.5, 10 % Glycerol	Resolution 1.61 Å R-free 0.198
7BL1 human complex II-BATS bound to membrane-attached Rab5a-GTP Deposited 2021-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain EEE 1–450（450 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；Blot force 20, blot time 6 s	Resolution 9.80 Å
9C82 Structure of human ULK1C:PI3KC3-C1 supercomplex Deposited 2024-06-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；added 0.05% (w/v) octylglucopyranoside as surfactant	Resolution 6.84 Å
9MHF Cryo-EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L) Deposited 2024-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–450（450 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9MHG Cryo EM reconstruction of PI3KC3-C1 in complex with Human RAB1A(Q70L), VPS34 kinase domain in the inactive conformation Deposited 2024-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–450（450 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 MYR MYRISTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05% cryo-EM vitrification conditions Cryogen ETHANE；100% humidity, 3 s wait time, blot force -15	Resolution 3.20 Å
9MHH PI3KC3-C1 in complex with RAB1A. VPS34 kinase domain active conformation Deposited 2024-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–450（450 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；OG supplemented at time of grid preparation 0.05% cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
9RX5 VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L) Deposited 2025-07-10	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 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.15 Å
9RX6 VPS34-CII (VPS34 199-REIE-202 to 199-ERIR-202 mutant) bound to RAB5A (Q79L) on the VPS15 subunit Deposited 2025-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.52 Å
9RX8 Apo VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) Deposited 2025-07-10	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 C 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.87 Å
9RX9 VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS34 subunit Deposited 2025-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.99 Å
9RXA VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS15 subunit Deposited 2025-07-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 4.00 Å
9RXB VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) bound to RAB5A (Q79L) on the VPS34 and VPS15 subunits Deposited 2025-07-10	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 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 4.03 Å
9S47 Human complex II-BATS bound to membrane-attached Rab5a-GTP Deposited 2025-07-25	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 9.88 Å
9ZPC Cryo-EM structure of human PI3KC3-C2 Deposited 2025-12-16	Different construct 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 D 1–450（450 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.83 Å
9ZPD Cryo-EM structure of human PI3KC3-C2 in complex with Rubicon Middle Region of C terminus Deposited 2025-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–450（450 aa） Chain E 1–450（450 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å

29 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BECN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 241–450

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ddp
Deposition date deposition_date	2012-01-19
Structure title title	crystal structure of Beclin 1 evolutionarily conserved domain(ECD)
Keywords keywords	Beclin 1, ECD, autophagy, membrane binding, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	17.18 Å
Radius of gyration Rg (electron density) rg_electron	15.89 Å
Forward intensity I(0) i0	8969870.00
Molecular weight molecular_weight	22495.0 kDa
Excluded volume excluded_volume	28316 Å³
Envelope volume envelope_volume	31848 Å³
Hydration-shell volume shell_volume	16440 Å³
Envelope diameter envelope_diameter	54.8 Å
Shell Rg shell_rg	22.30 Å
Envelope Rg envelope_rg	16.30 Å
Shape Rg shape_rg	15.90 Å
Total Rg total_rg	16.97 Å
Total atoms total_atoms	3116
Residues n_residues	195
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	66.7 Å
Rg (real space) rg_real	17.05 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	8.9700e+06
I(0) uncertainty (real space) i0_real_error	1.1920e+05
Rg (reciprocal space) rg_reciprocal	17.06 Å
I(0) (reciprocal space) i0_reciprocal	8970000.0000
Solution quality estimate total_estimate	0.5679
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.090
Kurtosis Kurtosis kurtosis	-0.399
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3333000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.434; Stabil: 1.000; Sysdev: 0.379; Positv: 1.000; Valcen: 0.942; Smooth: 0.000

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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4ddpA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	40 — Autophagy protein 6/Beclin 1

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8. Citations (1)

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Unit-cell length a length_a	80.746 Å
Unit-cell length b length_b	33.563 Å
Unit-cell length c length_c	74.765 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.49 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.547 Å
Low-resolution limit resolution_low	32.408 Å
R factor r_factor	0.1770
R_work r_work	0.1755
R_free r_free	0.2034

Description description	Beclin-1
Molecular weight formula_weight	24459.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3231

crystal structure of Beclin 1 evolutionarily conserved domain(ECD)

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

Beclin-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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	115

fit	/app/data/saxs_computation/dd/4ddp/4ddp.fit
pddf	/app/data/pr_computation/dd/4ddp/4ddp.pr.out
profile	/app/data/saxs_computation/dd/4ddp/4ddp.dat