8d9x

Cryo-EM structure of human DELE1 in oligomeric form

Method: ELECTRON MICROSCOPY D_max: 143.4 Å Quality: GOOD

▼

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

Maltodextrin-binding protein,DAP3-binding cell death enhancer 1 short form

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	Insufficient information Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 27–387 Chain B； UniProt 27–387 Chain C； UniProt 27–387 Chain D； UniProt 27–387 Chain E； UniProt 27–387 Chain F； UniProt 27–387 Chain G； UniProt 27–387 Chain H； UniProt 27–387	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.80 Å

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 8D9X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6I4Y X-ray structure of the human mitochondrial PRELID3b-TRIAP1 complex Deposited 2018-11-12	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 × 4 PDB declaration: tetrameric	Chain A 27–393（367 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；Tacsimate (60% v/v) pH 7	Resolution 2.91 Å R-free 0.296
6QF7 Crystal structures of the recombinant beta-Factor XIIa protease with bound Thr-Arg and Pro-Arg substrate mimetics Deposited 2019-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–393（368 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；292 K；0.1 M sodium citrate, pH 5.6 with 10% PEG 4000 and 0.15 M MgCl2	Resolution 4.00 Å R-free 0.356
6QF7 Crystal structures of the recombinant beta-Factor XIIa protease with bound Thr-Arg and Pro-Arg substrate mimetics Deposited 2019-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 26–393（368 aa）	Not recorded	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；292 K；0.1 M sodium citrate, pH 5.6 with 10% PEG 4000 and 0.15 M MgCl2	Resolution 4.00 Å R-free 0.356
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	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 Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 10 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain J 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 11 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain K 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 12 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain L 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain E 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain F 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain G 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain H 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6QUG GHK tagged MBP-Nup98(1-29) Deposited 2019-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 9 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain I 27–392（366 aa）	Not recorded	CU COPPER (II) ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG550, PEG20,000, MOPS, HEPES, sodium Phosphate, sodium nitrate, ammonium sulphate	Resolution 2.70 Å R-free 0.226
6SJV Structure of HPV18 E6 oncoprotein in complex with mutant E6AP LxxLL motif Deposited 2019-08-14	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 Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–392（366 aa）	Mutation：;K84A,K240A,E360A,K363A,D364A,F1049R,L2386F,E2393R,K84A,K240A,E360A,K363A,D364A,F1049R,L2386F,E2393R,K84A,K240A,E360A,K363A,D364A,F1049R,L2386F,E2393R ;	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；Sodium Cacodylate 100 mM pH 6.5, PEG 8000 5%, 2-methyl-2,4-pentanediol 40%	Resolution 2.03 Å R-free 0.242
6WBH Crystal structure of mRECK(CC4) in fusion with engineered MBP at medium resolution Deposited 2020-03-26	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 Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–392（364 aa）	Mutation：D84A,K85A,E174A,N175A,A217H,K221H,K241A,A314V,I319V,E361A,K364A,D365A	CL CHLORIDE ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, 25% PEG 4000	Resolution 2.46 Å R-free 0.220
6WBJ High resolution crystal structure of mRECK(CC4) in fusion with engineered MBP Deposited 2020-03-26	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 Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–392（364 aa）	Mutation：D84A,K85A,E174A,N175A,A217H,K221H,K241A,A314V,I319V,E361A,K364A,D365A	SO4 SULFATE ION × 1 ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, 25% PEG 4000	Resolution 1.65 Å R-free 0.177
7B01 ADAMTS13-CUB12 Deposited 2020-11-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–387（361 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；21% (v/v) PEG1500, 100 mM Sodium propionate, sodium cacodylate trihydrate, 200 mM MnCl2, Bis-Tris propane, pH 5	Resolution 2.80 Å R-free 0.292
7CY5 Crystal Structure of CMD1 in complex with vitamin C Deposited 2020-09-03	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 Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–392（366 aa） Fragment：dioxygenase,dioxygenase	Mutation：D108A, K109A, E198A, N199A, E385A, K388A, D389A	FE FE (III) ION × 1 ASC ASCORBIC ACID × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.6；290 K；2% Tacsimate, 0.1M CIT pH 5.6, 16% PEG 3350	Resolution 2.20 Å R-free 0.221
7CY6 Crystal Structure of CMD1 in complex with 5mC-DNA Deposited 2020-09-03	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 Monomer；Protein × 1 PDB declaration: trimeric	Chain A 27–392（366 aa）	Mutation：D108A, K109A, E198A, N199A, E385A, K388A, D389A	PG4 TETRAETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 13 FE2 FE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；290 K；15% (v/v) 2-propanol, 0.1 M sodium citrate, pH 5.0, and 10% (w/v) PEG 10000	Resolution 2.10 Å R-free 0.227
7CY7 Crystal Structure of CMD1 in complex with DNA Deposited 2020-09-03	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 Monomer；Protein × 1 PDB declaration: trimeric	Chain A 27–392（366 aa）	Mutation：D108A, K109A, E198A, N199A, E385A, K388A, D389A	EDO 1,2-ETHANEDIOL × 8 IPA ISOPROPYL ALCOHOL × 1 FE2 FE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；290 K；15% (v/v) 2-propanol, 0.1 M sodium citrate, pH 5.0, and 10% (w/v) PEG 10000	Resolution 2.15 Å R-free 0.221
7CY8 Crystal Structure of CMD1 in complex with 5mC-DNA and vitamin C Deposited 2020-09-03	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 Monomer；Protein × 1 PDB declaration: trimeric	Chain A 27–392（366 aa）	Mutation：D108A, K109A, E198A, N199A, E385A, K388A, D389A	ASC ASCORBIC ACID × 1 EDO 1,2-ETHANEDIOL × 2 IPA ISOPROPYL ALCOHOL × 1 FE2 FE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；290 K；15% (v/v) 2-propanol, 0.1 M sodium citrate, pH 5.0, and 10% (w/v) PEG 10000	Resolution 2.40 Å R-free 0.235
7U0G structure of LIN28b nucleosome bound 3 OCT4 Deposited 2022-02-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain K 26–392（367 aa） Chain L 26–392（367 aa） Chain M 26–392（367 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
7U0I Structure of LIN28b nucleosome bound 2 OCT4 Deposited 2022-02-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain L 26–392（367 aa） Chain M 26–392（367 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
7XMN Structure of SARS-CoV-2 ORF8 Deposited 2022-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 27–392（366 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 SO4 SULFATE ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NNH NOR-N-OMEGA-HYDROXY-L-ARGININE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M MES pH6.1, 2%Polyethylene glycol 400, 2.1 M Ammonium sulfate	Resolution 2.30 Å R-free 0.245
8CDY N-terminal domain of human apolipoprotein E Deposited 2023-02-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–392（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；HEPES, PEG 6000	Resolution 1.90 Å R-free 0.231
8CE0 N-terminal domain of human apolipoprotein E Deposited 2023-02-01	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 Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–396（373 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；NaCl, Hepes, PEG 8000	Resolution 1.75 Å R-free 0.215
8JYX Crystal structure of the gasdermin-like protein RCD-1-1 from Neurospora crassa Deposited 2023-07-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–392（366 aa）	Mutation：D108A, K109A, E198A, N199A, K265A, K388A, D389A, K174A, K175A, K176A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；0.1 M Bicine pH 7.4, 11% PEG 3350, 3% (w/v) D(+)-Glucose monohydrate	Resolution 2.35 Å R-free 0.248
8JYX Crystal structure of the gasdermin-like protein RCD-1-1 from Neurospora crassa Deposited 2023-07-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–392（366 aa）	Mutation：D108A, K109A, E198A, N199A, K265A, K388A, D389A, K174A, K175A, K176A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；0.1 M Bicine pH 7.4, 11% PEG 3350, 3% (w/v) D(+)-Glucose monohydrate	Resolution 2.35 Å R-free 0.248
8SPS High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Deposited 2023-05-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain L 26–387（362 aa） Chain M 26–387（362 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8SPU Structure of ESRRB nucleosome bound OCT4 at site c Deposited 2023-05-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric	Chain L 26–387（362 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

19 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A376KDN7_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–362； UniProt 27–387 Author chain B； PDBConstruct 2–362； UniProt 27–387 Author chain C； PDBConstruct 2–362； UniProt 27–387 Author chain D； PDBConstruct 2–362； UniProt 27–387 Author chain E； PDBConstruct 2–362； UniProt 27–387 Author chain F； PDBConstruct 2–362； UniProt 27–387 Author chain G； PDBConstruct 2–362； UniProt 27–387 Author chain H； PDBConstruct 2–362； UniProt 27–387

Maltodextrin-binding protein,DAP3-binding cell death enhancer 1 short form

Homo sapiens

UniProt Q14154

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 224–515 Chain B； UniProt 224–515 Chain C； UniProt 224–515 Chain D； UniProt 224–515 Chain E； UniProt 224–515 Chain F； UniProt 224–515 Chain G； UniProt 224–515 Chain H； UniProt 224–515	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.80 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	DELE1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 372–663； UniProt 224–515 Author chain B； PDBConstruct 372–663； UniProt 224–515 Author chain C； PDBConstruct 372–663； UniProt 224–515 Author chain D； PDBConstruct 372–663； UniProt 224–515 Author chain E； PDBConstruct 372–663； UniProt 224–515 Author chain F； PDBConstruct 372–663； UniProt 224–515 Author chain G； PDBConstruct 372–663； UniProt 224–515 Author chain H； PDBConstruct 372–663； UniProt 224–515

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8d9x
Deposition date deposition_date	2022-06-11
Structure title title	Cryo-EM structure of human DELE1 in oligomeric form
Keywords keywords	Oligomer, Mitochondria, Integrated Stress Response, Kinase, Tetratricopeptide repeat, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	43.77 Å
Radius of gyration Rg (electron density) rg_electron	44.05 Å
Forward intensity I(0) i0	511957000.00
Molecular weight molecular_weight	179630.0 kDa
Excluded volume excluded_volume	222580 Å³
Envelope volume envelope_volume	346380 Å³
Hydration-shell volume shell_volume	68403 Å³
Envelope diameter envelope_diameter	151.9 Å
Shell Rg shell_rg	46.97 Å
Envelope Rg envelope_rg	42.45 Å
Shape Rg shape_rg	44.05 Å
Total Rg total_rg	44.18 Å
Total atoms total_atoms	12670
Residues n_residues	1680
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	143.4 Å
Rg (real space) rg_real	43.88 Å
Rg uncertainty (real space) rg_real_error	1.15 Å
I(0) (real space) i0_real	5.1200e+08
I(0) uncertainty (real space) i0_real_error	9.1160e+06
Rg (reciprocal space) rg_reciprocal	43.77 Å
I(0) (reciprocal space) i0_reciprocal	511900000.0000
Solution quality estimate total_estimate	0.8297
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.8 Å
Skewness Skewness skewness	0.470
Kurtosis Kurtosis kurtosis	-0.271
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	533300000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.719; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.628

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

Resolution resolution	3.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	92455

Description description	Maltodextrin-binding protein,DAP3-binding cell death enhancer 1 short form
Molecular weight formula_weight	73343.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	12670

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 'BL21-Gold(DE3)pLysS AG' ;

fit	/app/data/saxs_computation/d9/8d9x/8d9x.fit
pddf	/app/data/pr_computation/d9/8d9x/8d9x.pr.out
profile	/app/data/saxs_computation/d9/8d9x/8d9x.dat

Cryo-EM structure of human DELE1 in oligomeric form

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

Maltodextrin-binding protein,DAP3-binding cell death enhancer 1 short form

State in the Current Structure

Other States of the Same Protein in the Database

Maltodextrin-binding protein,DAP3-binding cell death enhancer 1 short form

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)