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NMR structure of the human NOTCH-1 ligand binding region

Method: SOLUTION NMR Dmax: 59.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurogenic locus notch homolog protein 1

Homo sapiens

UniProt P46531

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 411–526 Fragment：NOTCH-1 EGF 11-13 Mutation：M477I No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.1；298 K；Ionic strength (raw mmCIF value) 15mM CaCl2；Pressure ambient NMR sample composition：0.5-1mM protein | 90% H2O, 10% D2O, 15mM CaCl2, 0.02% NaN3 Resolution not provided

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 1TOZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1PB5 NMR Structure of a Prototype LNR Module from Human Notch1 Deposited 2003-05-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1447–1481（35 aa） Fragment：First LNR module
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 10mM Ca2+；Pressure ambient
NMR measurement conditions pH 7；283 K；Ionic strength (raw mmCIF value) 10mM Ca2+, 50mM PIPES；Pressure ambient
NMR sample composition 1mM LNRA U-15N, 10mM Ca2+, 0.5mM DSS pH 6.5 | 90% H2O/10% D2O
NMR sample composition 1mM LNRA U-15N,13C, 10mM Ca2+, 0.5mM DSS pH 6.5 | 90% H2O/10% D2O
NMR sample composition 1.5mM LNRA U-15N,13C, 10 mM Ca2+, 0.5mM DSS, 50 mM deuterated PIPES pH 7.0 | 90% H2O/10% D2O
Resolution not provided
1YYH Crystal structure of the human Notch 1 ankyrin domain Deposited 2005-02-25 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1873–2115（243 aa） Fragment：ankyrin domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；ammonium hydrogen phosphate, sodium chloride, imidazole, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.193
1YYH Crystal structure of the human Notch 1 ankyrin domain Deposited 2005-02-25 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1873–2115（243 aa） Fragment：ankyrin domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；ammonium hydrogen phosphate, sodium chloride, imidazole, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.193
2F8X Crystal structure of activated Notch, CSL and MAML on HES-1 promoter DNA sequence Deposited 2005-12-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain K 1873–2127（255 aa） Fragment：[Contains: Notch 1 extracellular truncation; Notch 1 intracellular domain]
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions HANGING DROP；pH 7.9；298 K；50mM HEPES, 6% PEG 3350, and 5% ethylene glycol, pH 7.9, HANGING DROP, temperature 298K
Resolution 3.25 Å R-free 0.257
2F8Y Crystal structure of human Notch1 ankyrin repeats to 1.55A resolution. Deposited 2005-12-04 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1906–2127（222 aa） Fragment：ankyrin repeat domain, repeats 1-7
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.55 Å R-free 0.187
2F8Y Crystal structure of human Notch1 ankyrin repeats to 1.55A resolution. Deposited 2005-12-04 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1906–2127（222 aa） Fragment：ankyrin repeat domain, repeats 1-7
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.55 Å R-free 0.187
2HE0 Crystal structure of a human Notch1 ankyrin domain mutant Deposited 2006-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1873–2115（243 aa） Fragment：Ankyrin Domain, residues 1873-2115
Chain B 1873–2115（243 aa） Fragment：Ankyrin Domain, residues 1873-2115
Mutation：E58A, R66A Mutation：E58A, R66A EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.55M Sodium/Potassium Tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.231
2VJ3 Human Notch-1 EGFs 11-13 Deposited 2007-12-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 411–526（116 aa） Fragment：EGFS 11-13, RESIDUES 411-526
Not recorded CA CALCIUM ION × 4 NA SODIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.7；30% (W/V) PEG-5000-MME, 100MM SODIUM ACETATE, PH5.7
Resolution 2.60 Å R-free 0.244
3ETO 2 Angstrom Xray structure of the NOTCH1 Negative Regulatory Region (NRR) Deposited 2008-10-08 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1447–1734（288 aa） Fragment：NOTCH1 Negative Regulatory Region, residues 1447-1734
Not recorded CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；0.1M Sodium acetate pH 4.0, 1.0-1.5M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.252
3ETO 2 Angstrom Xray structure of the NOTCH1 Negative Regulatory Region (NRR) Deposited 2008-10-08 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1447–1734（288 aa） Fragment：NOTCH1 Negative Regulatory Region, residues 1447-1734
Not recorded CA CALCIUM ION × 3 CL CHLORIDE ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；0.1M Sodium acetate pH 4.0, 1.0-1.5M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.252
3I08 Crystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR) Deposited 2009-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1446–1664（219 aa） Fragment：Notch1 NRR (Residues 1446-1665)
Chain B 1666–1734（69 aa） Fragment：Notch1 NRR (Residues 1666-1734)
Not recorded CA CALCIUM ION × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；0.1M NaOAc, 2.0 M NaCl, 10% glycerol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.286
3I08 Crystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR) Deposited 2009-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1446–1664（219 aa） Fragment：Notch1 NRR (Residues 1446-1665)
Chain D 1666–1734（69 aa） Fragment：Notch1 NRR (Residues 1666-1734)
Not recorded CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；0.1M NaOAc, 2.0 M NaCl, 10% glycerol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.286
3I08 Crystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR) Deposited 2009-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1446–1664（219 aa） Fragment：Notch1 NRR (Residues 1446-1665)
Chain B 1666–1734（69 aa） Fragment：Notch1 NRR (Residues 1666-1734)
Chain C 1446–1664（219 aa） Fragment：Notch1 NRR (Residues 1446-1665)
Chain D 1666–1734（69 aa） Fragment：Notch1 NRR (Residues 1666-1734)
Not recorded CA CALCIUM ION × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；0.1M NaOAc, 2.0 M NaCl, 10% glycerol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.286
3L95 Crystal structure of the human Notch1 Negative Regulatory Region (NRR) bound to the fab fragment of an antagonist antibody Deposited 2010-01-04 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 × 5 PDB declaration: pentameric
Chain X 1448–1621（174 aa） Fragment：Negative regulatory region (NRR1)
Chain X 1670–1728（59 aa） Fragment：Negative regulatory region (NRR1)
Chain Y 1448–1621（174 aa） Fragment：Negative regulatory region (NRR1)
Chain Y 1670–1728（59 aa） Fragment：Negative regulatory region (NRR1)
Not recorded SO4 SULFATE ION × 1 CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；Equal volumes of protein and well solutions. Protein: 6 mg/mL in 150 mM NaCl, 20 mM Bis-Tris pH 6.5. Well solution: 300 mM di-Ammonium Sulfate, 20% PEG 5000 MME, 100 mM Tris pH 7.5, VAPOR DIFFUSION, temperature 292K
Resolution 2.19 Å R-free 0.271
3L95 Crystal structure of the human Notch1 Negative Regulatory Region (NRR) bound to the fab fragment of an antagonist antibody Deposited 2010-01-04 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 × 4 PDB declaration: tetrameric
Chain X 1448–1621（174 aa） Fragment：Negative regulatory region (NRR1)
Chain X 1670–1728（59 aa） Fragment：Negative regulatory region (NRR1)
Chain Y 1448–1621（174 aa） Fragment：Negative regulatory region (NRR1)
Chain Y 1670–1728（59 aa） Fragment：Negative regulatory region (NRR1)
Not recorded CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；292 K；Equal volumes of protein and well solutions. Protein: 6 mg/mL in 150 mM NaCl, 20 mM Bis-Tris pH 6.5. Well solution: 300 mM di-Ammonium Sulfate, 20% PEG 5000 MME, 100 mM Tris pH 7.5, VAPOR DIFFUSION, temperature 292K
Resolution 2.19 Å R-free 0.271
3NBN Crystal structure of a dimer of Notch Transcription Complex trimers on HES1 DNA Deposited 2010-06-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain B 1872–2126（255 aa） Fragment：residues 1872-2126
Chain E 1872–2126（255 aa） Fragment：residues 1872-2126
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；3% PEG3350, 10% ethylene glycol, 0.15M NaCl, 0.1M magnesium chloride, 0.1M BIS-TRIS, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.45 Å R-free 0.298
3V79 Structure of human Notch1 transcription complex including CSL, RAM, ANK, and MAML-1 on HES-1 promoter DNA sequence Deposited 2011-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain K 1872–2126（255 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；6% PEG 3350, 5% Ethylene glycol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.85 Å R-free 0.245
4CUD Human Notch1 EGF domains 11-13 mutant fucosylated at T466 Deposited 2014-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 410–526（117 aa） Fragment：EGF 11-13, RESIDUES 410-526
Not recorded FUC alpha-L-fucopyranose × 2 CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 1.85 Å R-free 0.260
4CUE Human Notch1 EGF domains 11-13 mutant T466V Deposited 2014-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 411–526（116 aa） Fragment：EGF 11-13, RESIDUES 411-526
Mutation：YES CA CALCIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；pH 5.5
Resolution 3.00 Å R-free 0.282
4CUF Human Notch1 EGF domains 11-13 mutant T466S Deposited 2014-03-18 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 411–526（116 aa） Fragment：EGF 11-13, RESIDUES 411-526
Mutation：YES CA CALCIUM ION × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.29 Å R-free 0.286
4D0E Human Notch1 EGF domains 11-13 mutant GlcNAc-fucose disaccharide modified at T466 Deposited 2014-04-25 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 Monomer；Protein × 1 PDB declaration: monomeric
Chain A 411–526（116 aa） Fragment：EGF 11-13, RESIDUES 411-526
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；pH 6.0
Resolution 1.61 Å R-free 0.270
4D0F Human Notch1 EGF domains 11-13 mutant T466A Deposited 2014-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 411–526（116 aa） Fragment：EGF 11-13
Mutation：YES CA CALCIUM ION × 6 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.80 Å R-free 0.265
5FM9 human Notch 1, EGF 4-7 Deposited 2015-11-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 140–294（155 aa） Fragment：EGF DOMAINS 4-7, UNP RESIDUES 140-294
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；PH 8.5
Resolution 2.92 Å R-free 0.237
5FMA human Notch 1, EGF 4-7 Deposited 2015-11-02 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 142–294（153 aa） Fragment：EGF DOMAINS 4-7, RESIDUES 142-294
Not recorded CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.46 Å R-free 0.263
5FMA human Notch 1, EGF 4-7 Deposited 2015-11-02 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 142–294（153 aa） Fragment：EGF DOMAINS 4-7, RESIDUES 142-294
Not recorded CA CALCIUM ION × 2 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.46 Å R-free 0.263
5KZO Notch1 transmembrane and associated juxtamembrane segment Deposited 2016-07-25 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1721–1771（51 aa） Fragment：UNP residues 1721-1771
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；318 K；Ionic strength (raw mmCIF value) 65 mM imidazole；Pressure 1
NMR sample composition 350 uM [U-99% 15N] Notch1, 150 mg/mL DHPC/DMPC bicelle, 1 mM EDTA, 65 mM imidazole, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 uM [U-99% 13C; U-99% 15N] Notch1, 150 mg/mL DHPC/DMPC bicelle, 100% D2O | 100% D2O
NMR sample composition 500 uM [U-99% 13C; U-99% 15N] Notch1, 150 mg/mL DHPC/DMPC, 1 mM EDTA, 65 mM imidazole, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5L0R human POGLUT1 in complex with Notch1 EGF12 and UDP Deposited 2016-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 452–491（40 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 UDP URIDINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% glycerol
Resolution 1.50 Å R-free 0.171
5UB5 human POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP Deposited 2016-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 452–491（40 aa） Fragment：UNP residues 452-491
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 UDP URIDINE-5'-DIPHOSPHATE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% (v/v) PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% (v/v) 2-methyl-2,4-pentanediol
Resolution 2.09 Å R-free 0.193
6PY8 Crystal structure of the RBPJ-NOTCH1-NRARP ternary complex bound to DNA Deposited 2019-07-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain F 1759–2127（369 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；50 mM Hepes pH 6.8, 200 mM Sodium Fluoride, 18% PEG 3350
Resolution 3.75 Å R-free 0.315
6PY8 Crystal structure of the RBPJ-NOTCH1-NRARP ternary complex bound to DNA Deposited 2019-07-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain K 1759–2127（369 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；50 mM Hepes pH 6.8, 200 mM Sodium Fluoride, 18% PEG 3350
Resolution 3.75 Å R-free 0.315
8OR5 Solution NMR structure of Notch1 TMD Deposited 2023-04-13 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1734–1760（27 aa） Fragment：Notch1 transmembrane domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Pressure 1
NMR sample composition 500 uM Notch1 WT TMD, trifluoroethanol/water 80/20 | trifluoroethanol/water 80/20
Resolution not provided
8ORY Solution NMR structure of Notch1 L1740-1743 TMD Deposited 2023-04-17 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1734–1757（24 aa）
Mutation：A1740L, A1741L, A1742L, A1743L No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Pressure 1
NMR sample composition 500 uM Notch1 L1740-1743 TMD, trifluoroethanol/water 80/20 | trifluoroethanol/water 80/20
Resolution not provided
8ORZ Solution NMR structure of Notch1 G1740-1743 TMD Deposited 2023-04-17 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1734–1757（24 aa） Fragment：Notch1 transmembrane domain
Mutation：A1740G, A1741G, A1742G, A1743G No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Pressure 1
NMR sample composition 500 uM Notch1 G1740-1743 TMD, trifluoroethanol/water 80/20 | trifluoroethanol/water 80/20
Resolution not provided
9B3G Human Notch-1 EGFs 21-23 Deposited 2024-03-19 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 790–906（117 aa） Fragment：Human Notch1 EGF domains 21-23
Not recorded BA BARIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M Ammonium acetate 0.1 M BIS-Tris pH 5.5 25% (w/v) PEG3350
Resolution 1.55 Å R-free 0.218
9B3N Human Notch-1 EGFs 20-24 Deposited 2024-03-19 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 Monomer；Protein × 1 PDB declaration: monomeric
Chain A 753–944（192 aa） Fragment：Human Notch1 EGFs 20-24
Not recorded BGC beta-D-glucopyranose × 1 FUC alpha-L-fucopyranose × 4 CA CALCIUM ION × 4 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M Imidazole Malate pH 6 8% (w/v) PEG4K
Resolution 1.50 Å R-free 0.198

27 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOTC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–116； UniProt 411–526

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1toz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1toz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1toz
Deposition date deposition_date2004-06-15
Structure title titleNMR structure of the human NOTCH-1 ligand binding region
Keywords keywordsNOTCH, EGF, CALCIUM BINDING, LIGAND BINDING, MODULE, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.92 Å
Radius of gyration Rg (electron density) rg_electron23.45 Å
Forward intensity I(0) i01165990000.00
Molecular weight molecular_weight251220.0 kDa
Excluded volume excluded_volume298010 ų
Envelope volume envelope_volume59505 ų
Hydration-shell volume shell_volume18184 ų
Envelope diameter envelope_diameter103.1 Å
Shell Rg shell_rg33.92 Å
Envelope Rg envelope_rg30.13 Å
Shape Rg shape_rg23.48 Å
Total Rg total_rg23.55 Å
Total atoms total_atoms32760
Residues n_residues2320
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax59.6 Å
Rg (real space) rg_real21.33 Å
Rg uncertainty (real space) rg_real_error0.13 Å
I(0) (real space) i0_real1.1120e+09
I(0) uncertainty (real space) i0_real_error1.2570e+07
Rg (reciprocal space) rg_reciprocal23.25 Å
I(0) (reciprocal space) i0_reciprocal1166000000.0000
Solution quality estimate total_estimate0.6264
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary13.8 Å
Skewness Skewness skewness0.269
Kurtosis Kurtosis kurtosis-0.913
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha2.5510
Highest regularization parameter α highest_alpha83240.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.003; Oscil: 0.930; Stabil: 0.983; Sysdev: 0.000; Positv: 1.000; Valcen: 0.411; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1toza1
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.11 — EGF/Laminin
Family Family familyg.3.11.1 — EGF-type module
Domain ID domain_idd1toza2
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.11 — EGF/Laminin
Family Family familyg.3.11.1 — EGF-type module
Domain ID domain_idd1toza3
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.11 — EGF/Laminin
Family Family familyg.3.11.1 — EGF-type module

CATH v4.4 (2 domains)

Domain ID domain_id1tozA01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
Domain ID domain_id1tozA02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
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8. Citations (2)

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9. Files and Curves (10)