3i08

Crystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR)

Method: X-RAY DIFFRACTION D_max: 77.1 Å Quality: EXCELLENT

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

Neurogenic locus notch homolog protein 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1446–1664 Chain B； UniProt 1666–1734	Fragment：Notch1 NRR (Residues 1446-1665) Fragment：Notch1 NRR (Residues 1666-1734)	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1446–1664 Chain D； UniProt 1666–1734	Fragment：Notch1 NRR (Residues 1446-1665) Fragment：Notch1 NRR (Residues 1666-1734)	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
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1446–1664 Chain B； UniProt 1666–1734 Chain C； UniProt 1446–1664 Chain D； UniProt 1666–1734	Fragment：Notch1 NRR (Residues 1446-1665) Fragment：Notch1 NRR (Residues 1666-1734)	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

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 3I08	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 oligomeric state 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 1447–1481（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
1TOZ NMR structure of the human NOTCH-1 ligand binding region Deposited 2004-06-15	Different construct Different mutation/modification Different oligomeric state 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：NOTCH-1 EGF 11-13	Mutation：M477I	No recorded non-water small molecule	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
1YYH Crystal structure of the human Notch 1 ankyrin domain Deposited 2005-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 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 ligand/ion 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 ligand/ion 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state 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 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 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 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 ligand/ion 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 ligand/ion 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state Different ligand/ion 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 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 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NOTC1_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 2–220； UniProt 1446–1664 Author chain C； PDBConstruct 2–220； UniProt 1446–1664 Author chain B； PDBConstruct 1–69； UniProt 1666–1734 Author chain D； PDBConstruct 1–69； UniProt 1666–1734

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	3i08
Deposition date deposition_date	2009-06-24
Structure title title	Crystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR)
Keywords keywords	;SEA domain, Lin-12 Notch repeat, LNR, Heterodimerization Domain, HD, Activator, ANK repeat, Calcium, Cell membrane, Developmental protein, Differentiation, Disulfide bond, EGF-like domain, Glycoprotein, Membrane, Metal-binding, Notch signaling pathway, Nucleus, Phosphoprotein, Polymorphism, Receptor, Transcription, Transcription regulation, Transmembrane, furin, T-ALL, leukemia, oncogene, metalloprotease, gamma-secretase, SIGNALING PROTEIN ;; SIGNALING 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	24.68 Å
Radius of gyration Rg (electron density) rg_electron	23.63 Å
Forward intensity I(0) i0	51761600.00
Molecular weight molecular_weight	51322.0 kDa
Excluded volume excluded_volume	62163 Å³
Envelope volume envelope_volume	77374 Å³
Hydration-shell volume shell_volume	27188 Å³
Envelope diameter envelope_diameter	81.2 Å
Shell Rg shell_rg	30.96 Å
Envelope Rg envelope_rg	23.76 Å
Shape Rg shape_rg	23.62 Å
Total Rg total_rg	24.47 Å
Total atoms total_atoms	3573
Residues n_residues	466
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	77.1 Å
Rg (real space) rg_real	24.54 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	5.1760e+07
I(0) uncertainty (real space) i0_real_error	7.0790e+05
Rg (reciprocal space) rg_reciprocal	24.57 Å
I(0) (reciprocal space) i0_reciprocal	51760000.0000
Solution quality estimate total_estimate	0.9077
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.6 Å
Skewness Skewness skewness	0.147
Kurtosis Kurtosis kurtosis	-0.510
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3268000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Neurogenic locus notch homolog protein 1
Molecular weight formula_weight	24595.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3594

GEEACELPECQEDAGNKVCSLQCNNHACGWDGGDCSLNFNDPWKNCTQSLQCWKYFSDGHCDSQCNSAGCLFDGFDCQRAEGQCNPLYDQYCKDHFSDGHCDQGCNSAECEWDGLDCAEHVPERLAAGTLVVVVLMPPEQLRNSSFHFLRELSRVLHTNVVFKRDAHGQQMIFPYYGREEELRKHPIKRAAEGWAAPDALLGQVKASLLPGGSEGGRRRR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Neurogenic locus notch homolog protein 1
Molecular weight formula_weight	7383.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

ELDPMDVRGSIVYLEIDNRQCVQASSQCFQSATDVAAFLGALASLGSLNIPYKIEAVQSETVEPPPPAQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3i08A01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3i08A02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3i08B01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	470 —

Domain ID domain_id	3i08C01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3i08C02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3i08D01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	470 —

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8. Citations (1)

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Unit-cell length a length_a	65.868 Å
Unit-cell length b length_b	65.868 Å
Unit-cell length c length_c	322.586 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	46.320 Å
R factor r_factor	0.2320
R_work r_work	0.2290
R_free r_free	0.2860

fit	/app/data/saxs_computation/i0/3i08/3i08.fit
pddf	/app/data/pr_computation/i0/3i08/3i08.pr.out
profile	/app/data/saxs_computation/i0/3i08/3i08.dat

Crystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR)

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

Neurogenic locus notch homolog protein 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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)