3I08: S1-cleaved Notch1 Negative Regulatory Region

Crystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR). Determined by X-ray diffraction at 3.2 Å resolution. Released 1 Sept 2009.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,594
Mol. weight: 64.23 kDa
Ligands: CA
Released: 1 Sept 2009

Explore 3I08 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3I08 contains 33 α-helices and 20 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1455-1458	4
α-helix	1466-1468	3
α-helix	1471-1473	3
α-helix	1474-1477	4
α-helix	1493-1495	3
α-helix	1497-1499	3
α-helix	1508-1510	3
α-helix	1513-1520	8
α-helix	1531-1538	8
α-helix	1548-1550	3
α-helix	1553-1560	8
β-strand	1570	1	1
α-helix	1571	1
β-strand	1572	1	2
β-strand	1574-1580	7	1
α-helix	1583-1588	6
α-helix	1590-1601	12
β-strand	1604-1607	4	1
β-strand	1609	1	3
β-strand	1615	1	3
β-strand	1617-1620	4	1

Chain B: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1674-1682	9	1
α-helix	1686-1689	4
β-strand	1696	1	2
α-helix	1697-1709	13
β-strand	1718-1725	8	1

Chain C: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	1455-1458	4
α-helix	1466-1468	3
α-helix	1476-1478	3
α-helix	1487-1490	4
α-helix	1493-1495	3
α-helix	1497-1499	3
α-helix	1508-1510	3
α-helix	1513-1520	8
α-helix	1529-1530	2
α-helix	1531-1540	10
α-helix	1548-1550	3
α-helix	1553-1560	8
β-strand	1570	1	4
α-helix	1571	1
β-strand	1572	1	5
β-strand	1575-1579	5	4
α-helix	1583-1588	6
α-helix	1590-1601	12
β-strand	1604-1607	4	4
β-strand	1609	1	6
β-strand	1615	1	6
β-strand	1617-1620	4	4

Chain D: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	1674-1682	9	4
α-helix	1686-1689	4
β-strand	1696	1	5
α-helix	1697-1709	13
β-strand	1719-1724	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neurogenic locus notch homolog protein 1	A, C	protein	220	Homo sapiens	P46531 (AlphaFold model)
Neurogenic locus notch homolog protein 1	B, D	protein	69	Homo sapiens	P46531 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3I08_1 Neurogenic locus notch homolog protein 1 (chains A, C)
GEEACELPECQEDAGNKVCSLQCNNHACGWDGGDCSLNFNDPWKNCTQSLQCWKYFSDGH
CDSQCNSAGCLFDGFDCQRAEGQCNPLYDQYCKDHFSDGHCDQGCNSAECEWDGLDCAEH
VPERLAAGTLVVVVLMPPEQLRNSSFHFLRELSRVLHTNVVFKRDAHGQQMIFPYYGREE
ELRKHPIKRAAEGWAAPDALLGQVKASLLPGGSEGGRRRR

Sequence of entity 2 (B, D), FASTA

>3I08_2 Neurogenic locus notch homolog protein 1 (chains B, D)
ELDPMDVRGSIVYLEIDNRQCVQASSQCFQSATDVAAFLGALASLGSLNIPYKIEAVQSE
TVEPPPPAQ

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6

Water and common crystallization additives (CL) are not listed.

Primary citation

Effects of S1 cleavage on the structure, surface export, and signaling activity of human Notch1 and Notch2. Gordon, W.R., Vardar-Ulu, D., L'Heureux, S. et al. PLoS One (2009) 4:e6613-e6613. DOI 10.1371/journal.pone.0006613 · PubMed

Other PDB entries of the same protein (UniProt P46531 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5L0R 1.5 Å, human POGLUT1 in complex with Notch1 EGF12 and UDP
9B3N 1.5 Å, Human Notch-1 EGFs 20-24
2F8Y 1.55 Å, Crystal structure of human Notch1 ankyrin repeats to 1.55A resolution.
9B3G 1.55 Å, Human Notch-1 EGFs 21-23
4D0E 1.61 Å, Human Notch1 EGF domains 11-13 mutant GlcNAc-fucose disaccharide modified at T466
4CUD 1.85 Å, Human Notch1 EGF domains 11-13 mutant fucosylated at T466
2HE0 1.9 Å, Crystal structure of a human Notch1 ankyrin domain mutant
1YYH 1.9 Å, Crystal structure of the human Notch 1 ankyrin domain
3ETO 2.0 Å, 2 Angstrom Xray structure of the NOTCH1 Negative Regulatory Region (NRR)
5UB5 2.09 Å, human POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP
3L95 2.19 Å, Crystal structure of the human Notch1 Negative Regulatory Region (NRR) bound to the fab…
4CUF 2.29 Å, Human Notch1 EGF domains 11-13 mutant T466S

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