3L95: Human Notch1 Negative Regulatory Region

Crystal structure of the human Notch1 Negative Regulatory Region (NRR) bound to the fab fragment of an antagonist antibody. Determined by X-ray diffraction at 2.19 Å resolution. Released 9 Mar 2010.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,113
Mol. weight: 150.12 kDa
Ligands: CA
Released: 9 Mar 2010

Explore 3L95 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3L95 contains 60 α-helices and 108 β-strands across 6 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: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-65	4	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-150	7	5
β-strand	153-154	2	5
β-strand	159-163	5	4
β-strand	173-182	10	4
α-helix	183-188	6
β-strand	191-198	8	5
β-strand	205-210	6	5

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-52	8	7
β-strand	56-59	4	7
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	7
β-strand	100K-103	4	7
β-strand	107-111	5	7
α-helix	115-116	2
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
α-helix	128-130	3
β-strand	131	1	9
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	10
β-strand	159	1	10
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-185	10	9
α-helix	188-191	4
β-strand	194-200	7	10
α-helix	201-203	3
β-strand	205-211	7	10

Chain H: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	10-11	2	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	34-39	6	20
β-strand	45-52	8	20
β-strand	56-59	4	20
α-helix	61-63	3
β-strand	68-72	5	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-94	7	20
β-strand	102-103	2	20
β-strand	107-110	4	20
α-helix	114-116	3
β-strand	117	1	21
α-helix	118-119	2
β-strand	120-124	5	22
β-strand	131	1	22
β-strand	135-145	11	22
β-strand	146	1	21
β-strand	151-154	4	23
β-strand	159	1	23
β-strand	163-165	3	22
β-strand	169-170	2	22
α-helix	171	1
β-strand	176-185	10	22
β-strand	194-200	7	23
β-strand	205-211	7	23

Chain L: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-14	5	15
β-strand	19-25	7	14
β-strand	33-38	6	15
β-strand	45-49	5	15
β-strand	53-54	2	15
α-helix	55	1
β-strand	62-65	4	14
β-strand	70-75	6	14
β-strand	84-90	7	15
β-strand	97-98	2	15
β-strand	102-107	6	15
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	16
β-strand	145-150	6	17
β-strand	153-154	2	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-186	4
β-strand	191	1	18
β-strand	193-197	5	17
β-strand	205-206	2	17
β-strand	210	1	18

Chain X: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1448-1451	4
α-helix	1453-1458	6
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	1516-1520	5
α-helix	1528-1530	3
α-helix	1531-1533	3
α-helix	1534-1539	6
α-helix	1548-1550	3
α-helix	1556-1560	5
α-helix	1567-1568	2
β-strand	1570	1	11
α-helix	1571	1
β-strand	1572	1	12
β-strand	1574-1579	6	11
α-helix	1583-1588	6
α-helix	1590-1601	12
β-strand	1604-1607	4	11
β-strand	1609	1	13
β-strand	1615	1	13
β-strand	1617-1619	3	11
β-strand	1675-1682	8	11
β-strand	1696	1	12
α-helix	1697-1709	13
β-strand	1719-1725	7	11

Chain Y: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1464-1465	2
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	1516-1520	5
α-helix	1534-1539	6
α-helix	1548-1550	3
α-helix	1553-1560	8
α-helix	1567-1568	2
β-strand	1570	1	24
α-helix	1571	1
β-strand	1572	1	25
β-strand	1574-1579	6	24
α-helix	1583-1588	6
α-helix	1590-1601	12
β-strand	1604-1607	4	24
β-strand	1609	1	26
β-strand	1615	1	26
β-strand	1617-1619	3	24
β-strand	1675-1682	8	24
α-helix	1686-1689	4
β-strand	1696	1	25
α-helix	1697-1709	13
β-strand	1719-1725	7	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-NRR1 fab fragment light chain	A, L	protein	214	Homo sapiens
anti-NRR1 fab fragment heavy chain	B, H	protein	227	Homo sapiens
Neurogenic locus notch homolog protein 1	X, Y	protein	244	Homo sapiens	P46531 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>3L95_1 anti-NRR1 fab fragment light chain (chains A, L)
DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQFYTTPSTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, H), FASTA

>3L95_2 anti-NRR1 fab fragment heavy chain (chains B, H)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYWIHWVRQAPGKGLEWVARINPPNRSNQY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGSGFRWVMDYWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (X, Y), FASTA

>3L95_3 Neurogenic locus notch homolog protein 1 (chains X, Y)
GSACELPECQEDAGNKVCSLQCNNHACGWDGGDCSLNFNDPWKNCTQSLQCWKYFSDGHC
DSQCNSAGCLFDGFDCQRAEGQCNPLYDQYCKDHFSDGHCDQGCNSAECEWDGLDCAEHV
PERLAAGTLVVVVLMPPEQLRNSSFHFLRELSRVLHTNVVFKRDAHGQQMIFPYYGDVRG
SIVYLEIDNRQCVQASSQCFQSATDVAAFLGALASLGSLNIPYKIEAVQSETVEPANSHH
HHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

Therapeutic antibody targeting of individual Notch receptors. Wu, Y., Cain-Hom, C., Choy, L. et al. Nature (2010) 464:1052-1057. DOI 10.1038/nature08878 · 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
4CUF 2.29 Å, Human Notch1 EGF domains 11-13 mutant T466S
5FMA 2.46 Å, human Notch 1, EGF 4-7

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