3V79: Neurogenic locus notch homolog protein 1

Structure of human Notch1 transcription complex including CSL, RAM, ANK, and MAML-1 on HES-1 promoter DNA sequence. Determined by X-ray diffraction at 3.85 Å resolution. Released 15 Feb 2012.

Method: X-ray diffraction
Resolution: 3.85 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,421
Mol. weight: 98.13 kDa
Released: 15 Feb 2012

Explore 3V79 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3V79 contains 27 α-helices and 54 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 C: 11 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	19-27	9
β-strand	32-39	8	2
β-strand	41-43	3	3
α-helix	44	1
β-strand	45	1	4
α-helix	46	1
β-strand	58	1	2
α-helix	65-74	10
β-strand	86-87	2	5
β-strand	88-89	2	6
β-strand	90-91	2	5
β-strand	99-100	2	6
β-strand	110	1	2
β-strand	117	1	4
β-strand	124-125	2	3
β-strand	127-132	6	5
β-strand	138-143	6	5
β-strand	147-150	4	3
β-strand	166	1	7
β-strand	168	1	8
β-strand	172-173	2	9
β-strand	176-177	2	10
β-strand	187-188	2	10
β-strand	191-192	2	11
β-strand	195-196	2	11
β-strand	206-211	6	9
β-strand	227	1	8
β-strand	229	1	12
β-strand	233-238	6	9
β-strand	243-244	2	9
β-strand	248-252	5	9
β-strand	253-254	2	13
β-strand	257-259	3	13
α-helix	264	1
β-strand	265	1	12
α-helix	266	1
β-strand	267	1	7
β-strand	271	1	10
β-strand	272-275	4	9
β-strand	284-286	3	14
β-strand	291-293	3	14
β-strand	302	1	13
β-strand	305-307	3	13
α-helix	314	1
β-strand	315	1	10
α-helix	316	1
β-strand	319-326	8	2
β-strand	329	1	15
β-strand	331	1	15
β-strand	342-349	8	16
α-helix	352-354	3
β-strand	356-362	7	16
β-strand	368-372	5	17
β-strand	375-377	3	17
α-helix	378	1
β-strand	379-383	5	16
β-strand	386-390	5	16
α-helix	394-396	3
β-strand	408-409	2	18
β-strand	413-416	4	17
β-strand	421-423	3	17
β-strand	429-430	2	18

Chain K: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1912-1915	4
α-helix	1923-1925	3
α-helix	1932-1938	7
α-helix	1942-1950	9
α-helix	1965-1971	7
α-helix	1975-1982	8
α-helix	1999-2005	7
α-helix	2011-2017	7
β-strand	2025	1	1
β-strand	2031	1	1
α-helix	2032-2038	7
α-helix	2042-2050	9
α-helix	2065-2072	8
α-helix	2075-2083	9
α-helix	2098-2105	8
α-helix	2108-2116	9

Chain M: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	17-68	52

Chain R: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	943-944	2	9
α-helix	951-953	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neurogenic locus notch homolog protein 1	K	protein	256	Homo sapiens	P46531 (AlphaFold model)
Recombining binding protein suppressor of hairless	C	protein	434	Homo sapiens	Q06330 (AlphaFold model)
Mastermind-like protein 1	M	protein	63	Homo sapiens	Q92585 (AlphaFold model)
DNA 5'-d(gptptpapcptpgptpgpgpgpapapapgpapapa)-3'	X	DNA	18
DNA 5'-d(tptptpcptptptpcpcpcpapcpapgptpapapc)-3'	Y	DNA	18
RAM	R	protein	19	Homo sapiens	P46531 (AlphaFold model)

Sequence of entity 1 (K), FASTA

>3V79_1 Neurogenic locus notch homolog protein 1 (chains K)
GMDVNVRGPDGFTPLMIASCSGGGLETGNSEEEEDAPAVISDFIYQGASLHNQTDRTGET
ALHLAARYSRSDAAKRLLEASADANIQDNMGRTPLHAAVSADAQGVFQILIRNRATDLDA
RMHDGTTPLILAARLAVEGMLEDLINSHADVNAVDDLGKSALHWAAAVNNVDAAVVLLKN
GANKDMQNNREETPLFLAAREGSYETAKVLLDHFANRDITDHMDRLPRDIAQERMHHDIV
RLLDEYNLVRSPQLHG

Sequence of entity 2 (C), FASTA

>3V79_2 Recombining binding protein suppressor of hairless (chains C)
MGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWK
KKKEQMERDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFML
SVKMFYGNSDDIGVFLSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTR
YLHVEGGNFHASSQQWGAFFIHLLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPR
LIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMYLCLSQERIIQFQATPCPKEPNKEM
INDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGDVAMLELTGQNFTPN
LRVWFGDVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGIIYSTSLT
FTYTPEPGHHHHHH

Sequence of entity 3 (M), FASTA

>3V79_3 Mastermind-like protein 1 (chains M)
GLPRHSAVMERLRRRIELCRRHHSTCEARYEAVSPERLELERQHTFALHQRCIQAKAKRA
GKH

Sequence of entity 4 (X), FASTA

>3V79_4 DNA 5'-D(*GP*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*AP*AP*A)-3' (chains X)
GTTACTGTGGGAAAGAAA

Sequence of entity 5 (Y), FASTA

>3V79_5 DNA 5'-D(*TP*TP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*TP*AP*AP*C)-3' (chains Y)
TTTCTTTCCCACAGTAAC

Sequence of entity 6 (R), FASTA

>3V79_6 RAM (chains R)
KRRRQHGQLWFPEGFKVSE

Primary citation

Conformational Locking upon Cooperative Assembly of Notch Transcription Complexes. Choi, S.H., Wales, T.E., Nam, Y. et al. Structure (2012) 20:340-349. DOI 10.1016/j.str.2011.12.011 · 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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