3NBN: PDB entry 3NBN

Crystal structure of a dimer of Notch Transcription Complex trimers on HES1 DNA. Determined by X-ray diffraction at 3.45 Å resolution. Released 3 Nov 2010.

Method: X-ray diffraction
Resolution: 3.45 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,198
Mol. weight: 192.05 kDa
Released: 3 Nov 2010

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

Secondary structure: helices and β-sheets

3NBN contains 37 α-helices and 101 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: 4 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
α-helix	19-23	5
β-strand	32-39	8	2
β-strand	41-43	3	3
β-strand	45	1	4
α-helix	56-57	2
β-strand	58-60	3	2
α-helix	66-74	9
β-strand	85-89	5	5
β-strand	99-100	2	5
β-strand	110	1	2
β-strand	117	1	4
β-strand	125	1	6
β-strand	128	1	7
β-strand	130-133	4	5
β-strand	138	1	5
β-strand	143	1	7
β-strand	147	1	6
β-strand	148-150	3	3
β-strand	168	1	8
β-strand	172-177	6	9
β-strand	187-192	6	9
β-strand	195-199	5	9
β-strand	206-210	5	9
β-strand	227	1	8
β-strand	229	1	10
β-strand	233-238	6	9
β-strand	244-252	9	9
β-strand	254	1	11
β-strand	257-259	3	11
β-strand	265	1	10
β-strand	270-276	7	9
β-strand	279	1	12
β-strand	281	1	12
β-strand	283-285	3	9
β-strand	292-294	3	9
β-strand	305-307	3	11
β-strand	314-318	5	9
β-strand	319-326	8	2
β-strand	327	1	13
α-helix	340-341	2
β-strand	342-347	6	14
β-strand	357-362	6	14
β-strand	370-372	3	13
β-strand	375-376	2	13
β-strand	379-383	5	14
β-strand	386-389	4	14
β-strand	408-415	8	13
β-strand	418	1	1
β-strand	421-430	10	13

Chain B: 13 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1932-1938	7
α-helix	1944-1950	7
α-helix	1965-1971	7
α-helix	1975-1983	9
β-strand	1984	1	15
α-helix	1999-2005	7
α-helix	2011-2017	7
β-strand	2025	1	16
β-strand	2031	1	16
α-helix	2032-2038	7
α-helix	2042-2049	8
α-helix	2065-2072	8
α-helix	2075-2081	7
α-helix	2082-2084	3
α-helix	2098-2105	8
α-helix	2108-2116	9

Chains C and F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	18-57	40
α-helix	60-63	4

Chain D: 4 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	17
α-helix	19-23	5
β-strand	32-39	8	18
β-strand	41-43	3	19
β-strand	45	1	20
α-helix	56-57	2
β-strand	58-60	3	18
α-helix	66-74	9
β-strand	85	1	21
β-strand	88-89	2	22
β-strand	99-100	2	22
β-strand	110	1	18
β-strand	117	1	20
β-strand	125	1	23
β-strand	128	1	24
β-strand	130	1	22
β-strand	132	1	25
β-strand	133	1	21
β-strand	138	1	25
β-strand	143	1	24
β-strand	147	1	23
β-strand	148-150	3	19
β-strand	168	1	26
β-strand	172-177	6	27
β-strand	187-192	6	27
β-strand	195-199	5	27
β-strand	206-208	3	27
β-strand	227	1	26
β-strand	229	1	28
β-strand	233-238	6	27
β-strand	244-252	9	27
β-strand	254	1	29
β-strand	257-259	3	29
β-strand	265	1	28
β-strand	270-276	7	27
β-strand	279	1	30
β-strand	281	1	30
β-strand	283-285	3	27
β-strand	292-294	3	27
β-strand	305-307	3	29
β-strand	314-318	5	27
β-strand	319-326	8	18
β-strand	327	1	31
β-strand	342-347	6	32
β-strand	357-362	6	32
β-strand	368-372	5	31
β-strand	375-376	2	31
β-strand	379-383	5	32
β-strand	386-389	4	32
α-helix	394-396	3
β-strand	408-416	9	31
β-strand	418	1	17
β-strand	421-430	10	31

Chain E: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1932-1938	7
α-helix	1944-1950	7
α-helix	1965-1971	7
α-helix	1975-1983	9
β-strand	1984	1	15
α-helix	1999-2005	7
α-helix	2011-2017	7
β-strand	2025	1	33
β-strand	2031	1	33
α-helix	2032-2038	7
α-helix	2042-2049	8
α-helix	2065-2072	8
α-helix	2075-2081	7
α-helix	2098-2105	8
α-helix	2108-2116	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Recombining binding protein suppressor of hairless	A, D	protein	433	Homo sapiens	Q06330 (AlphaFold model)
Neurogenic locus notch homolog protein 1	B, E	protein	256	Homo sapiens	P46531 (AlphaFold model)
Mastermind-like protein 1	C, F	protein	63	Homo sapiens	Q92585 (AlphaFold model)
DNA, HES1 promoter	X	DNA	37
DNA, HES1 promoter	Y	DNA	37

Sequence of entity 1 (A, D), FASTA

>3NBN_1 Recombining binding protein suppressor of hairless (chains A, D)
MGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWK
KKKEQMERDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFML
SVKMFYGNSDDIGVFLSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTR
YLHVEGGNFHASSQQWGAFFIHLLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPR
LIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMYLCLSQERIIQFQATPCPKEPNKEM
INDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGDVAMLELTGQNFTPN
LRVWFGDVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGIIYSTSLT
FTYTPEPHHHHHH

Sequence of entity 2 (B, E), FASTA

>3NBN_2 Neurogenic locus notch homolog protein 1 (chains B, E)
GMDVNVRGPDGFTPLMIASCSGGGLETGNSEEEEDAPAVISDFIYQGASLHNQTDRTGET
ALHLAARYSRSDAAKRLLEASADANIQDNMGRTPLHAAVSADAQGVFQILIRNRATDLDA
RMHDGTTPLILAARLAVEGMLEDLINSHADVNAVDDLGKSALHWAAAVNNVDAAVVLLKN
GANKDMQNNREETPLFLAAREGSYETAKVLLDHFANRDITDHMDRLPRDIAQERMHHDIV
RLLDEYNLVRSPQLHG

Sequence of entity 3 (C, F), FASTA

>3NBN_3 Mastermind-like protein 1 (chains C, F)
GLPRHSAVMERLRRRIELCRRHHSTCEARYEAVSPERLELERQHTFALHQRCIQAKAKRA
GKH

Sequence of entity 4 (X), FASTA

>3NBN_4 DNA, HES1 promoter (chains X)
TACTGTGGGAAAGAAAGTTTGGAAAATTTCACACGAG

Sequence of entity 5 (Y), FASTA

>3NBN_5 DNA, HES1 promoter (chains Y)
ACTCGTGTGAAACTTCCCAAACTTTCTTTCCCACAGT

Primary citation

Structural and mechanistic insights into cooperative assembly of dimeric Notch transcription complexes. Arnett, K.L., Hass, M., McArthur, D.G. et al. Nat Struct Mol Biol (2010) 17:1312-1317. DOI 10.1038/nsmb.1938 · PubMed

Other PDB entries of the same protein (UniProt Q06330 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2F8X 3.25 Å, Crystal structure of activated Notch, CSL and MAML on HES-1 promoter DNA sequence
6PY8 3.75 Å, Crystal structure of the RBPJ-NOTCH1-NRARP ternary complex bound to DNA
3V79 3.85 Å, Structure of human Notch1 transcription complex including CSL, RAM, ANK, and MAML-1 on…

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