5CVD: Human NRMT1

Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide. Determined by X-ray diffraction at 1.3 Å resolution. Released 25 Nov 2015.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,625
Mol. weight: 58.23 kDa
Ligands: SAH
Released: 25 Nov 2015

Explore 5CVD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CVD contains 35 α-helices and 24 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: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	9-21	13
α-helix	27-30	4
α-helix	35-37	3
α-helix	38-54	17
α-helix	59-61	3
β-strand	65-68	4	1
α-helix	74-75	2
α-helix	76-80	5
β-strand	87-91	5	1
α-helix	94-103	10
α-helix	105-110	6
β-strand	111-116	6	1
α-helix	119-121	3
α-helix	124-125	2
β-strand	129-135	7	1
α-helix	138-140	3
α-helix	143-156	14
β-strand	157-170	14	1
β-strand	174-177	4	1
β-strand	182-186	5	1
α-helix	187-196	10
β-strand	201-206	6	1
α-helix	207-208	2
β-strand	214	1	2
α-helix	215	1
β-strand	216-222	7	1

Chain B: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	9-21	13
α-helix	27-30	4
α-helix	35-37	3
α-helix	38-53	16
α-helix	59-61	3
β-strand	64-68	5	3
α-helix	74-75	2
α-helix	76-80	5
β-strand	86-91	6	3
α-helix	94-103	10
α-helix	105-110	6
β-strand	111-116	6	3
α-helix	119-121	3
α-helix	124-125	2
β-strand	129-135	7	3
α-helix	138-140	3
α-helix	143-154	12
β-strand	157-169	13	3
β-strand	170	1	4
β-strand	174-177	4	5
β-strand	182-185	4	5
β-strand	186	1	4
α-helix	187-196	10
β-strand	201-206	6	3
α-helix	207-208	2
β-strand	214	1	6
α-helix	215	1
β-strand	216-222	7	3

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	2

Chain E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	6
α-helix	5-6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-terminal Xaa-Pro-Lys N-methyltransferase 1	A, B	protein	243	Homo sapiens	Q9BV86 (AlphaFold model)
N-teminal peptide from Histone H3-like centromeric protein A	D, E	protein	9	Homo sapiens	P49450 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5CVD_1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 (chains A, B)
MGSSHHHHHHSSGLVPRGSHMTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSI
DINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQA
KTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPN
GIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSF
ALR

Sequence of entity 2 (D, E), FASTA

>5CVD_2 N-teminal peptide from Histone H3-like centromeric protein A (chains D, E)
XPRRRSRKP

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Primary citation

Molecular basis for histone N-terminal methylation by NRMT1. Wu, R., Yue, Y., Zheng, X. et al. Genes Dev (2015) 29:2337-2342. DOI 10.1101/gad.270926.115 · PubMed

Other PDB entries of the same protein (UniProt Q9BV86 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WJ7 1.42 Å, The structure of NTMT1 in complex with compound C2A
5E1D 1.45 Å, NTMT1 in complex with YPKRIA peptide
6DTN 1.48 Å, The structure of NTMT1 in complex with compound DC100-1
6KDQ 1.5 Å, Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A…
5CVE 1.5 Å, Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH
6PVB 1.5 Å, The structure of NTMT1 in complex with compound 6
5E1B 1.65 Å, Crystal structure of NRMT1 in complex with SPKRIA peptide
6WH8 1.73 Å, The structure of NTMT1 in complex with compound BM-30
2EX4 1.75 Å, Crystal Structure of Human methyltransferase AD-003 in complex with…
5E1M 1.75 Å, Crystal structure of NTMT1 in complex with PPKRIA peptide
5E2A 1.75 Å, Crystal structure of NTMT1 in complex with N-terminally methylated SPKRIA peptide
6PVA 1.84 Å, The structure of NTMT1 in complex with compound 11

Browse structure collections

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