4NDY: Human MHF1-MHF2 DNA complex

Human MHF1-MHF2 DNA complex. Determined by X-ray diffraction at 7.0 Å resolution. Released 22 Jan 2014.

Method: X-ray diffraction
Resolution: 7.0 Å
Organisms: Synthetic DNA, Homo sapiens
Chains: 24
Atoms: 15,914
Mol. weight: 236.83 kDa
Released: 22 Jan 2014

Explore 4NDY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NDY contains 73 α-helices and 38 β-strands across 20 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	16-38	23
β-strand	42	1	4
α-helix	44-71	28
β-strand	76-77	2	5
α-helix	79-85	7
α-helix	90-105	16

Chains B, H, U, V and W: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
β-strand	29-30	2	5
α-helix	32-59	28
β-strand	65	1	4
α-helix	67-80	14

Chain C: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	15-38	24
α-helix	44-71	28
β-strand	76-77	2	1
α-helix	79-85	7
α-helix	86-88	3
α-helix	90-105	16

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-20	9
β-strand	29-30	2	1
α-helix	32-59	28
α-helix	67-80	14

Chain G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	15-38	24
β-strand	42	1	2
α-helix	44-71	28
β-strand	76-77	2	3
α-helix	79-85	7
α-helix	86-88	3
α-helix	90-105	16

Chain I: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	15-38	24
β-strand	41-42	2	6
α-helix	44-71	28
β-strand	76-77	2	7
α-helix	79-85	7
α-helix	86-88	3
α-helix	90-113	24

Chain J: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	15-38	24
β-strand	42	1	8
α-helix	44-71	28
β-strand	77	1	9
α-helix	79-85	7
α-helix	90-105	16

Chains K, Q and T: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	15-38	24
β-strand	42	1	10
α-helix	44-71	28
β-strand	76-77	2	11
α-helix	79-85	7
α-helix	90-113	24

5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (26-mer)	E, O	DNA	26	Synthetic DNA
DNA (26-mer)	F, P	DNA	26	Synthetic DNA
Centromere protein S	A, C, G, I, J, K, Q, R, S, T	protein	105	Homo sapiens	Q8N2Z9 (AlphaFold model)
Centromere protein X	B, D, H, L, M, N, U, V, W, X	protein	74	Homo sapiens	A8MT69 (AlphaFold model)

Sequence of entity 1 (E, O), FASTA

>4NDY_1 DNA (26-MER) (chains E, O)
AAAAAAAAAAAAAAAAAAAAAAAAAA

Sequence of entity 2 (F, P), FASTA

>4NDY_2 DNA (26-MER) (chains F, P)
TTTTTTTTTTTTTTTTTTTTTTTTTT

Sequence of entity 3 (A, C, G, I, J, K, Q, R, S, T), FASTA

>4NDY_3 Centromere protein S (chains A, C, G, I, J, K, Q, R, S, T)
SYQQRLKAAVHYTVGCLCEEVALDKAMQFSKQTIAAISELTFRQCENFAKDLEMFARHAK
RTTINTEDVKLLARRSNSLLKYITDKSEEIAQANLERKAQKKKKS

Sequence of entity 4 (B, D, H, L, M, N, U, V, W, X), FASTA

>4NDY_4 Centromere protein X (chains B, D, H, L, M, N, U, V, W, X)
SGFRKELVSRLLHLHFKDDKTKVSGDALQLMVELLKVFVVEAAVRGVRQAQAEDALRVDV
DQLEKVLPQLLLDF

Primary citation

The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes. Zhao, Q., Saro, D., Sachpatzidis, A. et al. Nat Commun (2014) 5:2987-2987. DOI 10.1038/ncomms3987 · PubMed

Other PDB entries of the same protein (UniProt Q8N2Z9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NE3 1.8 Å, Human MHF1-MHF2 complex
4E45 2.0 Å, Crystal structure of the hMHF1/hMHF2 Histone-Fold Tetramer in Complex with Fanconi…
4E44 2.1 Å, Crystal structure of the hMHF1/hMHF2 Histone-Fold Tetramer
4NE6 2.1 Å, Human MHF1-MHF2 complex
4DRA 2.41 Å, Crystal structure of MHF complex
4NE5 2.5 Å, Human MHF1-MHF2 complex
4DRB 2.63 Å, The crystal structure of FANCM bound MHF complex
28OP 2.7 Å, Structure of the human inner kinetochore CCAN and CENP-C bound to DNA
7R5S 2.83 Å, Structure of the human CCAN bound to alpha satellite DNA
7XHO 3.29 Å, Structure of human inner kinetochore CCAN complex
9TAW 3.54 Å, Structure of the human inner kinetochore CCAN bound to DNA
7XHN 3.71 Å, Structure of human inner kinetochore CCAN-DNA complex

Browse structure collections

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