4S0H: TBX5 DB, NKX2.5 HD, ANF DNA Complex

TBX5 DB, NKX2.5 HD, ANF DNA Complex. Determined by X-ray diffraction at 2.82 Å resolution. Released 16 Dec 2015.

Method: X-ray diffraction
Resolution: 2.82 Å
Organisms: Homo sapiens, synthetic construct
Chains: 8
Atoms: 5,350
Mol. weight: 79.16 kDa
Released: 16 Dec 2015

Explore 4S0H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4S0H contains 22 α-helices and 32 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: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	55-58	4	1
α-helix	61-68	8
β-strand	73-75	3	2
β-strand	77	1	3
β-strand	81-82	2	3
β-strand	87-92	6	1
β-strand	99-108	10	2
β-strand	112-116	5	4
β-strand	121-126	6	4
α-helix	127-128	2
β-strand	135-137	3	2
β-strand	143-144	2	2
α-helix	145-150	6
β-strand	153-155	3	1
β-strand	159-161	3	3
α-helix	170	1
β-strand	171-172	2	3
β-strand	178-187	10	2
β-strand	202-205	4	2
α-helix	207-209	3
β-strand	211-214	4	2
α-helix	220-229	10
α-helix	231-236	6

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	144-146	3
α-helix	147-159	13
α-helix	167-175	9
α-helix	179-192	14

Chain E: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	55-58	4	5
α-helix	61-70	10
β-strand	73-75	3	6
β-strand	77	1	7
β-strand	81-82	2	7
β-strand	88-92	5	5
β-strand	99-100	2	8
β-strand	101-116	16	6
β-strand	121-125	5	6
α-helix	126-130	5
β-strand	136-137	2	6
β-strand	143-144	2	8
α-helix	145-149	5
β-strand	153-154	2	5
β-strand	159-161	3	7
α-helix	170	1
β-strand	171-172	2	7
β-strand	177-186	10	6
β-strand	202-204	3	6
α-helix	207-209	3
β-strand	211-214	4	6
α-helix	220-229	10
α-helix	231-236	6

Chain F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	107-109	3
α-helix	110-120	11
α-helix	128-138	11
α-helix	142-155	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-box transcription factor TBX5	A, E	protein	186	Homo sapiens	Q99593 (AlphaFold model)
Homeobox protein Nkx-2.5	B, F	protein	53	Homo sapiens	P52952 (AlphaFold model)
5'-d(tpcptpcpapcpapcpcptptptpgpapapgptpgp*g)-3'	C, G	DNA	19	synthetic construct
5'-d(cpcpapcptptpcpapapapgpgptpgptpgpapgp*a)-3'	D, H	DNA	19	synthetic construct

Sequence of entity 1 (A, E), FASTA

>4S0H_1 T-box transcription factor TBX5 (chains A, E)
GIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDH
RYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHII
LNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPF
AKGFRG

Sequence of entity 2 (B, F), FASTA

>4S0H_2 Homeobox protein Nkx-2.5 (chains B, F)
RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK

Sequence of entity 3 (C, G), FASTA

>4S0H_3 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP*TP*GP*AP*AP*GP*TP*GP*G)-3' (chains C, G)
TCTCACACCTTTGAAGTGG

Sequence of entity 4 (D, H), FASTA

>4S0H_4 5'-D(*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP*A)-3' (chains D, H)
CCACTTCAAAGGTGTGAGA

Primary citation

Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5. Pradhan, L., Gopal, S., Li, S. et al. Biochemistry (2016) 55:1702-1710. DOI 10.1021/acs.biochem.6b00171 · PubMed

Other PDB entries of the same protein (UniProt Q99593 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X6U 1.9 Å, Crystal structure of human TBX5 in the DNA-free form
2X6V 2.2 Å, Crystal structure of human TBX5 in the DNA-bound and DNA-free form
5BQD 2.58 Å, Crystal Structure of TBX5 (1-239) Dimer

Browse structure collections

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