2X6V: Human TBX5 in the DNA-bound and DNA-free form

Crystal structure of human TBX5 in the DNA-bound and DNA-free form. Determined by X-ray diffraction at 2.2 Å resolution. Released 28 Apr 2010.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: HOMO SAPIENS, SYNTHETIC CONSTRUCT
Chains: 4
Atoms: 3,759
Mol. weight: 53.91 kDa
Ligands: PE4, MG
Released: 28 Apr 2010

Explore 2X6V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2X6V contains 16 α-helices and 35 β-strands across 2 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: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	55-58	4	1
α-helix	61-70	10
β-strand	73-75	3	2
β-strand	77	1	3
β-strand	81-82	2	3
β-strand	88-92	5	1
β-strand	99-100	2	4
β-strand	101-108	8	2
β-strand	112-117	6	5
β-strand	120-126	7	5
α-helix	127-129	3
β-strand	130	1	6
α-helix	131-135	5
β-strand	136-137	2	2
β-strand	143-144	2	4
α-helix	145-150	6
β-strand	153-154	2	1
β-strand	159-161	3	3
α-helix	170	1
β-strand	171-172	2	3
β-strand	178-186	9	2
β-strand	200-205	6	2
α-helix	207-209	3
β-strand	211-214	4	2
α-helix	220-229	10
α-helix	231-236	6

Chain B: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	55-58	4	7
α-helix	61-70	10
β-strand	73-75	3	2
β-strand	77	1	8
β-strand	81-82	2	8
α-helix	86-87	2
β-strand	88-92	5	7
β-strand	99-108	10	2
β-strand	112-116	5	9
β-strand	121-126	6	9
α-helix	127-129	3
β-strand	130	1	6
α-helix	131-135	5
β-strand	136-137	2	2
β-strand	143-144	2	2
α-helix	145-150	6
β-strand	153-154	2	7
β-strand	159-161	3	8
α-helix	170	1
β-strand	171-172	2	8
β-strand	178-187	10	2
β-strand	200-204	5	2
α-helix	207-209	3
β-strand	211-214	4	2
α-helix	220-229	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-box transcription factor TBX5	A, B	protein	203	HOMO SAPIENS	Q99593 (AlphaFold model)
5'-d(tpcptpcpapcpapcpcptp*tp)-3'	C	DNA	11	SYNTHETIC CONSTRUCT
5'-d(tpapapgpgptpgptpgpap*gp)-3'	D	DNA	11	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A, B), FASTA

>2X6V_1 T-BOX TRANSCRIPTION FACTOR TBX5 (chains A, B)
GAMEGIKVFLHERELWLKFHEVGTEMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVP
ADDHRYKFADNKWSVTGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPF
GHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIE
NNPFAKGFRGSDDMELHRMSRMQ

Sequence of entity 2 (C), FASTA

>2X6V_2 5'-D(*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP)-3' (chains C)
TCTCACACCTT

Sequence of entity 3 (D), FASTA

>2X6V_3 5'-D(*TP*AP*AP*GP*GP*TP*GP*TP*GP*AP*GP)-3' (chains D)
TAAGGTGTGAG

Ligands and cofactors

ID	Name	Formula	Copies
PE4	2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-etha…	C16 H34 O8	1
MG	Magnesium ion	Mg	2

Primary citation

Structural Basis of Tbx5-DNA Recognition: The T-Box Domain in its DNA-Bound and -Unbound Form. Stirnimann, C.U., Ptchelkine, D., Grimm, C. et al. J Mol Biol (2010) 400:71. DOI 10.1016/J.JMB.2010.04.052 · 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
5BQD 2.58 Å, Crystal Structure of TBX5 (1-239) Dimer
4S0H 2.82 Å, TBX5 DB, NKX2.5 HD, ANF DNA Complex

Browse structure collections

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