2VI6: Nanog Homeodomain

Name: PDB 2VI6: Crystal Structure of the Nanog Homeodomain
Published: 2008-01-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal Structure of the Nanog Homeodomain. Determined by X-ray diffraction at 2.6 Å resolution. Released 15 Jan 2008.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: MUS MUSCULUS
Chains: 8
Atoms: 3,832
Mol. weight: 60.81 kDa
Released: 15 Jan 2008

Explore 2VI6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VI6 contains 33 α-helices and 0 β-strands across 8 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, 0 β-strands

Element	Residues	Length
α-helix	10-22	13
α-helix	28-38	11
α-helix	42-54	13
α-helix	57-59	3

Chains B, C and G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-22	13
α-helix	28-38	11
α-helix	42-53	12
α-helix	57-59	3

Chains D and H: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-20	11
α-helix	28-38	11
α-helix	42-55	14
α-helix	57-59	3

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-20	11
α-helix	28-37	10
α-helix	42-54	13
α-helix	57-59	3

Chain F: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-9	3
α-helix	10-22	13
α-helix	28-38	11
α-helix	42-54	13
α-helix	57-59	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Homeobox protein nanog	A, B, C, D, E, F, G, H	protein	62	MUS MUSCULUS	Q80Z64 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>2VI6_1 HOMEOBOX PROTEIN NANOG (chains A, B, C, D, E, F, G, H)
GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR
WQ

Primary citation

Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog. Jauch, R., Ng, C.K.L., Saitakendu, K.S. et al. J Mol Biol (2008) 376:758. DOI 10.1016/J.JMB.2007.11.091 · PubMed

Other PDB entries of the same protein (UniProt Q80Z64 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YDD 2.5 Å, Crystal structure of Nanog(R100A) in complex with Wdr5

Browse structure collections

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