3NKE: Protein ygbT

High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from Escherichia coli str. K-12. Determined by X-ray diffraction at 1.4 Å resolution. Released 25 Aug 2010.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Escherichia coli
Chains: 3
Atoms: 5,145
Mol. weight: 67.24 kDa
Ligands: SO3
Released: 25 Aug 2010

Explore 3NKE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NKE contains 30 α-helices and 0 β-strands across 3 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: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	95-107	13
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
α-helix	175-197	23
α-helix	214-223	10
α-helix	228-238	11
α-helix	243-258	16
α-helix	260-273	14
α-helix	278-279	2

Chain B: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	94-107	14
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
α-helix	175-198	24
α-helix	214-223	10
α-helix	228-237	10
α-helix	243-258	16
α-helix	260-273	14
α-helix	278-280	3

Chain C: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	93-107	15
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-156	23
α-helix	175-197	23
α-helix	214-223	10
α-helix	228-238	11
α-helix	243-258	16
α-helix	260-273	14
α-helix	277-280	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
protein ygbT	A, B, C	protein	200	Escherichia coli	Q46896 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3NKE_1 protein ygbT (chains A, B, C)
GGARSDKLLYQAKLALDEDLRLKVVRKMFELRFGEPAPARRSVEQLRGIEGSRVRATYAL
LAKQYGVTWNGRRYDPKDWEKGDTINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGK
PLSFVYDIADIIKFDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDV
LAAGEIQPPAPPEDAQPVAI

Ligands and cofactors

ID	Name	Formula	Copies
SO3	Sulfite ion	O3 S	2

Water and common crystallization additives (EDO, SO4) are not listed.

Primary citation

A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Babu, M., Beloglazova, N., Flick, R. et al. Mol Microbiol (2011) 79:484-502. DOI 10.1111/j.1365-2958.2010.07465.x · PubMed

Other PDB entries of the same protein (UniProt Q46896 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NKD 1.95 Å, Structure of CRISP-associated protein Cas1 from Escherichia coli str. K-12
4P6I 2.3 Å, Crystal structure of the Cas1-Cas2 complex from Escherichia coli
5DLJ 2.6 Å, Crystal Structure of Cas-DNA-N1 complex
4QDL 2.7 Å, Crystal structure of E.coli Cas1-Cas2 complex
5DQZ 2.7 Å, Crystal Structure of Cas-DNA-PAM complex
5VVK 2.9 Å, Cas1-Cas2 bound to full-site mimic
5DS5 2.95 Å, Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA and Mg
5DQT 3.1 Å, Crystal Structure of Cas-DNA-22 complex
5DS4 3.2 Å, Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA
5VVL 3.31 Å, Cas1-Cas2 bound to full-site mimic with Ni
5DS6 3.35 Å, Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with…
5WFE 3.64 Å, Cas1-Cas2-IHF-DNA holo-complex

Browse structure collections

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