3NKD: CRISPR-associated protein Cas1

Structure of CRISP-associated protein Cas1 from Escherichia coli str. K-12. Determined by X-ray diffraction at 1.95 Å resolution. Released 25 Aug 2010.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Escherichia coli
Chains: 2
Atoms: 4,242
Mol. weight: 66.47 kDa
Released: 25 Aug 2010

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

Secondary structure: helices and β-sheets

3NKD contains 32 α-helices and 16 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: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	1
β-strand	23-28	6	2
β-strand	31-36	6	2
β-strand	41-43	3	2
α-helix	46-48	3
β-strand	51-54	4	1
β-strand	58-60	3	2
α-helix	62-70	9
β-strand	74-78	5	1
α-helix	80-82	3
β-strand	85-89	5	1
α-helix	96-107	12
α-helix	109-124	16
α-helix	127-129	3
α-helix	134-143	10
α-helix	145-156	12
α-helix	175-184	10
α-helix	187-198	12
α-helix	214-223	10
α-helix	224-228	5
α-helix	229-238	10
α-helix	244-252	9
α-helix	253-256	4
α-helix	258-262	5
α-helix	264-273	10
α-helix	278-279	2

Chain B: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	15-20	6	1
β-strand	24-28	5	2
β-strand	31-35	5	2
β-strand	42-43	2	2
α-helix	46-48	3
β-strand	49-54	6	1
β-strand	59-61	3	2
α-helix	62-70	9
β-strand	74-78	5	1
α-helix	80-82	3
β-strand	84-89	6	1
α-helix	96-107	12
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	228-236	9
α-helix	244-258	15
α-helix	260-273	14
α-helix	277-279	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CRISPR-associated protein Cas1	A, B	protein	305	Escherichia coli	Q46896 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3NKD_1 CRISPR-associated protein Cas1 (chains A, B)
MTWLPLNPIPLKDRVSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRV
SHAAVRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLKVVRKMF
ELRFGEPAPARRSVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPKDWEKGDTINQCI
SAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIKFDTVVPKAFEIARRNP
GEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAAGEIQPPAPPEDAQPVAIPLPVSLGDA
GHRSS

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:

3NKE 1.4 Å, High resolution structure of the C-terminal domain CRISP-associated protein Cas1 from…
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

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