5L2L: Nab2 Zn fingers 5-7

Nab2 Zn fingers 5-7 bound to A11G RNA. Determined by X-ray diffraction at 1.55 Å resolution. Released 21 Dec 2016.

Method: X-ray diffraction
Resolution: 1.55 Å
Organisms: Saccharomyces cerevisiae YJM1574, Saccharomyces cerevisiae
Chains: 8
Atoms: 4,031
Mol. weight: 52.44 kDa
Ligands: ZN
Released: 21 Dec 2016

Explore 5L2L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L2L contains 20 α-helices and 24 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.

Chains A, B, E and F: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	414	1	1
α-helix	415	1
α-helix	418-420	3
β-strand	429	1	1
β-strand	436	1	2
α-helix	437	1
α-helix	440-442	3
β-strand	451	1	2
β-strand	457	1	3
α-helix	461-463	3
β-strand	472	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nab2p	A, B, E, F	protein	77	Saccharomyces cerevisiae YJM1574	P32505 (AlphaFold model)
RNA (5'-r(apapapapapapapapapg)-3')	C, D, G, H	RNA	12	Saccharomyces cerevisiae

Sequence of entity 1 (A, B, E, F), FASTA

>5L2L_1 Nab2p (chains A, B, E, F)
GSEKSLEQCKFGTHCTNKRCKYRHARSHIMCREGANCTRIDCLFGHPINEDCRFGVNCKN
IYCLFRHPPGRVLPEKK

Sequence of entity 2 (C, D, G, H), FASTA

>5L2L_2 RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*G)-3') (chains C, D, G, H)
AAAAAAAAAAAG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	14

Primary citation

Structural basis for the dimerization of Nab2 generated by RNA binding provides insight into its contribution to both poly(A) tail length determination and transcript compaction in Saccharomyces cerevisiae. Aibara, S., Gordon, J.M., Riesterer, A.S. et al. Nucleic Acids Res (2017) 45:1529-1538. DOI 10.1093/nar/gkw1224 · PubMed

Other PDB entries of the same protein (UniProt P32505 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2V75 1.8 Å, N-terminal domain of Nab2
3LCN 2.0 Å, Nab2:Gfd1 complex
4JLQ 3.05 Å, Crystal structure of human Karyopherin-beta2 bound to the PY-NLS of Saccharomyces…
2JPS NAB2 N-terminal domain
2LHN RNA-binding zinc finger protein
3ZJ1 Structure of Nab2p tandem zinc finger 12
3ZJ2 Structure of Nab2p tandem zinc finger 34

Browse structure collections

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