8VHI: NPM2-H1.8 isolated from Xenopus egg extract

NPM2-H1.8 isolated from Xenopus egg extract. Determined by electron microscopy at 5.0 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 5.0 Å
Organism: Xenopus laevis
Chains: 5
Atoms: 4,285
Mol. weight: 109.75 kDa
Released: 11 Dec 2024

Explore 8VHI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VHI contains 5 α-helices and 50 β-strands across 5 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, C, D and E: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	1
β-strand	29-32	4	2
α-helix	38-40	3
β-strand	44-52	9	1
β-strand	61-69	9	2
β-strand	72-81	10	2
β-strand	82	1	3
β-strand	86	1	3
β-strand	88-96	9	1
β-strand	100-106	7	2
β-strand	111-118	8	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nucleoplasmin isoform X1	A, B, C, D, E	protein	199	Xenopus laevis	P05221 (AlphaFold model)

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

>8VHI_1 Nucleoplasmin isoform X1 (chains A, B, C, D, E)
MASTVSNTSKLEKPVSLIWGCELNEQNKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEF
HIVEIVTQEEGAEKSVPIATLKPSILPMATMVGIELTPPVTFRLKAGSGPLYISGQHVAM
EEDYSWAEEEDEGEAEGEEEEEEEEDQESPPKAVKRPAATKKAGQAKKKLDKEDESSEED
SPTKKGKGAGRGRKPAAKK

Primary citation

MagIC-Cryo-EM, structural determination on magnetic beads for scarce macromolecules in heterogeneous samples. Arimura, Y., Konishi, H.A., Funabiki, H. Elife (2025) 13. DOI 10.7554/eLife.103486 · PubMed

Other PDB entries of the same protein (UniProt P05221 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3UL1 1.9 Å, Mouse importin alpha: nucleoplasmin cNLS peptide complex
1K5J 2.3 Å, The Crystal Structure of Nucleoplasmin-Core
4BPL 2.3 Å, rice importin_alpha in complex with nucleoplasmin NLS
1EE5 2.4 Å, Yeast karyopherin (importin) alpha in a complex with a nucleoplasmin nls peptide
2VTX 2.5 Å, Activation of nucleoplasmin, an oligomeric histone chaperone, challenges its stability
1EJY 2.9 Å, Mouse importin alpha-nucleoplasmin nls peptide complex
8VHK 5.16 Å, NPM2-H1.8 isolated from Xenopus egg extract (Stretched form)
8VHJ 5.9 Å, NPM2-H1.8 isolated from Xenopus egg extract (Bent form)

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