5KP9: EPN-01*

Structure of Nanoparticle Released from Enveloped Protein Nanoparticle. Determined by electron microscopy at 5.7 Å resolution. Released 7 Dec 2016.

Method: Electron microscopy
Resolution: 5.7 Å
Organisms: Thermotoga maritima, Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Chains: 1
Atoms: 1,518
Mol. weight: 30.3 kDa
Released: 7 Dec 2016

Explore 5KP9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KP9 contains 11 α-helices and 10 β-strands across 1 chain. 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 B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
β-strand	10-14	5	1
α-helix	19-31	13
β-strand	36-40	5	1
α-helix	46-53	8
α-helix	54-59	6
β-strand	62-66	5	1
α-helix	71-79	9
β-strand	84-86	3	1
α-helix	92-101	10
β-strand	104-106	3	1
β-strand	108-109	2	2
α-helix	112-120	9
β-strand	125-128	4	2
α-helix	131-143	13
β-strand	150-153	4	2
β-strand	154	1	1
α-helix	162-168	7
β-strand	173-175	3	1
α-helix	177-180	4
α-helix	184-199	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
EPN-01*	B	protein	282	Thermotoga maritima, Human immunodeficiency virus type 1 group M subtype B (isolate BH10)	P03347, Q9WXS1 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5KP9_1 EPN-01* (chains B)
MGARASGSKSGSGSDSGSKMEELFKKHKIVAVLRANSVEEAKKKALAVFLGGVHLIEITF
TVPDADTVIKELSFLKEMGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEK
GVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDN
VCEWFKAGVLAVGVGSALVKGTPVEVAEKAKAFVEKIRGCTEQKLISEEDLQSRPEPTAP
PEESFRSGVETTTPPQKQEPIDKELYPLTSLRSLFGNDPSSQ

Primary citation

Designed proteins induce the formation of nanocage-containing extracellular vesicles. Votteler, J., Ogohara, C., Yi, S. et al. Nature (2016) 540:292-295. DOI 10.1038/nature20607 · PubMed

Other PDB entries of the same protein (UniProt P03347), best resolution first:

2BUO 1.7 Å, HIV-1 capsid C-terminal domain in complex with an inhibitor of particle assembly
6BHR 2.91 Å, HIV-1 immature CTD-SP1 hexamer in complex with IP6

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