6PEK: Spastin Hexamer

Structure of Spastin Hexamer (Subunit A-E) in complex with substrate peptide. Determined by electron microscopy at 4.2 Å resolution. Released 4 Dec 2019.

Method: Electron microscopy
Resolution: 4.2 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 11,106
Mol. weight: 276.47 kDa
Ligands: ADP, BEF, MG
Released: 4 Dec 2019

Explore 6PEK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PEK contains 74 α-helices and 34 β-strands across 6 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: 17 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	325-331	7
α-helix	341-343	3
α-helix	348-363	16
α-helix	373-375	3
β-strand	377-381	5	1
α-helix	388-398	11
β-strand	402-406	5	1
α-helix	419-432	14
β-strand	436-440	5	1
α-helix	456-471	16
β-strand	481-485	5	1
α-helix	494-497	4
β-strand	502-505	4	1
α-helix	507-509	3
α-helix	511-521	11
α-helix	531-540	10
α-helix	546-556	11
α-helix	559-562	4
α-helix	566-571	6
α-helix	577-580	4
α-helix	582-589	8
α-helix	598-608	11

Chain B: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	324-331	8
α-helix	348-363	16
β-strand	377-381	5	2
α-helix	388-399	12
β-strand	402-406	5	2
β-strand	415	1	3
α-helix	418-432	15
β-strand	436-441	6	2
α-helix	456-469	14
β-strand	480-485	6	2
α-helix	494-499	6
β-strand	502-505	4	2
α-helix	507-509	3
α-helix	511-521	11
α-helix	531-540	10
α-helix	546-562	17
α-helix	566-571	6
α-helix	582-589	8
α-helix	598-608	11

Chain C: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	325-332	8
β-strand	333-334	2	4
α-helix	348-363	16
α-helix	373-375	3
β-strand	377-381	5	4
α-helix	388-398	11
β-strand	402-406	5	4
α-helix	408-411	4
β-strand	415	1	5
α-helix	418-432	15
β-strand	436-441	6	4
α-helix	456-470	15
β-strand	480-486	7	4
α-helix	489-491	3
α-helix	494-499	6
β-strand	502-505	4	4
α-helix	511-521	11
α-helix	531-540	10
α-helix	546-562	17
α-helix	566-571	6
α-helix	578-580	3
α-helix	582-588	7
α-helix	598-608	11

Chain D: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	322-331	10
α-helix	348-363	16
β-strand	377-381	5	6
α-helix	388-399	12
β-strand	402-406	5	6
β-strand	415	1	7
α-helix	419-432	14
β-strand	436-441	6	6
α-helix	443-446	4
α-helix	456-469	14
β-strand	480-485	6	6
α-helix	489-491	3
α-helix	494-499	6
β-strand	502-505	4	6
α-helix	511-521	11
α-helix	531-540	10
α-helix	546-563	18
α-helix	566-571	6
α-helix	582-588	7
α-helix	598-609	12

Chain E: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	325-332	8
β-strand	333	1	8
α-helix	341-343	3
α-helix	348-363	16
β-strand	379-381	3	9
α-helix	388-399	12
β-strand	404-405	2	8
α-helix	418-432	15
β-strand	438-439	2	8
α-helix	443-445	3
α-helix	456-468	13
β-strand	482-483	2	8
β-strand	484-486	3	9
α-helix	489-491	3
α-helix	494-499	6
β-strand	503-505	3	9
α-helix	507-509	3
α-helix	511-521	11
α-helix	531-539	9
α-helix	546-553	8
α-helix	598-609	12

Chain G: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	3
β-strand	6	1	5
β-strand	8	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spastin	A, B, C, D, E	protein	498	Homo sapiens	Q9UBP0 (AlphaFold model)
substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU	G	protein	10	synthetic construct

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

>6PEK_1 Spastin (chains A, B, C, D, E)
MAAKRSSGAAPAPASASAPAPVPGGEAERVRVFHKQAFEYISIALRIDEDEKAGQKEQAV
EWYKKGIEELEKGIAVIVTGQGEQCERARRLQAKMMTNLVMAKDRLQLLESGAVPKRKDP
LTHTSNSLPRSKTVMKTGSAGLSGHHRAPSYSGLSMVSGVKQGSGPAPTTHKGTPKTNRT
NKPSTPTTATRKKKDLKNFRNVDSNLANLIMNEIVDNGTAVKFDDIAGQDLAKQALQEIV
ILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGE
GEKLVRALFAVARELQPSIIFIDEVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDD
RVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLA
RMTDGYSGSDLTALAKDAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRSVSP
QTLEAYIRWNKDFGDTTV

Sequence of entity 2 (G), FASTA

>6PEK_2 substrate peptide, TYR-GLU-TYR-GLU-TYR-GLU-TYR-GLU (chains G)
EYEYEYEYEY

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5
BEF	Beryllium trifluoride ion	Be F3	4
MG	Magnesium ion	Mg	4

Primary citation

Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation. Han, H., Schubert, H.L., McCullough, J. et al. J Biol Chem (2020) 295:435-443. DOI 10.1074/jbc.AC119.009890 · PubMed

Other PDB entries of the same protein (UniProt Q9UBP0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7S7J 1.15 Å, Structure of Human SPASTIN-IST1 complex.
3EAB 2.5 Å, Crystal structure of Spastin MIT in complex with ESCRT III
5Z6Q 3.0 Å, Crystal structure of AAA of Spastin
5Z6R 3.0 Å, Spastin aaa with ATP
3VFD 3.3 Å, Human spastin AAA domain
6PEN 4.2 Å, Structure of Spastin Hexamer (whole model) in complex with substrate peptide

Browse structure collections

About this viewer

MolViewer shows 6PEK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.