4TXR: LIP5 N-terminal domain

Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM and CHMP5 MIM. Determined by X-ray diffraction at 1.0 Å resolution. Released 11 Feb 2015.

Method: X-ray diffraction
Resolution: 1.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,349
Mol. weight: 28.32 kDa
Released: 11 Feb 2015

Explore 4TXR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4TXR contains 14 α-helices and 0 β-strands across 3 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: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	5-11	7
α-helix	12-17	6
α-helix	18-26	9
α-helix	32-49	18
α-helix	54-73	20
α-helix	78-81	4
α-helix	83-106	24
α-helix	112-128	17
α-helix	129-131	3
α-helix	134-135	2
α-helix	136-158	23

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	187-196	10

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	160-175	16
α-helix	182-188	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Charged multivesicular body protein 1b	B	protein	25	Homo sapiens	Q7LBR1 (AlphaFold model)
Vacuolar protein sorting-associated protein VTA1 homolog	A	protein	163	Homo sapiens	Q9NP79 (AlphaFold model)
Charged multivesicular body protein 5	C	protein	58	Homo sapiens	Q9NZZ3 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>4TXR_1 Charged multivesicular body protein 1b (chains B)
SVGTSVASAEQDELSQRLARLRDQV

Sequence of entity 2 (A), FASTA

>4TXR_2 Vacuolar protein sorting-associated protein VTA1 homolog (chains A)
SMAALAPLPPLPAQFKSIQHHLRTAQEHDKRDPVVAYYCRLYAMQTGMKIDSKTPECRKF
LSKLMDQLEALKKQLGDNEAITQEIVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSFY
TASLLIDVITVFGELTDENVKHRKYARWKATYIHNCLKNGETP

Sequence of entity 3 (C), FASTA

>4TXR_3 Charged multivesicular body protein 5 (chains C)
SMEDANEIQEALSRSYGTPELDEDDLEAELDALGDELLADEDSSYLDEAASAPAIPEG

Primary citation

A Novel Mechanism of Regulating the ATPase VPS4 by Its Cofactor LIP5 and the Endosomal Sorting Complex Required for Transport (ESCRT)-III Protein CHMP5. Vild, C.J., Li, Y., Guo, E.Z. et al. J Biol Chem (2015) 290:7291-7303. DOI 10.1074/jbc.M114.616730 · PubMed

Other PDB entries of the same protein (UniProt Q7LBR1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TXQ 2.21 Å, Crystal structure of LIP5 N-terminal domain complexed with CHMP1B MIM
3EAB 2.5 Å, Crystal structure of Spastin MIT in complex with ESCRT III
8V2S 2.72 Å, CHMP1B/IST1 dsDNA bound copolymer
6E8G 2.9 Å, CryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ssDNA at 2.9 Angstrom…
8V2Q 2.95 Å, CHMP1B/IST1 ssRNA bound copolymer
8V2R 3.01 Å, CHMP1B/IST1 ssDNA bound copolymer
6TZ5 3.1 Å, CryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B+IST1…
6TZ4 3.2 Å, CryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B+IST1…
3JC1 4.0 Å, Electron cryo-microscopy of the IST1-CHMP1B ESCRT-III copolymer
6TZ9 6.2 Å, CryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B only

Browse structure collections

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