4PT2: Myxococcus xanthus encapsulin protein

Myxococcus xanthus encapsulin protein (EncA). Determined by electron microscopy at 4.6 Å resolution. Released 30 Jul 2014.

Method: Electron microscopy
Resolution: 4.6 Å
Organism: Myxococcus xanthus
Chains: 3
Atoms: 6,462
Mol. weight: 95.08 kDa
Released: 30 Jul 2014

Explore 4PT2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PT2 contains 29 α-helices and 29 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: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	39	1
β-strand	40	1	4
α-helix	41-43	3
α-helix	72-74	3
α-helix	82-86	5
β-strand	88-94	7	4
α-helix	96-99	4
α-helix	112-130	19
α-helix	163-174	12
β-strand	181-185	5	5
α-helix	187-192	6
α-helix	204-212	9
β-strand	213-218	6	5
β-strand	227-231	5	5
β-strand	237-249	13	4
β-strand	253	1	6
β-strand	255	1	6
β-strand	257-269	13	4

Chain B: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-30	17
β-strand	40	1	7
α-helix	82-86	5
β-strand	88-94	7	8
α-helix	98-101	4
α-helix	109-110	2
α-helix	114-130	17
α-helix	161-174	14
β-strand	181-185	5	9
α-helix	187-193	7
α-helix	204-211	8
β-strand	213-218	6	9
β-strand	227-231	5	9
β-strand	237-241	5	7
β-strand	246-249	4	8
β-strand	257-263	7	8
β-strand	265-269	5	7
β-strand	276	1	9

Chain P: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-30	17
α-helix	39	1
β-strand	40	1	1
α-helix	41-43	3
α-helix	82-86	5
β-strand	88-94	7	2
α-helix	98-102	5
α-helix	108-110	3
α-helix	112-130	19
α-helix	163-173	11
α-helix	174-176	3
β-strand	181-185	5	3
α-helix	187-194	8
α-helix	204-212	9
β-strand	213-218	6	3
β-strand	228-231	4	3
β-strand	237-241	5	1
β-strand	246-249	4	2
β-strand	257-263	7	2
β-strand	265-269	5	1
β-strand	276	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Encapsulin protein	A, B, P	protein	287	Myxococcus xanthus	Q1D6H4 (AlphaFold model)

Sequence of entity 1 (A, B, P), FASTA

>4PT2_1 Encapsulin protein (chains A, B, P)
MPDFLGHAENPLREEEWARLNETVIQVARRSLVGRRILDIYGPLGAGVQTVPYDEFQGVS
PGAVDIVGEQETAMVFTDARKFKTIPIIYKDFLLHWRDIEAARTHNMPLDVSAAAGAAAL
CAQQEDELIFYGDARLGYEGLMTANGRLTVPLGDWTSPGGGFQAIVEATRKLNEQGHFGP
YAVVLSPRLYSQLHRIYEKTGVLEIETIRQLASDGVYQSNRLRGESGVVVSTGRENMDLA
VSMDMVAAYLGASRMNHPFRVLEALLLRIKHPDAICTLEGAGATERR

Primary citation

A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. McHugh, C.A., Fontana, J., Nemecek, D. et al. EMBO J (2014) 33:1896-1911. DOI 10.15252/embj.201488566 · PubMed

Other PDB entries of the same protein (UniProt Q1D6H4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VJO 2.4 Å, Cryo-EM structure of Myxococcus xanthus EncA encapsulin shell loaded with EncD cargo
8V4N 2.43 Å, Myxococcus xanthus EncA 3xHis pore mutant with T=1 icosahedral symmetry
8TK7 2.53 Å, Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein
8V4Q 2.71 Å, Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry
9B9I 2.86 Å, Myxococcus xanthus EncA encapsulin engineered pore mutant with T=1 icosahedral symmetry
7S4Q 3.12 Å, M. xanthus encapsulin EncA bound to EncC targeting peptide
9B9Q 3.14 Å, Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3…
7S20 3.4 Å, M. xanthus encapsulin shell protein EncA with T=3 symmetry
7S21 3.4 Å, M. xanthus encapsulin shell protein EncA with T=1 symmetry
7S2T 3.45 Å, M. xanthus encapsulin EncA bound to EncB targeting peptide
9BC8 3.46 Å, Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=4…

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