8V4Q: Type 1 encapsulin shell protein EncA

Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry. Determined by electron microscopy at 2.71 Å resolution. Released 22 May 2024.

Method: Electron microscopy
Resolution: 2.71 Å
Organism: Myxococcus xanthus DK 1622
Chains: 3
Atoms: 5,993
Mol. weight: 95.46 kDa
Released: 22 May 2024

Explore 8V4Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V4Q contains 29 α-helices and 43 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, 15 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	34-36	3
β-strand	40-41	2	1
β-strand	50-52	3	2
β-strand	82-84	3	2
α-helix	85-86	2
β-strand	88-94	7	1
α-helix	96-105	10
α-helix	107-110	4
α-helix	112-131	20
β-strand	133	1	3
β-strand	138	1	3
β-strand	148-150	3	4
α-helix	160-174	15
β-strand	181-185	5	4
α-helix	187-192	6
α-helix	204-209	6
β-strand	215-218	4	4
β-strand	227-231	5	4
β-strand	237-249	13	1
β-strand	253	1	5
β-strand	256	1	5
β-strand	257-269	13	1
α-helix	272-274	3
β-strand	275-278	4	4

Chain B: 10 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	14-29	16
α-helix	34-36	3
β-strand	40-41	2	6
β-strand	50-52	3	7
β-strand	82-84	3	7
α-helix	85-86	2
β-strand	87-94	8	6
α-helix	96-105	10
α-helix	108-110	3
α-helix	112-131	20
β-strand	133	1	8
β-strand	138	1	8
β-strand	148-150	3	9
α-helix	160-173	14
β-strand	181-185	5	9
α-helix	187-192	6
α-helix	204-209	6
β-strand	216-218	3	9
β-strand	227-231	5	9
β-strand	237-249	13	6
β-strand	253	1	10
β-strand	256	1	10
β-strand	257-269	13	6
α-helix	272-274	3
β-strand	275-278	4	9

Chain C: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	14-29	16
α-helix	34-36	3
β-strand	40	1	11
β-strand	87-94	8	11
α-helix	96-105	10
α-helix	108-110	3
α-helix	112-131	20
β-strand	133	1	12
β-strand	138	1	12
β-strand	148-150	3	13
α-helix	160-174	15
β-strand	181-185	5	13
α-helix	187-192	6
α-helix	204-211	8
β-strand	215-218	4	13
β-strand	227-231	5	13
β-strand	237-249	13	11
β-strand	253	1	14
β-strand	256	1	14
β-strand	257-269	13	11
α-helix	272-274	3
β-strand	275-278	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Type 1 encapsulin shell protein EncA	A, B, C	protein	287	Myxococcus xanthus DK 1622	Q1D6H4 (AlphaFold model)

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

>8V4Q_1 Type 1 encapsulin shell protein EncA (chains A, B, C)
MPDFLGHAENPLREEEWARLNETVIQVARRSLVGRRILDIYGPLGAGVQTVPYDEFQGVS
PGAVDIVGEQETAMVFTDARKFKTIPIIYKDFLLHWRDIEAARTHNMPLDVSAAAGAAAL
CAQQEDELIFYGDARLGYEGLMTANGRLTVPLGDWTSPGGGFQAIVEATRKLNEQGHFGP
YAVVLSPRLYSQLHRIYEHHHVLEIETIRQLASDGVYQSNRLRGESGVVVSTGRENMDLA
VSMDMVAAYLGASRMNHPFRVLEALLLRIKHPDAICTLEGAGATERR

Primary citation

Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. Szyszka, T.N., Andreas, M.P., Lie, F. et al. Proc Natl Acad Sci U S A (2024) 121:e2321260121-e2321260121. DOI 10.1073/pnas.2321260121 · 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
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…
4PT2 4.6 Å, Myxococcus xanthus encapsulin protein (EncA)

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