9BC8: Type 1 encapsulin shell protein EncA

Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=4 icosahedral symmetry. Determined by electron microscopy at 3.46 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 3.46 Å
Organism: Myxococcus xanthus DK 1622
Chains: 8
Atoms: 8,740
Mol. weight: 129.27 kDa
Released: 30 Oct 2024

Explore 9BC8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BC8 contains 55 α-helices and 45 β-strands across 4 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: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	34-37	4
α-helix	39	1
β-strand	40-41	2	1
α-helix	42-43	2
β-strand	50-51	2	2
β-strand	83-84	2	2
α-helix	85	1
β-strand	87-94	8	1
α-helix	96-105	10
α-helix	107-109	3
α-helix	112-130	19
α-helix	158-175	18
β-strand	181-185	5	3
α-helix	187-196	10
α-helix	198-206	9
β-strand	207-212	6	3
β-strand	221-225	5	3
β-strand	232-243	12	1
β-strand	251-262	12	1
α-helix	266-268	3
β-strand	269-271	3	3

Chain B: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	33-37	5
α-helix	41-43	3
β-strand	50-51	2	4
α-helix	72-75	4
β-strand	83-84	2	4
α-helix	85	1
β-strand	88-95	8	5
α-helix	96-105	10
α-helix	108-110	3
α-helix	112-130	19
α-helix	160-175	16
β-strand	181-185	5	6
α-helix	187-194	8
α-helix	198-206	9
β-strand	207-212	6	6
β-strand	221-225	5	6
β-strand	228	1	7
β-strand	231	1	7
β-strand	232-243	12	5
β-strand	250-262	13	5
α-helix	266-268	3
β-strand	271	1	6

Chain C: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	14-31	18
α-helix	34-37	4
α-helix	39	1
β-strand	40-43	4	8
β-strand	50	1	9
α-helix	72-74	3
α-helix	83	1
β-strand	84	1	9
α-helix	85	1
β-strand	88-94	7	8
α-helix	96-100	5
α-helix	101-105	5
α-helix	107-109	3
α-helix	112-130	19
α-helix	160-174	15
β-strand	181-185	5	10
α-helix	187-195	9
α-helix	199-206	8
β-strand	210-212	3	10
β-strand	221-225	5	10
β-strand	232-243	12	8
β-strand	247	1	11
β-strand	250	1	11
β-strand	251-262	12	8
α-helix	266-268	3
β-strand	269-271	3	10

Chain D: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	14-31	18
α-helix	34-37	4
α-helix	39	1
β-strand	40-41	2	12
α-helix	42	1
β-strand	50	1	13
β-strand	63-65	3	1
β-strand	73	1	1
α-helix	74-77	4
α-helix	83	1
β-strand	84	1	13
α-helix	85	1
β-strand	88-94	7	12
α-helix	96-105	10
α-helix	108-110	3
α-helix	112-130	19
α-helix	158-175	18
β-strand	181-185	5	14
α-helix	187-192	6
α-helix	193-196	4
α-helix	198-206	9
β-strand	207-212	6	14
β-strand	221-225	5	14
β-strand	232-243	12	12
β-strand	251-262	12	12
α-helix	266-268	3
β-strand	269-271	3	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Type 1 encapsulin shell protein EncA	A, B, C, D	protein	281	Myxococcus xanthus DK 1622	Q1D6H4 (AlphaFold model)
Encapsulin nanocompartment cargo protein EncC	E, F, G, H	protein	12	Myxococcus xanthus DK 1622	Q1D3Y8 (AlphaFold model)

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

>9BC8_1 Type 1 encapsulin shell protein EncA (chains A, B, C, D)
MPDFLGHAENPLREEEWARLNETVIQVARRSLVGRRILDIYGPLGAGVQTVPYDEFQGVS
PGAVDIVGEQETAMVFTDARKFKTIPIIYKDFLLHWRDIEAARTHNMPLDVSAAAGAAAL
CAQQEDELIFYGDARLGYEGLMTANGRLTVPLGDWTSPGGGFQAIVEATRKLNEQGHFGP
YAVVLSPRLYSQLHRGGEIETIRQLASDGVYQSNRLRGESGVVVSTGRENMDLAVSMDMV
AAYLGASRMNHPFRVLEALLLRIKHPDAICTLEGAGATERR

Sequence of entity 2 (E, F, G, H), FASTA

>9BC8_2 Encapsulin nanocompartment cargo protein EncC (chains E, F, G, H)
PEKRLTVGSLRR

Primary citation

Pore Engineering as a General Strategy to Improve Protein-Based Enzyme Nanoreactor Performance. Kwon, S., Andreas, M.P., Giessen, T.W. ACS Nano (2024) 18:25740-25753. DOI 10.1021/acsnano.4c08186 · 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
4PT2 4.6 Å, Myxococcus xanthus encapsulin protein (EncA)

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