9B9Q: Type 1 encapsulin shell protein EncA

Cargo-loaded Myxococcus xanthus EncA encapsulin engineered pore mutant with T=3 icosahedral symmetry. Determined by electron microscopy at 3.14 Å resolution. Released 18 Sept 2024.

Method: Electron microscopy
Resolution: 3.14 Å
Organism: Myxococcus xanthus DK 1622
Chains: 6
Atoms: 6,569
Mol. weight: 96.95 kDa
Released: 18 Sept 2024

Explore 9B9Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B9Q contains 33 α-helices and 34 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: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	39	1
β-strand	40	1	1
α-helix	41-43	3
β-strand	50-51	2	2
α-helix	75-77	3
β-strand	83-84	2	2
α-helix	85-86	2
β-strand	88-94	7	1
α-helix	96-103	8
α-helix	107-110	4
α-helix	112-130	19
α-helix	160-174	15
β-strand	181-185	5	3
α-helix	187-192	6
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: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	34-36	3
β-strand	40-43	4	4
β-strand	50-51	2	5
α-helix	72-75	4
β-strand	83-84	2	5
α-helix	85	1
β-strand	88-94	7	4
α-helix	96-105	10
α-helix	112-130	19
α-helix	162-175	14
β-strand	181-185	5	6
α-helix	187-195	9
α-helix	198-206	9
β-strand	210-212	3	6
β-strand	221-225	5	6
β-strand	231-243	13	4
β-strand	247	1	7
β-strand	250	1	7
β-strand	251-263	13	4
α-helix	266-268	3
β-strand	269-271	3	6

Chain C: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	34-36	3
β-strand	42-43	2	8
β-strand	50-53	4	9
α-helix	73-75	3
β-strand	81-84	4	9
α-helix	85-86	2
β-strand	88-94	7	8
α-helix	96-105	10
α-helix	107-110	4
α-helix	112-130	19
α-helix	160-173	14
β-strand	181-185	5	10
α-helix	187-192	6
α-helix	198-205	8
β-strand	209-212	4	10
β-strand	221-225	5	10
β-strand	231-243	13	8
β-strand	247	1	11
β-strand	250	1	11
β-strand	251-263	13	8
α-helix	266-268	3
β-strand	269-271	3	10

Molecules and chains

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

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

>9B9Q_1 Type 1 encapsulin shell protein EncA (chains A, B, C)
MPDFLGHAENPLREEEWARLNETVIQVARRSLVGRRILDIYGPLGAGVQTVPYDEFQGVS
PGAVDIVGEQETAMVFTDARKFKTIPIIYKDFLLHWRDIEAARTHNMPLDVSAAAGAAAL
CAQQEDELIFYGDARLGYEGLMTANGRLTVPLGDWTSPGGGFQAIVEATRKLNEQGHFGP
YAVVLSPRLYSQLHRGGEIETIRQLASDGVYQSNRLRGESGVVVSTGRENMDLAVSMDMV
AAYLGASRMNHPFRVLEALLLRIKHPDAICTLEGAGATERR

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

>9B9Q_2 Encapsulin nanocompartment cargo protein EncC (chains 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
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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