8TK7: Type 1 encapsulin shell protein EncA

Myxococcus xanthus EncA protein shell with compartmentalized SNAP-tag cargo protein. Determined by electron microscopy at 2.53 Å resolution. Released 13 Sept 2023.

Method: Electron microscopy
Resolution: 2.53 Å
Organisms: Myxococcus xanthus DK 1622, Homo sapiens
Chains: 6
Atoms: 6,702
Mol. weight: 159.52 kDa
Released: 13 Sept 2023

Explore 8TK7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TK7 contains 29 α-helices and 49 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	13-30	18
α-helix	33-36	4
β-strand	39-42	4	7
β-strand	49-54	6	8
β-strand	78-83	6	8
β-strand	87-93	7	7
α-helix	95-104	10
α-helix	107-109	3
α-helix	111-129	19
β-strand	147-148	2	9
α-helix	159-172	14
β-strand	180-184	5	9
α-helix	186-192	7
α-helix	203-211	9
β-strand	212-217	6	9
β-strand	226-230	5	9
β-strand	236-248	13	7
β-strand	252	1	10
β-strand	255	1	10
β-strand	256-268	13	7
α-helix	271-273	3
β-strand	274-276	3	9

Chain B: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	33-35	3
β-strand	39-40	2	1
β-strand	49-52	4	2
β-strand	80-83	4	2
β-strand	86-93	8	1
α-helix	95-103	9
α-helix	106-108	3
α-helix	111-129	19
β-strand	132	1	3
β-strand	137	1	3
β-strand	147-148	2	4
α-helix	159-172	14
α-helix	179	1
β-strand	180-184	5	4
α-helix	186-191	6
β-strand	195-196	2	5
β-strand	201-202	2	5
α-helix	203-211	9
β-strand	212-217	6	4
β-strand	226-230	5	4
β-strand	236-248	13	1
β-strand	252	1	6
β-strand	255	1	6
β-strand	256-268	13	1
β-strand	274-276	3	4

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	33-35	3
β-strand	39-40	2	11
β-strand	49-51	3	12
β-strand	62-64	3	1
α-helix	72-73	2
β-strand	74	1	1
β-strand	81-83	3	12
β-strand	87-93	7	11
α-helix	95-102	8
α-helix	107-109	3
α-helix	111-129	19
β-strand	132	1	13
β-strand	137	1	13
β-strand	148	1	14
α-helix	159-174	16
β-strand	180-184	5	14
α-helix	186-191	6
β-strand	195	1	15
β-strand	202	1	15
α-helix	203-210	8
β-strand	214-217	4	14
β-strand	226-230	5	14
β-strand	236-248	13	11
β-strand	252	1	16
β-strand	255	1	16
β-strand	256-268	13	11
α-helix	271-273	3
β-strand	274-276	3	14

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)
Methylated-DNA--protein-cysteine methyltransferase	D, E, F	protein	203	Homo sapiens	E5BBQ0 (AlphaFold model)

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

>8TK7_1 Type 1 encapsulin shell protein EncA (chains A, B, C)
MPDFLGHAENPLREEEWARLNETVIQVARRSLVGRRILDIYGPLGAGVQTVPYDEFQGVS
PGAVDIVGEQETAMVFTDARKFKTIPIIYKDFLLHWRDIEAARTHNMPLDVSAAAGAAAL
CAQQEDELIFYGDARLGYEGLMTANGRLTVPLGDWTSPGGGFQAIVEATRKLNEQGHFGP
YAVVLSPRLYSQLHRIYEKTGVLEIETIRQLASDGVYQSNRLRGESGVVVSTGRENMDLA
VSMDMVAAYLGASRMNHPFRVLEALLLRIKHPDAICTLEGAGATERR

Sequence of entity 2 (D, E, F), FASTA

>8TK7_2 Methylated-DNA--protein-cysteine methyltransferase (chains D, E, F)
MGPGSDKDCEMKRTTLDSPLGKLELSGCEQGLHEIIFLGKGTSAADAVEVPAPAAVLGGP
EPLMQATAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYSH
LAALAGNPAATAAVKTALSGNPVPILIPCHRVVQGDLDVGGYEGGLAVKEWLLAHEGHRL
GKRGGGSGGGSPEKRLTVGSLRR

Primary citation

Structure and heterogeneity of a highly cargo-loaded encapsulin shell. Kwon, S., Andreas, M.P., Giessen, T.W. J Struct Biol (2023) 215:108022-108022. DOI 10.1016/j.jsb.2023.108022 · 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
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…
4PT2 4.6 Å, Myxococcus xanthus encapsulin protein (EncA)

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