7S2T: M. xanthus encapsulin EncA

M. xanthus encapsulin EncA bound to EncB targeting peptide. Determined by electron microscopy at 3.45 Å resolution. Released 2 Feb 2022.

Method: Electron microscopy
Resolution: 3.45 Å
Organism: Myxococcus xanthus
Chains: 6
Atoms: 6,568
Mol. weight: 104.58 kDa
Released: 2 Feb 2022

Explore 7S2T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S2T contains 29 α-helices and 36 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: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	38	1
β-strand	39-40	2	1
α-helix	41	1
β-strand	49-50	2	2
α-helix	59-61	3
β-strand	82-83	2	2
β-strand	87	1	3
β-strand	90-91	2	4
α-helix	96-100	5
α-helix	111-128	18
α-helix	140-142	3
α-helix	159-173	15
β-strand	180-184	5	5
α-helix	186-191	6
α-helix	203-211	9
β-strand	215-217	3	5
β-strand	226-230	5	5
β-strand	237-240	4	1
β-strand	245-248	4	4
β-strand	258-261	4	4
β-strand	262	1	3
β-strand	264-267	4	1

Chain B: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	33-35	3
α-helix	38-39	2
β-strand	40-42	3	10
β-strand	49	1	11
β-strand	83	1	11
β-strand	87-92	6	12
α-helix	96-100	5
α-helix	108-109	2
α-helix	111-129	19
α-helix	161-173	13
β-strand	180-184	5	13
α-helix	186-192	7
α-helix	204-211	8
β-strand	215-217	3	13
β-strand	226-230	5	13
β-strand	238-240	3	10
β-strand	245-248	4	12
β-strand	257-262	6	12
β-strand	264-266	3	10
β-strand	275	1	13

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	33-35	3
β-strand	39-40	2	6
α-helix	41	1
β-strand	49-51	3	7
α-helix	71-74	4
β-strand	81-83	3	7
β-strand	87-93	7	6
α-helix	95-103	9
α-helix	111-129	19
α-helix	162-173	12
β-strand	180-184	5	8
α-helix	186-191	6
α-helix	203-211	9
β-strand	215-217	3	8
β-strand	226-230	5	8
β-strand	237-248	12	6
β-strand	252	1	9
β-strand	255	1	9
β-strand	256-267	12	6

Chain H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
EncA	A, B, C	protein	301	Myxococcus xanthus	Q1D6H4 (AlphaFold model)
EncB targeting peptide	F, G, H	protein	12	Myxococcus xanthus	Q1D6H3 (AlphaFold model)

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

>7S2T_1 EncA (chains A, B, C)
MHHHHHHMPLEPHFMPDFLGHAENPLREEEWARLNETVIQVARRSLVGRRILDIYGPLGA
GVQTVPYDEFQGVSPGAVDIVGEQETAMVFTDARKFKTIPIIYKDFLLHWRDIEAARTHN
MPLDVSAAAGAAALCAQQEDELIFYGDARLGYEGLMTANGRLTVPLGDWTSPGGGFQAIV
EATRKLNEQGHFGPYAVVLSPRLYSQLHRIYEKTGVLEIETIRQLASDGVYQSNRLRGES
GVVVSTGRENMDLAVSMDMVAAYLGASRMNHPFRVLEALLLRIKHPDAICTLEGAGATER
R

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

>7S2T_2 EncB targeting peptide (chains F, G, H)
ESHPLTVGSLRR

Primary citation

Structural characterization of the Myxococcus xanthus encapsulin and ferritin-like cargo system gives insight into its iron storage mechanism. Eren, E., Wang, B., Winkler, D.C. et al. Structure (2022) 30:551-563.e4. DOI 10.1016/j.str.2022.01.008 · 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
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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