7S4Q: M. xanthus encapsulin EncA

M. xanthus encapsulin EncA bound to EncC targeting peptide. Determined by electron microscopy at 3.12 Å resolution. Released 2 Feb 2022.

Method: Electron microscopy
Resolution: 3.12 Å
Organism: Myxococcus xanthus
Chains: 6
Atoms: 6,652
Mol. weight: 101.88 kDa
Released: 2 Feb 2022

Explore 7S4Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S4Q contains 24 α-helices and 36 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	33-35	3
β-strand	39-40	2	1
β-strand	49-50	2	2
β-strand	82-83	2	2
β-strand	87	1	3
β-strand	93	1	4
α-helix	95-103	9
α-helix	111-129	19
α-helix	161-173	13
β-strand	180-184	5	5
α-helix	186-192	7
β-strand	196	1	6
β-strand	202	1	6
α-helix	203-211	9
β-strand	215-217	3	5
β-strand	226-230	5	5
β-strand	236-248	13	1
β-strand	256	1	4
β-strand	258-268	11	1
β-strand	274-275	2	5

Chain B: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	33-35	3
α-helix	38	1
β-strand	39-42	4	7
β-strand	49-50	2	8
β-strand	82-83	2	8
β-strand	87-93	7	7
α-helix	97-100	4
α-helix	108-109	2
α-helix	111-129	19
α-helix	161-173	13
β-strand	180-184	5	9
α-helix	186-192	7
α-helix	203-211	9
β-strand	215-217	3	9
β-strand	226-230	5	9
β-strand	237-248	12	7
β-strand	256-267	12	7
β-strand	274-275	2	9

Chain C: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	33-35	3
β-strand	39-40	2	10
β-strand	49-51	3	11
α-helix	71-74	4
β-strand	81-83	3	11
β-strand	87-93	7	10
α-helix	95-103	9
α-helix	111-129	19
α-helix	160-173	14
β-strand	180-184	5	12
α-helix	186-190	5
α-helix	203-211	9
β-strand	215-217	3	12
β-strand	226-230	5	12
β-strand	238-248	11	10
β-strand	252	1	13
β-strand	255	1	13
β-strand	256-265	10	10
β-strand	275	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
EncA	A, B, C	protein	294	Myxococcus xanthus	Q1D6H4 (AlphaFold model)
EncC targeting peptide	F, G, H	protein	12	Myxococcus xanthus	Q1D3Y8 (AlphaFold model)

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

>7S4Q_1 EncA (chains A, B, C)
MPLEPHFMPDFLGHAENPLREEEWARLNETVIQVARRSLVGRRILDIYGPLGAGVQTVPY
DEFQGVSPGAVDIVGEQETAMVFTDARKFKTIPIIYKDFLLHWRDIEAARTHNMPLDVSA
AAGAAALCAQQEDELIFYGDARLGYEGLMTANGRLTVPLGDWTSPGGGFQAIVEATRKLN
EQGHFGPYAVVLSPRLYSQLHRIYEKTGVLEIETIRQLASDGVYQSNRLRGESGVVVSTG
RENMDLAVSMDMVAAYLGASRMNHPFRVLEALLLRIKHPDAICTLEGAGATERR

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

>7S4Q_2 EncC targeting peptide (chains F, G, H)
PEKRLTVGSLRR

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
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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