8VJO: EncA

Cryo-EM structure of Myxococcus xanthus EncA encapsulin shell loaded with EncD cargo. Determined by electron microscopy at 2.4 Å resolution. Released 8 May 2024.

Method: Electron microscopy
Resolution: 2.4 Å
Organism: Myxococcus xanthus
Chains: 6
Atoms: 6,585
Mol. weight: 103.1 kDa
Released: 8 May 2024

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

Secondary structure: helices and β-sheets

8VJO contains 32 α-helices and 40 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, 12 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	34-37	4
β-strand	39-40	2	1
β-strand	50-53	4	2
β-strand	81-84	4	2
α-helix	85-86	2
β-strand	87-94	8	1
α-helix	96-103	8
α-helix	108-110	3
α-helix	112-131	20
β-strand	133	1	3
β-strand	138	1	3
α-helix	149-151	3
α-helix	160-174	15
β-strand	181-185	5	4
α-helix	187-192	6
α-helix	196-198	3
α-helix	204-212	9
β-strand	213-218	6	4
β-strand	227-231	5	4
β-strand	237-249	13	1
β-strand	257-269	13	1
α-helix	272-274	3
β-strand	275-277	3	4

Chain B: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	14-31	18
α-helix	34-36	3
β-strand	40-41	2	5
β-strand	50-53	4	6
α-helix	72-74	3
β-strand	81-84	4	6
α-helix	85-86	2
β-strand	87-94	8	5
α-helix	96-104	9
α-helix	112-130	19
β-strand	148-150	3	7
α-helix	160-174	15
β-strand	181-185	5	7
α-helix	187-192	6
α-helix	204-211	8
β-strand	216-218	3	7
β-strand	227-231	5	7
β-strand	237-249	13	5
β-strand	253	1	8
β-strand	256	1	8
β-strand	257-269	13	5
α-helix	272-274	3
β-strand	275-278	4	7

Chain C: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	14-31	18
α-helix	34-36	3
β-strand	40-43	4	9
β-strand	50-52	3	10
α-helix	73-75	3
β-strand	82-84	3	10
α-helix	85-86	2
β-strand	87-94	8	9
α-helix	96-104	9
α-helix	112-130	19
β-strand	148-150	3	11
α-helix	161-174	14
β-strand	181-185	5	11
α-helix	187-192	6
β-strand	196	1	12
β-strand	203	1	12
α-helix	204-211	8
β-strand	216-218	3	11
β-strand	227-231	5	11
β-strand	237-249	13	9
β-strand	253	1	13
β-strand	256	1	13
β-strand	257-269	13	9
β-strand	275-278	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
EncA	A, B, C	protein	301	Myxococcus xanthus	Q1D6H4 (AlphaFold model)
Encapsulin nanocompartment cargo protein EncD	F, G, H	protein	9	Myxococcus xanthus	Q1D9P3 (AlphaFold model)

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

>8VJO_1 EncA (chains A, B, C)
MHHHHHHMPLEPHFMPDFLGHAENPLREEEWARLNETVIQVARRSLVGRRILDIYGPLGA
GVQTVPYDEFQGVSPGAVDIVGEQETAMVFTDARKFKTIPIIYKDFLLHWRDIEAARTHN
MPLDVSAAAGAAALCAQQEDELIFYGDARLGYEGLMTANGRLTVPLGDWTSPGGGFQAIV
EATRKLNEQGHFGPYAVVLSPRLYSQLHRIYEKTGVLEIETIRQLASDGVYQSNRLRGES
GVVVSTGRENMDLAVSMDMVAAYLGASRMNHPFRVLEALLLRIKHPDAICTLEGAGATER
R

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

>8VJO_2 Encapsulin nanocompartment cargo protein EncD (chains F, G, H)
GLTVGSLRG

Primary citation

Myxococcus xanthus encapsulin cargo protein EncD is a flavin-binding protein with ferric reductase activity. Eren, E., Watts, N.R., Conway, J.F. et al. Proc Natl Acad Sci U S A (2024) 121:e2400426121-e2400426121. DOI 10.1073/pnas.2400426121 · PubMed

Other PDB entries of the same protein (UniProt Q1D6H4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
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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