6JKY: MvcA

Crystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila. Determined by X-ray diffraction at 2.45 Å resolution. Released 18 Dec 2019.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Legionella pneumophila subsp. pneumophila str. Philadelphia 1, Homo sapiens, Schistosoma margrebowiei
Chains: 6
Atoms: 9,776
Mol. weight: 139.93 kDa
Released: 18 Dec 2019

Explore 6JKY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6JKY contains 72 α-helices and 48 β-strands across 6 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: 26 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
α-helix	16-31	16
α-helix	32-36	5
α-helix	40-51	12
α-helix	61-72	12
α-helix	83-95	13
α-helix	97-105	9
α-helix	107-108	2
β-strand	109-110	2	1
α-helix	111-112	2
α-helix	116-123	8
β-strand	132-141	10	1
β-strand	146-149	4	2
α-helix	152-154	3
α-helix	161	1
β-strand	164-167	4	2
β-strand	172-175	4	2
β-strand	181-183	3	2
α-helix	188-198	11
β-strand	203-205	3	2
α-helix	209-213	5
α-helix	218-232	15
α-helix	234-236	3
β-strand	240-250	11	1
α-helix	251-253	3
α-helix	257-259	3
β-strand	262-264	3	1
β-strand	267	1	3
β-strand	271	1	3
α-helix	273-278	6
α-helix	281-286	6
α-helix	290-302	13
α-helix	306-317	12
α-helix	319	1
α-helix	329-331	3
β-strand	337-345	9	1
α-helix	348-363	16
α-helix	370-392	23

Chain B: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	4
β-strand	34-40	7	4
α-helix	41-42	2
β-strand	51-57	7	4
β-strand	68-71	4	4
β-strand	85	1	4
α-helix	101-113	13
α-helix	124-131	8
α-helix	133-147	15

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	5
β-strand	12-17	6	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-70	5	5

Chain D: 28 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	16-31	16
α-helix	32-36	5
α-helix	40-50	11
α-helix	52-54	3
α-helix	63-76	14
α-helix	83-95	13
α-helix	97-104	8
α-helix	107-108	2
β-strand	109-110	2	7
α-helix	111-112	2
α-helix	116-124	9
β-strand	132-141	10	7
β-strand	146-149	4	8
α-helix	152-154	3
α-helix	161	1
β-strand	164-167	4	8
β-strand	172-175	4	8
β-strand	181-183	3	8
α-helix	188-196	9
β-strand	203-205	3	8
α-helix	209-212	4
α-helix	218-232	15
α-helix	234-236	3
β-strand	240-250	11	7
α-helix	251-253	3
α-helix	257-259	3
β-strand	262-264	3	7
β-strand	267	1	9
β-strand	271	1	9
α-helix	273-278	6
α-helix	281-285	5
α-helix	286-288	3
α-helix	290-302	13
α-helix	306-317	12
α-helix	319	1
α-helix	323-326	4
α-helix	329-331	3
β-strand	337-345	9	7
α-helix	348-363	16
α-helix	370-391	22

Chain E: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
β-strand	23-27	5	10
β-strand	34-39	6	10
β-strand	52-57	6	10
α-helix	66-67	2
β-strand	68-71	4	10
β-strand	85	1	10
α-helix	101-113	13
α-helix	124-131	8
α-helix	133-147	15

Chain F: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	11
β-strand	12-17	6	11
β-strand	22	1	12
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	11
β-strand	48-50	3	11
β-strand	55	1	12
α-helix	56-58	3
β-strand	66-70	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MvcA	A, D	protein	385	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Q5ZTL3 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B, E	protein	152	Homo sapiens	P61088 (AlphaFold model)
Ub	C, F	protein	79	Schistosoma margrebowiei	A0A3P7ZMV6 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6JKY_1 MvcA (chains A, D)
ASLESPGFMVHKKLKSMSQSYGVMMTGVPAEVLGQMQAERSIPSINKTGNLKQQIAKEVS
KVCHMMTEPTQSAGQASNDVCELLLGKIEAEKFHFTKYEALSADGDNLKNVLENTAPSST
NLLIRFEIDREDPPIVLVKTKNENFNPETAVKNKIYLLENKLYFIDKMGNLFNLGPGKKK
CTQLFNAIGDSAEYSLCDPFVLEEPEKPEDFAISEIVDIFNEQKERFDFWIGSHSFTIYI
PQTLGESPRQFYPYQAYFGSHTLQDWFVSDKDEYLSRIGIDKYIEKLAVLGKTTNTKERS
DIYAEFFSKRGREAFFCAHLNEKRQPLRVKFKITEINPELALKNLQETQEFIDTHPGENP
SDKVENYRNRAKLAMTEHLESLLDI

Sequence of entity 2 (B, E), FASTA

>6JKY_2 Ubiquitin-conjugating enzyme E2 N (chains B, E)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDAWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 3 (C, F), FASTA

>6JKY_3 Ub (chains C, F)
CGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS
DYNIQKESTLHLVLRLRGG

Primary citation

Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination. Gan, N., Guan, H., Huang, Y. et al. EMBO J (2020) 39:e102806-e102806. DOI 10.15252/embj.2019102806 · PubMed

Other PDB entries of the same protein (UniProt Q5ZTL3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6K11 1.94 Å, Crystal structure of MvcA from Legionella pneumophila
5SUJ 2.36 Å, Crystal structure of uncharacterized protein LPG2148 from Legionella pneumophila
6LP2 2.48 Å, Structure of Lpg2148/UBE2N-Ub complex
5YM9 2.5 Å, Crystal Structure of the Deamidase from Legionella pneumophila
6LW4 2.7 Å, Structure of Lpg2148/Lpg2149 complex
7BXF 2.7 Å, MvcA-Lpg2149 complex

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