6UMP: MavC

Crystal structure of MavC in complex with substrate mimic in P65 space group. Determined by X-ray diffraction at 2.8 Å resolution. Released 27 May 2020.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Legionella pneumophila
Chains: 3
Atoms: 4,608
Mol. weight: 69.98 kDa
Released: 27 May 2020

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

Secondary structure: helices and β-sheets

6UMP contains 33 α-helices and 30 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: 23 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
α-helix	25-29	5
α-helix	33-44	12
α-helix	45-47	3
α-helix	54-63	10
α-helix	70-71	2
α-helix	74-86	13
α-helix	88-96	9
α-helix	98-99	2
β-strand	100-101	2	3
α-helix	107-110	4
β-strand	118-127	10	3
β-strand	132	1	4
β-strand	133-135	3	5
α-helix	138-140	3
α-helix	147	1
β-strand	150-153	4	5
β-strand	158-161	4	5
β-strand	167-169	3	5
α-helix	174-183	10
α-helix	187-189	3
β-strand	193	1	4
α-helix	205-220	16
α-helix	221-223	3
β-strand	227-237	11	3
β-strand	249-251	3	3
β-strand	254	1	6
β-strand	258	1	6
α-helix	260-265	6
α-helix	268-271	4
α-helix	277-289	13
α-helix	297-304	8
α-helix	306	1
β-strand	324-332	9	3
α-helix	335-352	18
α-helix	358-380	23

Chain C: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	7
β-strand	34-40	7	7
α-helix	41-42	2
β-strand	51-57	7	7
β-strand	68	1	7
β-strand	70	1	8
β-strand	71	1	7
β-strand	77	1	9
β-strand	80	1	9
β-strand	85	1	8
β-strand	86	1	9
α-helix	101-113	13
α-helix	115-117	3
α-helix	124-131	8
α-helix	133-147	15

Chain E: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-44	3	1
β-strand	49	1	1
β-strand	55	1	2
α-helix	56-58	3
β-strand	66-70	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	E	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
MavC	A	protein	389	Legionella pneumophila	Q5ZTL4 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	C	protein	152	Homo sapiens	P61088 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>6UMP_1 Ubiquitin (chains E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGC

Sequence of entity 2 (A), FASTA

>6UMP_2 MavC (chains A)
GPLGSMTTSKLEKTGLHVHEKIKHMVKNYGTMITGIPAEILGQNEAEISVGYVKKMGNMK
ENIAEVVRKSEMTQPTNSAGKASNEVCDLLLGTEGASEFEKSSYQVLSGDGSNLKGSLPN
KNLLVRVEMDRFNAPQKYQKIKREEFNPETAEKNKIYLLEDQLVYLDIFGKVIDLGQTSD
TCHRLFNAITTPFYQNYILYDEYIDPEESAEEAAMFEMGEIVKAKMKNIDCWTATHSFTI
FVPESDSEDTRTLYPYQAYWTSHTLQQWFSGDKDEKLSRLGIDGYIEKLALLGTTTDSKI
RSSIYGELFSPPGKEHVFCTGMNEKFSPLRVKFKVTEVNPEIALQNLEEVQEFIDTNYPG
ENAKDQCELYKIKAQEAMTKQLEMRLLIE

Sequence of entity 3 (C), FASTA

>6UMP_3 Ubiquitin-conjugating enzyme E2 N (chains C)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Primary citation

Legionella effector MavC targets the Ube2N~Ub conjugate for noncanonical ubiquitination. Puvar, K., Iyer, S., Fu, J. et al. Nat Commun (2020) 11:2365-2365. DOI 10.1038/s41467-020-16211-x · PubMed

Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
4HK2 1.4 Å, U7Ub25.2540
9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant

Browse structure collections

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