6KFP: MavC ternary complex

Crystal structure of MavC ternary complex. Determined by X-ray diffraction at 2.92 Å resolution. Released 1 Apr 2020.

Method: X-ray diffraction
Resolution: 2.92 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 3
Atoms: 4,753
Mol. weight: 68.99 kDa
Released: 1 Apr 2020

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

Secondary structure: helices and β-sheets

6KFP contains 33 α-helices and 27 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: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	25-29	5
α-helix	33-43	11
α-helix	55-64	10
α-helix	70-71	2
α-helix	74-96	23
α-helix	98-99	2
β-strand	100-101	2	1
α-helix	107-111	5
β-strand	118-127	10	1
β-strand	132-135	4	2
α-helix	138-140	3
α-helix	147	1
β-strand	150-153	4	2
β-strand	158-161	4	2
β-strand	167-169	3	2
α-helix	174-183	10
α-helix	188-190	3
β-strand	191-193	3	2
α-helix	205-220	16
α-helix	221-223	3
β-strand	227-237	11	1
β-strand	249-251	3	1
β-strand	254	1	3
β-strand	258	1	3
α-helix	260-265	6
α-helix	268-273	6
α-helix	277-289	13
α-helix	293-304	12
α-helix	306	1
β-strand	324-332	9	1
α-helix	335-352	18
α-helix	358-380	23

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
α-helix	19-20	2
β-strand	23-24	2	4
β-strand	27	1	4
β-strand	34-40	7	4
α-helix	41-42	2
β-strand	51-57	7	4
α-helix	66-67	2
β-strand	68-71	4	4
β-strand	80	1	5
β-strand	85	1	4
β-strand	86	1	5
α-helix	89-91	3
α-helix	101-113	13
α-helix	124-131	8
α-helix	133-147	15

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	6
β-strand	12-17	6	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	6
β-strand	48-49	2	6
α-helix	50-51	2
β-strand	55	1	7
α-helix	57-59	3
β-strand	66-70	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MavC	A	protein	378	Legionella pneumophila	Q5ZTL4 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B	protein	152	Homo sapiens	P61088 (AlphaFold model)
Ubiquitin-40S ribosomal protein S27a	D	protein	77	Homo sapiens	P62979 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6KFP_1 MavC (chains A)
EKTGLHVHEKIKHMVKNYGTMITGIPAEILGQNEAEISVGYVKKMGNMKENIAEVVRKSE
MTQPTNSAGKASNEVCDLLLGTEGASEFEKSSYQVLSGDGSNLKGSLPNKNLLVRVEMDR
FNAPQKYQKIKREEFNPETAEKNKIYLLEDQLVYLDIFGKVIDLGQTSDTCHRLFNAITT
PFYQNYILYDEYIDPEESAEEAAMFEMGEIVKAKMKNIDCWTATHSFTIFVPESDSEDTR
TLYPYQAYWTSHTLQQWFSGDKDEKLSRLGIDGYIEKLALLGTTTDSKIRSSIYGELFSP
PGKEHVFCTGMNEKFSPLRVKFKVTEVNPEIALQNLEEVQEFIDTNYPGENAKDQCELYK
IKAQEAMTKQLEMRLLIE

Sequence of entity 2 (B), FASTA

>6KFP_2 Ubiquitin-conjugating enzyme E2 N (chains B)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 3 (D), FASTA

>6KFP_3 Ubiquitin-40S ribosomal protein S27a (chains D)
HMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDY
NIQKESTLHLVLRLRGG

Primary citation

Structural insights into the mechanism and inhibition of transglutaminase-induced ubiquitination by the Legionella effector MavC. Mu, Y., Wang, Y., Huang, Y. et al. Nat Commun (2020) 11:1774-1774. DOI 10.1038/s41467-020-15645-7 · PubMed

Other PDB entries of the same protein (UniProt Q5ZTL4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6P5H 1.53 Å, Structure of MavC middle insertion domain
6ULH 1.97 Å, Structure of MavC in complex with its substrate in R3 spacegroup
6K3B 1.97 Å, Crystal structure of Lpg2147-Lpg2149 complex
5TSC 2.01 Å, The crystal structure of Lpg2147 from Legionella pneumophila
6P5B 2.1 Å, Crystal Structure of MavC in Complex with Ub-UbE2N
6UMS 2.34 Å, Crystal structure of MavC in complex with its substrate mimic in C222(1) space group
6KG6 2.39 Å, Crystal structure of MavC/UBE2N-Ub complex
7BXH 2.7 Å, MavC-Lpg2149 complex
7BXG 2.71 Å, MavC-UBE2N-Ub complex
6UMP 2.8 Å, Crystal structure of MavC in complex with substrate mimic in P65 space group
6KL4 2.85 Å, Crystal structure of MavC-UBE2N-Ub

Browse structure collections

About this viewer

MolViewer shows 6KFP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.