5MS8: Legionella pneumophila effector protein RavZ

Crystal structure of the legionella pneumophila effector protein RavZ_1-487. Determined by X-ray diffraction at 2.85 Å resolution. Released 19 Apr 2017.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Legionella pneumophila subsp. pneumophila ATCC 33215
Chains: 1
Atoms: 2,995
Mol. weight: 55.25 kDa
Ligands: BA
Released: 19 Apr 2017

Explore 5MS8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MS8 contains 20 α-helices and 16 β-strands across 1 chain. 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: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	1
α-helix	59-61	3
α-helix	65-71	7
α-helix	72-76	5
β-strand	87-89	3	2
α-helix	90-91	2
β-strand	99-104	6	2
β-strand	110-114	5	2
α-helix	115-116	2
β-strand	121-124	4	2
β-strand	127	1	3
β-strand	133-135	3	2
α-helix	137-151	15
β-strand	157-167	11	2
β-strand	176-185	10	2
β-strand	190-197	8	2
α-helix	204-206	3
α-helix	210-213	4
β-strand	216	1	3
α-helix	221-231	11
β-strand	238-239	2	2
α-helix	240-242	3
β-strand	243-246	4	2
α-helix	258-274	17
α-helix	289-292	4
α-helix	295-307	13
β-strand	310-311	2	1
α-helix	312-320	9
α-helix	329-343	15
α-helix	359-377	19
β-strand	382-383	2	4
α-helix	384-392	9
α-helix	394-397	4
α-helix	400-411	12
α-helix	418-422	5
β-strand	426-427	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Legionella pneumophila effector protein RavZ	A	protein	489	Legionella pneumophila subsp. pneumophila ATCC 33215	Q5ZUV9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MS8_1 Legionella pneumophila effector protein RavZ (chains A)
GPMKGKLTGKDKLIVDEFEELGEQESDIDEFDLLEGDEKLPGDSELDKTTSIYPPETSWE
VNKGMNSSRLHKLYSLFFDKSSAFYLGDDVSVLEDKPLTGAYGFQSKKNDQQIFLFRPDS
DYVAGYHVDAKSDAGWVNDKLDRRLSEISEFCSKATQPATFILPFVEMPTDITKGVQHQV
LLTISYDPKSKQLTPTVYDSIGRDTYSESLSSYFKGKYRTTCDEILTQSIEKAIKSTDFT
LGKFTRAAYNHQNRLTEGNCGSYTFRTIKEVISSSAQGTEVKIPGSGYITSNSYLTSQHV
QDIESCIKYRNLGVVDIESALTEGKTLPVQLSEFIVALEDYGKLRSQQSEKSMLNFIGYS
KTAKLTAVELLIGILNDIKGKNEISESQYDKLVKEVDCLMDSSLGKLVQFHLKNLGAESL
QKLVLPCVKFDDTIDDFVTIEKDELFDVPDITGEELASKKGIEQGALDKEALLKQKQIKT
DLLDLREED

Ligands and cofactors

ID	Name	Formula	Copies
BA	Barium ion	Ba	2

Water and common crystallization additives (PEG) are not listed.

Primary citation

Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins. Yang, A., Pantoom, S., Wu, Y.W. Elife (2017) 6. DOI 10.7554/eLife.23905 · PubMed

Other PDB entries of the same protein (UniProt Q5ZUV9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MS5 1.53 Å, Low-salt structure of RavZ LIR2-fused human LC3B
5XAD 1.88 Å, NLIR - LC3B fusion protein
5MS2 2.47 Å, Crystal structure of the Legionella pneumophila effector protein RavZ in complex with…
5HZY 2.55 Å, Crystal structure of the legionella pneumophila effector protein RavZ - P6322
5IO3 2.74 Å, Crystal structure of the legionella pneumophila effector protein RavZ - I422
5MS7 2.8 Å, Crystal structure of the legionella pneumophila effector protein RavZ_20-502
5IZV 2.81 Å, Crystal structure of the legionella pneumophila effector protein RavZ - F222
5CQC 2.98 Å, Crystal structure of the legionella pneumophila effector protein RavZ

Browse structure collections

About this viewer

MolViewer shows 5MS8 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.