5MS2: Legionella pneumophila effector protein RavZ

Crystal structure of the Legionella pneumophila effector protein RavZ in complex with human LC3B. Determined by X-ray diffraction at 2.47 Å resolution. Released 19 Apr 2017.

Method: X-ray diffraction
Resolution: 2.47 Å
Organisms: Legionella pneumophila subsp. pneumophila str. Philadelphia 1, Homo sapiens
Chains: 2
Atoms: 4,273
Mol. weight: 63.1 kDa
Released: 19 Apr 2017

Explore 5MS2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MS2 contains 27 α-helices and 27 β-strands across 2 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, 20 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	37-40	4
α-helix	41-43	3
β-strand	50-51	2	1
α-helix	59-61	3
α-helix	65-71	7
α-helix	72-74	3
β-strand	88-90	3	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	134-135	2	2
α-helix	137-152	16
β-strand	157-167	11	2
α-helix	175	1
β-strand	176-185	10	2
β-strand	190-198	9	2
α-helix	199	1
β-strand	200	1	4
α-helix	206-211	6
β-strand	216	1	3
α-helix	221-232	12
α-helix	237	1
β-strand	238-239	2	2
β-strand	243-247	5	2
β-strand	253	1	4
α-helix	255-275	21
β-strand	281-282	2	5
β-strand	284-286	3	5
α-helix	289-292	4
α-helix	295-307	13
β-strand	310-311	2	1
α-helix	312-321	10
α-helix	329-345	17
α-helix	359-379	21
β-strand	382-383	2	6
α-helix	384-397	14
α-helix	400-412	13
α-helix	418-422	5
α-helix	423-425	3
β-strand	426-427	2	6

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	13-21	9
β-strand	31-37	7	7
β-strand	51-54	4	7
β-strand	59	1	8
α-helix	60-70	11
β-strand	80-83	4	7
β-strand	86	1	7
β-strand	94	1	8
α-helix	95-102	8
β-strand	109-114	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Legionella pneumophila effector protein RavZ	A	protein	433	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Q5ZUV9 (AlphaFold model)
Microtubule-associated proteins 1A/1B light chain 3B	B	protein	124	Homo sapiens	Q9GZQ8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MS2_1 Legionella pneumophila effector protein RavZ (chains A)
GPMKGKLTGKDKLIVDEFEELGEQESDIDEFDLLEGDEKLPGDSELDKTTSIYPPETSWE
VNKGMNSSRLHKLYSLFFDKSSAFYLGDDVSVLEDKPLTGAYGFQSKKNDQQIFLFRPDS
DYVAGYHVDAKSDAGWVNDKLDRRLSEISEFCSKATQPATFILPFVEMPTDITKGVQHQV
LLTISYDPKSKQLTPTVYDSIGRDTYSESLSSYFKGKYRTTCDEILTQSIEKAIKSTDFT
LGKFTRAAYNHQNRLTEGNCGSYTFRTIKEVISSSAQGTEVKIPGSGYITSNSYLTSQHV
QDIESCIKYRNLGVVDIESALTEGKTLPVQLSEFIVALEDYGKLRSQQSEKSMLNFIGYS
KTAKLTAVELLIGILNDIKGKNEISESQYDKLVKEVDCLMDSSLGKLVQFHLKNLGAESL
QKLVLPCVKFDDT

Sequence of entity 2 (B), FASTA

>5MS2_2 Microtubule-associated proteins 1A/1B light chain 3B (chains B)
GHMGCMPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVP
DHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYAS
QETF

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
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
5MS8 2.85 Å, Crystal structure of the legionella pneumophila effector protein RavZ_1-487
5CQC 2.98 Å, Crystal structure of the legionella pneumophila effector protein RavZ

Browse structure collections

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