5IZV: Uncharacterized protein RavZ

Crystal structure of the legionella pneumophila effector protein RavZ - F222. Determined by X-ray diffraction at 2.81 Å resolution. Released 9 Nov 2016.

Method: X-ray diffraction
Resolution: 2.81 Å
Organism: Legionella pneumophila subsp. pneumophila strain Philadelphia 1
Chains: 2
Atoms: 5,873
Mol. weight: 112.59 kDa
Released: 9 Nov 2016

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

Secondary structure: helices and β-sheets

5IZV contains 37 α-helices and 36 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: 19 helices, 18 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	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	133-135	3	2
α-helix	137-152	16
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	212-214	3
β-strand	216	1	3
α-helix	221-231	11
α-helix	237	1
β-strand	238-239	2	2
β-strand	243-246	4	2
α-helix	258-275	18
β-strand	281-282	2	4
β-strand	284-286	3	4
α-helix	289-292	4
α-helix	295-307	13
β-strand	310-311	2	1
α-helix	312-320	9
α-helix	329-344	16
α-helix	359-377	19
β-strand	382-383	2	5
α-helix	384-397	14
α-helix	402-412	11
α-helix	418-422	5
α-helix	423-425	3
β-strand	426-427	2	5

Chain B: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	6
α-helix	59-61	3
α-helix	65-71	7
α-helix	72-76	5
β-strand	88-90	3	7
β-strand	99-104	6	7
β-strand	110-114	5	7
α-helix	115-116	2
β-strand	121-124	4	7
β-strand	127	1	8
β-strand	133-135	3	7
α-helix	137-151	15
β-strand	157-167	11	7
β-strand	176-185	10	7
β-strand	190-197	8	7
α-helix	212-214	3
β-strand	216	1	8
α-helix	221-231	11
β-strand	238-239	2	7
β-strand	243-246	4	7
α-helix	258-274	17
β-strand	281-282	2	9
β-strand	284-286	3	9
α-helix	289-292	4
α-helix	295-307	13
β-strand	310-311	2	6
α-helix	312-320	9
α-helix	326-328	3
α-helix	329-345	17
α-helix	359-377	19
β-strand	382-383	2	10
α-helix	384-397	14
α-helix	400-411	12
α-helix	418-422	5
α-helix	423-425	3
β-strand	426-427	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Uncharacterized protein RavZ	A, B	protein	502	Legionella pneumophila subsp. pneumophila strain Philadelphia 1	Q5ZUV9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IZV_1 Uncharacterized protein RavZ (chains A, B)
MKGKLTGKDKLIVDEFEELGEQESDIDEFDLLEGDEKLPGDSELDKTTSIYPPETSWEVN
KGMNSSRLHKLYSLFFDKSSAFYLGDDVSVLEDKPLTGAYGFQSKKNDQQIFLFRPDSDY
VAGYHVDAKSDAGWVNDKLDRRLSEISEFCSKATQPATFILPFVEMPTDITKGVQHQVLL
TISYDPKSKQLTPTVYDSIGRDTYSESLSSYFKGKYRTTCDEILTQSIEKAIKSTDFTLG
KFTRAAYNHQNRLTEGNSGSYTFRTIKEVISSSAQGTEVKIPGSGYITSNSYLTSQHVQD
IESCIKYRNLGVVDIESALTEGKTLPVQLSEFIVALEDYGKLRSQQSEKSMLNFIGYSKT
AKLTAVELLIGILNDIKGKNEISESQYDKLVKEVDCLMDSSLGKLVQFHLKNLGAESLQK
LVLPCVKFDDTIDDFVTIEKDELFDVPDITGEELASKKGIEQGALDKEALLKQKQIKTDL
LDLREEDKTGLKKPLHGGIKVK

Primary citation

The 1:2 complex between RavZ and LC3 reveals a mechanism for deconjugation of LC3 on the phagophore membrane. Kwon, D.H., Kim, S., Jung, Y.O. et al. Autophagy (2017) 13:70-81. DOI 10.1080/15548627.2016.1243199 · 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
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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