8ANP: Legionella effector Lem3 mutant D190A

Legionella effector Lem3 mutant D190A in complex with Mg2+. Determined by X-ray diffraction at 2.2 Å resolution. Released 12 Apr 2023.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Legionella pneumophila
Chains: 4
Atoms: 13,813
Mol. weight: 213.12 kDa
Ligands: MG
Released: 12 Apr 2023

Explore 8ANP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ANP contains 82 α-helices and 96 β-strands across 4 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: 20 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	1
α-helix	25-27	3
β-strand	29-32	4	2
α-helix	35-38	4
α-helix	43-48	6
β-strand	51-57	7	3
β-strand	60-66	7	3
β-strand	69-70	2	4
β-strand	75-79	5	2
β-strand	82-90	9	1
β-strand	96-106	11	1
α-helix	114-133	20
α-helix	138-145	8
β-strand	166-176	11	1
β-strand	180-188	9	1
β-strand	192-196	5	3
β-strand	202-206	5	3
β-strand	208-214	7	5
β-strand	217-219	3	5
α-helix	224-228	5
β-strand	237-243	7	1
β-strand	248-252	5	3
α-helix	254-257	4
α-helix	261	1
β-strand	262-267	6	5
β-strand	271-276	6	5
α-helix	278-283	6
α-helix	286-290	5
α-helix	296-327	32
α-helix	353-362	10
α-helix	380-389	10
β-strand	391-392	2	4
β-strand	395-402	8	3
α-helix	403-405	3
α-helix	406-416	11
α-helix	418-420	3
α-helix	421-431	11
α-helix	435-446	12
β-strand	449-450	2	6
β-strand	455-457	3	3
α-helix	458-460	3
β-strand	464-465	2	6
α-helix	469-484	16

Chain B: 24 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	7
β-strand	29-32	4	8
α-helix	35-38	4
α-helix	43-50	8
β-strand	51-57	7	9
β-strand	60-66	7	9
β-strand	69	1	10
β-strand	75-79	5	8
β-strand	82-90	9	7
β-strand	96-106	11	7
α-helix	114-133	20
α-helix	138-145	8
β-strand	166-176	11	7
β-strand	180-188	9	7
β-strand	192-196	5	9
β-strand	202-206	5	9
β-strand	208-214	7	11
β-strand	217-219	3	11
α-helix	223-228	6
α-helix	232-234	3
β-strand	237-243	7	7
β-strand	248-252	5	9
α-helix	254-257	4
β-strand	262-267	6	11
β-strand	271-276	6	11
α-helix	278-283	6
α-helix	286-288	3
α-helix	296-328	33
β-strand	337	1	12
α-helix	338-348	11
α-helix	351-358	8
α-helix	359-363	5
α-helix	377-378	2
β-strand	379	1	12
α-helix	380-389	10
β-strand	392	1	10
β-strand	395-402	8	9
α-helix	403-405	3
α-helix	406-416	11
α-helix	418-420	3
α-helix	421-424	4
α-helix	425-427	3
α-helix	428-431	4
α-helix	435-447	13
β-strand	449-450	2	13
β-strand	455-457	3	9
α-helix	458-460	3
β-strand	464-465	2	13
α-helix	469-485	17

Chain C: 21 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	14
β-strand	29-32	4	15
α-helix	35-38	4
α-helix	43-50	8
β-strand	51-57	7	16
β-strand	60-66	7	16
β-strand	69	1	17
β-strand	75-79	5	15
β-strand	82-90	9	14
β-strand	96-106	11	14
α-helix	114-133	20
α-helix	138-144	7
β-strand	166-176	11	14
β-strand	180-188	9	14
β-strand	192-196	5	16
β-strand	202-206	5	16
β-strand	208-214	7	18
β-strand	217-219	3	18
α-helix	224-228	5
α-helix	232-234	3
β-strand	236-243	8	14
β-strand	248-252	5	16
α-helix	254-257	4
α-helix	261	1
β-strand	262-267	6	18
β-strand	271-276	6	18
α-helix	278-283	6
α-helix	286-288	3
α-helix	296-328	33
β-strand	337	1	19
α-helix	338-346	9
α-helix	352-362	11
β-strand	379	1	19
α-helix	380-389	10
β-strand	392	1	17
β-strand	395-402	8	16
α-helix	403-405	3
α-helix	406-416	11
α-helix	418-420	3
α-helix	421-431	11
α-helix	435-447	13
β-strand	449-450	2	20
β-strand	455-457	3	16
α-helix	458-460	3
β-strand	464-465	2	20
α-helix	469-485	17

Chain D: 17 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	21
β-strand	29-30	2	22
α-helix	35-38	4
α-helix	43-50	8
β-strand	51-57	7	23
β-strand	60-66	7	23
β-strand	69-70	2	24
β-strand	78-79	2	22
β-strand	82-90	9	21
β-strand	96-106	11	21
α-helix	114-133	20
α-helix	138-145	8
β-strand	166-176	11	21
β-strand	180-188	9	21
β-strand	192-196	5	23
β-strand	202-206	5	23
β-strand	208-212	5	25
β-strand	218-219	2	25
α-helix	223-228	6
β-strand	237-242	6	21
β-strand	248-252	5	23
α-helix	254-257	4
β-strand	262-267	6	25
β-strand	271-276	6	25
α-helix	278-283	6
α-helix	284-286	3
α-helix	296-321	26
α-helix	384-389	6
β-strand	391-392	2	24
β-strand	395-402	8	23
α-helix	403-405	3
α-helix	406-416	11
α-helix	418-420	3
α-helix	421-431	11
α-helix	435-446	12
β-strand	449-450	2	26
β-strand	455-457	3	23
α-helix	458-460	3
β-strand	464-465	2	26
α-helix	469-485	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphocholine hydrolase Lem3	A, B, C, D	protein	468	Legionella pneumophila	Q5ZXN5 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8ANP_1 Phosphocholine hydrolase Lem3 (chains A, B, C, D)
GHDKIITGKKIIFSQSVAKDQTKNLSSFLSERFYSVNQSHNHSIIIGSSLSHQENDIEHD
TILDTSGVLVTTDTNGIVNGARVAITDGLGGGNGDQEEDDEIYRVSHSSCENFLNCDQNI
DTTLSLITQPKASDKKQTAPKTLQHTEASMAAFIYQNHPGKGYIGEFANIGAGLIIILDK
RFKIKHMVSACHIYRGFGTWTPPSLQALATTANKDALLVRQTLKLAEGDIIISMTDGVWG
ELKTSLIAQTNDRRDIGVDKEYFKTLFDELTDAPYPSSFDIARIITQRAMSRSLERRKTL
IKLINEIEQQHFHEKSVKTINEVLEYFIKTGHVETAQTLKAILFEDGLSDGITYFENIEI
PLEMVMHDLKSRTVGDCSTINVTRIPYHLDELIRGFINYPEKHQILAPLFKARVKSEADL
EEAFHRLSLEMVQPEIECPISETHFERAFKKETLDKTQAVLTHYFRIS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	7

Water and common crystallization additives (SO4, PGE) are not listed.

Primary citation

Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b. Kaspers, M.S., Pogenberg, V., Pett, C. et al. Nat Commun (2023) 14:2245-2245. DOI 10.1038/s41467-023-37621-7 · PubMed

Other PDB entries of the same protein (UniProt Q5ZXN5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ALK 2.15 Å, Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate…
8AGG 3.6 Å, Structure of the Legionella phosphocholine hydrolase Lem3

Browse structure collections

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