6PLM: SidJ protein

Legionella pneumophila SidJ/ Calmodulin 2 complex. Determined by X-ray diffraction at 2.59 Å resolution. Released 20 Nov 2019.

Method: X-ray diffraction
Resolution: 2.59 Å
Organisms: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513), Homo sapiens
Chains: 4
Atoms: 14,660
Mol. weight: 209.27 kDa
Ligands: AMP, POP, CA
Released: 20 Nov 2019

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

Secondary structure: helices and β-sheets

6PLM contains 112 α-helices and 66 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: 46 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	105-109	5	1
β-strand	121-124	4	2
β-strand	127-130	4	2
β-strand	131-133	3	3
α-helix	136-156	21
α-helix	160-162	3
α-helix	165-181	17
α-helix	185-205	21
α-helix	207-219	13
α-helix	224-227	4
α-helix	231-234	4
α-helix	237-245	9
α-helix	249-251	3
α-helix	252-260	9
α-helix	265-268	4
α-helix	271-280	10
β-strand	291-294	4	4
β-strand	297-300	4	4
α-helix	302-310	9
α-helix	314-315	2
β-strand	316-320	5	1
α-helix	329-330	2
α-helix	332-334	3
α-helix	343-345	3
β-strand	346-350	5	5
β-strand	353-357	5	5
β-strand	363-368	6	5
α-helix	369	1
β-strand	370	1	6
α-helix	375-390	16
α-helix	392-395	4
β-strand	403-411	9	5
α-helix	412-419	8
α-helix	425-431	7
β-strand	432	1	6
β-strand	437-445	9	5
α-helix	447-450	4
β-strand	452	1	7
α-helix	460-479	20
β-strand	482-483	2	8
β-strand	491-494	4	9
β-strand	502-505	4	9
α-helix	510-513	4
α-helix	520	1
β-strand	521	1	10
α-helix	522	1
β-strand	523	1	11
α-helix	528-530	3
β-strand	535-536	2	7
β-strand	539-540	2	7
β-strand	547-548	2	8
α-helix	549-552	4
α-helix	557-562	6
α-helix	564-568	5
α-helix	573-575	3
β-strand	576	1	3
β-strand	583-585	3	3
α-helix	587-591	5
α-helix	594-622	29
α-helix	628-654	27
α-helix	658-668	11
α-helix	671-681	11
α-helix	685-688	4
α-helix	691-702	12
α-helix	706-708	3
α-helix	712-714	3
β-strand	715	1	12
β-strand	719	1	12
β-strand	729	1	11
β-strand	735	1	10
α-helix	739-774	36
α-helix	781-794	14
α-helix	796	1
α-helix	800-816	17
α-helix	826-849	24

Chain B: 45 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	98-100	3
β-strand	105-109	5	13
α-helix	117-119	3
β-strand	121-124	4	14
β-strand	127-130	4	14
β-strand	131-133	3	15
α-helix	136-157	22
α-helix	160-162	3
α-helix	165-181	17
α-helix	185-205	21
α-helix	207-217	11
α-helix	224-227	4
α-helix	231-234	4
α-helix	237-245	9
α-helix	249-251	3
α-helix	252-260	9
α-helix	265-268	4
α-helix	271-280	10
β-strand	291-294	4	16
β-strand	297-300	4	16
α-helix	302-310	9
β-strand	316-320	5	13
α-helix	331-334	4
β-strand	346-350	5	17
β-strand	353-357	5	17
β-strand	363-368	6	17
α-helix	369	1
β-strand	370	1	18
α-helix	375-390	16
α-helix	392-395	4
β-strand	403-411	9	17
α-helix	412-419	8
α-helix	425-431	7
β-strand	432	1	18
β-strand	437-445	9	17
α-helix	447-450	4
β-strand	452	1	19
α-helix	460-480	21
β-strand	482-483	2	20
β-strand	491-494	4	21
β-strand	502-505	4	21
α-helix	510-513	4
α-helix	520	1
β-strand	521	1	22
α-helix	522	1
β-strand	523	1	23
α-helix	528-530	3
β-strand	535-536	2	19
β-strand	539-540	2	19
β-strand	547-548	2	20
α-helix	549-552	4
α-helix	557-562	6
α-helix	564-568	5
α-helix	573-575	3
β-strand	576-577	2	15
β-strand	582-585	4	15
α-helix	587-591	5
α-helix	594-622	29
α-helix	628-654	27
α-helix	658-668	11
α-helix	671-681	11
α-helix	685-688	4
α-helix	691-702	12
α-helix	706-708	3
α-helix	712-714	3
β-strand	715	1	24
β-strand	719	1	24
β-strand	729	1	23
β-strand	735	1	22
α-helix	739-774	36
α-helix	781-793	13
α-helix	796	1
α-helix	801-816	16
α-helix	826-852	27

Chain C: 11 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
β-strand	27	1	25
α-helix	29-31	3
α-helix	32-38	7
α-helix	42-44	3
α-helix	45-54	10
β-strand	63	1	25
α-helix	65-78	14
α-helix	81-92	12
β-strand	99-101	3	26
α-helix	102-109	8
α-helix	115-117	3
α-helix	118-126	9
β-strand	135-137	3	26
α-helix	138-144	7

Chain D: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	26-28	3	27
α-helix	29-38	10
α-helix	42-44	3
α-helix	45-53	9
β-strand	62-64	3	27
α-helix	65-78	14
α-helix	81-90	10
β-strand	99-101	3	28
α-helix	102-111	10
α-helix	115-117	3
α-helix	118-127	10
β-strand	135-137	3	28
α-helix	138-146	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SidJ protein	A, B	protein	757	Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)	Q5ZTK6 (AlphaFold model)
Calmodulin-2	C, D	protein	147	Homo sapiens	P0DP24 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6PLM_1 SidJ protein (chains A, B)
GHVKQYYFARRGETSTHDTSLPPPVKVLSGRSIPLKEIPFEATRNELVQIYLTSIDKLIK
SNKLNSIPSQQIASHYLFLRSLANSETDGIKKNQILSLAKPLGTYLASKEPHVWKMINEL
IEKSEYPIIHYLKNNRAHSNFMLALIHEYHKEPLTKNQSAFVQKFRDSSVFLFPNPIYTA
WLAHSYDEDSSFNPMFRERLSTNFYHSTLTDNLLLRTEPKEVTLSSEHHYKKEKGPIDSS
FRYQMSSDRLLRIQGRTLLFSTPQNDVVAVKVQKKGEPKSTLEEEFEMADYLLKHQRRLD
VHSKLPQPLGQYSVKKSEILEISRGSLDFERFKTLIDDSKDLEVYVYKAPQSYFTYLHDK
NQDLEDLTASVKTNVHDLFVLLREGIVFPQLADIFHTHFGEDEREDKGRYQALVQLLNVL
QFQLGRIDKWQKAVEYVNLRSSGLADLGDSLPITSLFTSSDFTKHYFSELLTGGYHPTFF
DKSSGTANSLFTGKRRLFGNYLYLNTIAEYLLVIQLTLGSYGDKVTRDMMDKPKKEAVWR
ELANVMFTSCAEAIHIMTGIPQSRALTLLKQRANIEKHFRQTQFWMTPDYSKLDEDTLQM
EQYSIYSGEPEYEFTDKLVSGVGLSVDGVHQDLGGYNRESPLRELEKLLYATVTLIEGTM
QLDKEFFKQLEQVEKILSGEIKTDANSCFEAVAQLLDLARPGCHFQKRLVLSYYEEAKLK
YPSAPTDAYDSRFQVVARTNAAITIQRFWREARKNLS

Sequence of entity 2 (C, D), FASTA

>6PLM_2 Calmodulin-2 (chains C, D)
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN
GTIDFPEFLTMMARKMKDTDSEEEIAEAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEE
VDEMIREADIDGDGQVNYEEFVQMMTA

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	2
POP	Pyrophosphate 2-	H2 O7 P2	2
CA	Calcium ion	Ca	6

Primary citation

Protein polyglutamylation catalyzed by the bacterial calmodulin-dependent pseudokinase SidJ. Sulpizio, A., Minelli, M.E., Wan, M. et al. Elife (2019) 8. DOI 10.7554/eLife.51162 · PubMed

Other PDB entries of the same protein (UniProt Q5ZTK6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6OQQ 2.1 Å, Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex
7MIR 2.5 Å, Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex
6K4K 2.71 Å, Crystal structure of SidJ-CaM binary complex at 2.71 A
7MIS 2.8 Å, Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex
7PPO 2.91 Å, Structure of SidJ/CaM bound to SdeA in pre-glutamylation state
6K4L 2.95 Å, Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A
6K4R 3.11 Å, Crystal structure of SidJ-CaM-AMP ternary complex at 3.11 A
7PQE 3.7 Å, Structure of SidJ/CaM bound to SdeA in post-catalysis state
6S5T 4.15 Å, Legionella pneumophila SidJ-Human calmodulin complex

Browse structure collections

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