6OQQ: Legionella pneumophila SidJ

Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 15 May 2019.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Legionella pneumophila, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 15,025
Mol. weight: 235.38 kDa
Ligands: CA, MG, POP, AMP
Released: 15 May 2019

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

Secondary structure: helices and β-sheets

6OQQ contains 109 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: 45 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	105-109	5	1
α-helix	117-119	3
β-strand	121-124	4	2
β-strand	127-130	4	2
β-strand	131-133	3	3
α-helix	134-135	2
α-helix	136-157	22
α-helix	159-162	4
α-helix	165-181	17
α-helix	185-205	21
α-helix	207-217	11
α-helix	223-227	5
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
β-strand	346-350	5	5
β-strand	353-357	5	5
β-strand	363-368	6	5
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	1	9
α-helix	497-499	3
β-strand	505	1	9
α-helix	510-513	4
β-strand	521	1	10
α-helix	522	1
β-strand	523	1	11
β-strand	524	1	9
α-helix	526-529	4
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	576-577	2	3
β-strand	582-585	4	3
α-helix	587-592	6
α-helix	594-623	30
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	706-709	4
α-helix	714	1
β-strand	715	1	12
β-strand	719	1	12
α-helix	727-728	2
β-strand	729	1	11
β-strand	735	1	10
α-helix	739-774	36
α-helix	781-793	13
α-helix	796	1
α-helix	800-816	17
α-helix	826-845	20

Chain B: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	27-29	3	13
α-helix	30-32	3
α-helix	33-39	7
α-helix	46-56	11
β-strand	63-65	3	13
α-helix	66-78	13
α-helix	82-90	9
β-strand	100	1	14
α-helix	103-112	10
α-helix	119-123	5
β-strand	137	1	14
α-helix	138-145	8

Chain C: 41 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	105-109	5	15
α-helix	117-119	3
β-strand	121-124	4	16
β-strand	127-130	4	16
β-strand	131-133	3	17
α-helix	136-157	22
α-helix	165-181	17
α-helix	185-205	21
α-helix	207-219	13
α-helix	223-227	5
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	18
β-strand	297-300	4	18
α-helix	302-310	9
α-helix	314-315	2
β-strand	316-320	5	15
α-helix	329-333	5
α-helix	343-345	3
β-strand	346-350	5	19
β-strand	353-356	4	19
β-strand	363-368	6	19
β-strand	370	1	20
α-helix	375-390	16
α-helix	392-395	4
β-strand	403-411	9	19
α-helix	412-419	8
α-helix	425-431	7
β-strand	432	1	20
β-strand	437-445	9	19
α-helix	447-450	4
β-strand	452	1	21
α-helix	460-480	21
β-strand	482-483	2	22
β-strand	491	1	23
β-strand	505	1	23
α-helix	510-513	4
β-strand	521	1	24
β-strand	523	1	25
α-helix	526-529	4
β-strand	535	1	26
β-strand	536	1	21
β-strand	540	1	26
β-strand	547-548	2	22
α-helix	549-553	5
α-helix	557-562	6
α-helix	564-568	5
α-helix	573-575	3
β-strand	576-577	2	17
β-strand	582-585	4	17
α-helix	587-592	6
α-helix	594-623	30
α-helix	628-654	27
α-helix	658-666	9
α-helix	671-682	12
α-helix	685-688	4
α-helix	691-702	12
α-helix	706-708	3
β-strand	715	1	27
β-strand	719	1	27
β-strand	729	1	25
β-strand	735	1	24
α-helix	739-772	34
α-helix	781-793	13
α-helix	796	1
α-helix	800-816	17
α-helix	823-841	19

Chain D: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	27-29	3	28
α-helix	30-32	3
α-helix	33-39	7
α-helix	43-45	3
α-helix	46-49	4
α-helix	52-55	4
α-helix	57-59	3
β-strand	63-65	3	28
α-helix	66-75	10
α-helix	77-79	3
α-helix	84-90	7
α-helix	91-93	3
α-helix	103-112	10
α-helix	119-123	5
α-helix	142-145	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Legionella pneumophila SidJ	A, C	protein	873	Legionella pneumophila	Q5ZTK6 (AlphaFold model)
Calmodulin	B, D	protein	147	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P06787 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6OQQ_1 Legionella pneumophila SidJ (chains A, C)
MFGFIKKVLDFFGVDQSEDNPSETAVETTDVSTKIKTTDTTQEESSVKTKTVVPTQPGGS
VKPETIAPDQQKKHQIKTETTTSTTKQKGPKVTLMDGHVKQYYFARRGETSTHDTSLPPP
VKVLSGRSIPLKEIPFEATRNELVQIYLTSIDKLIKSNKLNSIPSQQIASHYLFLRSLAN
SETDGIKKNQILSLAKPLGTYLASKEPHVWKMINELIEKSEYPIIHYLKNNRAHSNFMLA
LIHEYHKEPLTKNQSAFVQKFRDSSVFLFPNPIYTAWLAHSYDEDSSFNPMFRERLSTNF
YHSTLTDNLLLRTEPKEVTLSSEHHYKKEKGPIDSSFRYQMSSDRLLRIQGRTLLFSTPQ
NDVVAVKVQKKGEPKSTLEEEFEMADYLLKHQRRLDVHSKLPQPLGQYSVKKSEILEISR
GSLDFERFKTLIDDSKDLEVYVYKAPQSYFTYLHDKNQDLEDLTASVKTNVHDLFVLLRE
GIVFPQLADIFHTHFGEDEREDKGRYQALVQLLNVLQFQLGRIDKWQKAVEYVNLRSSGL
ADLGDSLPITSLFTSSDFTKHYFSELLTGGYHPTFFDKSSGTANSLFTGKRRLFGNYLYL
NTIAEYLLVIQLTLGSYGDKVTRDMMDKPKKEAVWRELANVMFTSCAEAIHIMTGIPQSR
ALTLLKQRANIEKHFRQTQFWMTPDYSKLDEDTLQMEQYSIYSGEPEYEFTDKLVSGVGL
SVDGVHQDLGGYNRESPLRELEKLLYATVTLIEGTMQLDKEFFKQLEQVEKILSGEIKTD
ANSCFEAVAQLLDLARPGCHFQKRLVLSYYEEAKLKYPSAPTDAYDSRFQVVARTNAAIT
IQRFWREARKNLSEKSDIDSEKPESERTTDKRL

Sequence of entity 2 (B, D), FASTA

>6OQQ_2 Calmodulin (chains B, D)
MSSNLTEEQIAEFKEAFALFDKDNNGSISSSELATVMRSLGLSPSEAEVNDLMNEIDVDG
NHQIEFSEFLALMSRQLKSNDSEQELLEAFKVFDKNGDGLISAAELKHVLTSIGEKLTDA
EVDDMLREVSDGSGEINIQQFAALLSK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
MG	Magnesium ion	Mg	7
POP	Pyrophosphate 2-	H2 O7 P2	3
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	2

Water and common crystallization additives (EDO, NA) are not listed.

Primary citation

Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases. Black, M.H., Osinski, A., Gradowski, M. et al. Science (2019) 364:787-792. DOI 10.1126/science.aaw7446 · PubMed

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

7MIR 2.5 Å, Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex
6PLM 2.59 Å, Legionella pneumophila SidJ/ Calmodulin 2 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

About this viewer

MolViewer shows 6OQQ 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.