6S5T: SidJ

Legionella pneumophila SidJ-Human calmodulin complex. Determined by electron microscopy at 4.15 Å resolution. Released 24 Jul 2019.

Method: Electron microscopy
Resolution: 4.15 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 2
Atoms: 6,958
Mol. weight: 117.7 kDa
Ligands: ANP
Released: 24 Jul 2019

Explore 6S5T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S5T contains 53 α-helices and 33 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: 43 helices, 29 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	136-157	22
α-helix	165-181	17
α-helix	185-205	21
α-helix	207-219	13
α-helix	231-234	4
α-helix	237-245	9
α-helix	249-251	3
α-helix	252-260	9
α-helix	266-268	3
α-helix	271-280	10
β-strand	291-294	4	4
β-strand	297-300	4	4
α-helix	304-310	7
β-strand	316-320	5	1
α-helix	330-332	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	375-390	16
α-helix	392-395	4
β-strand	403-406	4	5
β-strand	409-411	3	6
α-helix	412-418	7
α-helix	419-421	3
α-helix	425-431	7
β-strand	437-439	3	6
β-strand	440-445	6	5
α-helix	447-449	3
β-strand	452	1	7
α-helix	460-480	21
β-strand	482-483	2	8
β-strand	491	1	9
β-strand	505	1	9
α-helix	506-507	2
α-helix	520	1
β-strand	521	1	10
α-helix	522	1
β-strand	523	1	11
α-helix	526-529	4
β-strand	536	1	7
β-strand	539	1	7
β-strand	547-548	2	8
α-helix	549-552	4
α-helix	557-562	6
α-helix	564-567	4
α-helix	573-575	3
β-strand	576	1	3
β-strand	583-585	3	3
α-helix	588-591	4
α-helix	594-622	29
α-helix	628-653	26
α-helix	658-666	9
α-helix	671-681	11
α-helix	686-688	3
α-helix	691-701	11
α-helix	706-709	4
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	739-773	35
α-helix	781-792	12
α-helix	796	1
α-helix	801-816	16
α-helix	827-845	19

Chain B: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
β-strand	28-29	2	13
α-helix	30-32	3
α-helix	33-39	7
α-helix	46-56	11
β-strand	63-64	2	13
α-helix	66-76	11
α-helix	83-91	9
β-strand	100-101	2	14
α-helix	103-112	10
α-helix	116-118	3
α-helix	119-127	9
β-strand	137-138	2	14
α-helix	139-145	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SidJ	A	protein	873	Legionella pneumophila	Q5ZTK6 (AlphaFold model)
Calmodulin-2	B	protein	149	Homo sapiens	P0DP24 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6S5T_1 SidJ (chains A)
MFGFIKKVLDFFGVDQSEDNPSETAVETTDVSTKIKTTDTTQEESSVKTKTVVPTQPGGS
VKPETIAPDQQKKHQIKTETTTSTTKQKGPKVTLMDGHVKQYYFARRGETSTHDTSLPPP
VKVLSGRSIPLKEIPFEATRNELVQIYLTSIDKLIKSNKLNSIPSQQIASHYLFLRSLAN
SETDGIKKNQILSLAKPLGTYLASKEPHVWKMINELIEKSEYPIIHYLKNNRAHSNFMLA
LIHEYHKEPLTKNQSAFVQKFRDSSVFLFPNPIYTAWLAHSYDEDSSFNPMFRERLSTNF
YHSTLTDNLLLRTEPKEVTLSSEHHYKKEKGPIDSSFRYQMSSDRLLRIQGRTLLFSTPQ
NDVVAVKVQKKGEPKSTLEEEFEMADYLLKHQRRLDVHSKLPQPLGQYSVKKSEILEISR
GSLDFERFKTLIDDSKDLEVYVYKAPQSYFTYLHDKNQDLEDLTASVKTNVHDLFVLLRE
GIVFPQLADIFHTHFGEDEREDKGRYQALVQLLNVLQFQLGRIDKWQKAVEYVNLRSSGL
ADLGDSLPITSLFTSSDFTKHYFSELLTGGYHPTFFDKSSGTANSLFTGKRRLFGNYLYL
NTIAEYLLVIQLTLGSYGDKVTRDMMDKPKKEAVWRELANVMFTSCAEAIHIMTGIPQSR
ALTLLKQRANIEKHFRQTQFWMTPDYSKLDEDTLQMEQYSIYSGEPEYEFTDKLVSGVGL
SVDGVHQDLGGYNRESPLRELEKLLYATVTLIEGTMQLDKEFFKQLEQVEKILSGEIKTD
ANSCFEAVAQLLDLARPGCHFQKRLVLSYYEEAKLKYPSAPTDAYDSRFQVVARTNAAIT
IQRFWREARKNLSEKSDIDSEKPESERTTDKRL

Sequence of entity 2 (B), FASTA

>6S5T_2 Calmodulin-2 (chains B)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Primary citation

Inhibition of bacterial ubiquitin ligases by SidJ-calmodulin catalysed glutamylation. Bhogaraju, S., Bonn, F., Mukherjee, R. et al. Nature (2019) 572:382-386. DOI 10.1038/s41586-019-1440-8 · 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
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

Browse structure collections

About this viewer

MolViewer shows 6S5T 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.