6K4R: SidJ-CaM-AMP ternary complex

Crystal structure of SidJ-CaM-AMP ternary complex at 3.11 A. Determined by X-ray diffraction at 3.11 Å resolution. Released 24 Jul 2019.

Method: X-ray diffraction
Resolution: 3.11 Å
Organisms: Legionella pneumophila subsp. pneumophila str. Philadelphia 1, Homo sapiens
Chains: 4
Atoms: 12,715
Mol. weight: 235.69 kDa
Ligands: CA, AMP
Released: 24 Jul 2019

Explore 6K4R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K4R contains 96 α-helices and 55 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: 42 helices, 28 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	160-162	3
α-helix	165-181	17
α-helix	185-195	11
α-helix	197-205	9
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	266-268	3
α-helix	271-280	10
β-strand	291-293	3	4
β-strand	298-300	3	4
α-helix	302-310	9
α-helix	314-315	2
β-strand	316-320	5	1
α-helix	329-333	5
β-strand	346-350	5	5
β-strand	353-356	4	5
β-strand	363-368	6	5
β-strand	370	1	6
α-helix	375-390	16
α-helix	392-395	4
α-helix	401-402	2
β-strand	403-411	9	5
α-helix	412-418	7
β-strand	432	1	6
β-strand	437-445	9	5
α-helix	447-450	4
β-strand	452	1	7
α-helix	460-480	21
β-strand	482-483	2	8
β-strand	491	1	9
β-strand	505	1	9
α-helix	510-513	4
β-strand	523	1	10
β-strand	535	1	11
β-strand	536	1	7
β-strand	540	1	11
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	587-592	6
α-helix	594-622	29
α-helix	628-654	27
α-helix	658-668	11
α-helix	671-682	12
α-helix	685-688	4
α-helix	691-702	12
α-helix	706-707	2
α-helix	713-714	2
β-strand	715	1	12
β-strand	719	1	12
β-strand	729	1	10
α-helix	739-773	35
α-helix	785-793	9
α-helix	796	1
α-helix	800-816	17
α-helix	827-842	16

Chain B: 45 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	105	1	13
β-strand	108-109	2	14
α-helix	117-119	3
β-strand	121-124	4	15
β-strand	127-130	4	15
β-strand	131-133	3	16
α-helix	136-156	21
α-helix	159-162	4
α-helix	165-181	17
α-helix	185-195	11
α-helix	197-204	8
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	266-268	3
α-helix	271-280	10
β-strand	291-293	3	17
β-strand	298-300	3	17
α-helix	302-310	9
α-helix	314-315	2
β-strand	316-317	2	14
β-strand	320	1	13
α-helix	329-333	5
β-strand	346-350	5	18
β-strand	353-357	5	18
β-strand	363-368	6	18
α-helix	369-370	2
α-helix	375-390	16
α-helix	392-395	4
α-helix	401-402	2
β-strand	403-408	6	18
α-helix	412-419	8
α-helix	425-429	5
β-strand	440-445	6	18
α-helix	448-450	3
β-strand	452	1	19
α-helix	460-480	21
β-strand	482-483	2	20
α-helix	510-513	4
α-helix	522	1
β-strand	523	1	21
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	16
β-strand	582-585	4	16
α-helix	587-592	6
α-helix	594-622	29
α-helix	628-654	27
α-helix	658-668	11
α-helix	671-682	12
α-helix	685-688	4
α-helix	691-701	11
α-helix	706-707	2
α-helix	713	1
β-strand	714-715	2	22
β-strand	719-720	2	22
β-strand	729	1	21
α-helix	739-773	35
α-helix	785-793	9
α-helix	796	1
α-helix	800-816	17
α-helix	827-839	13

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	27-28	2	23
α-helix	30-40	11
β-strand	57-58	2	23
α-helix	59-70	12
α-helix	75-84	10
α-helix	97-101	5

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-20	14
α-helix	33-39	7
α-helix	59-64	6
α-helix	77-83	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SidJ	A, B	protein	873	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Q5ZTK6 (AlphaFold model)
Calmodulin-1	C, D	protein	149	Homo sapiens	P0DP23 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6K4R_1 SidJ (chains A, B)
MFGFIKKVLDFFGVDQSEDNPSETAVETTDVSTKIKTTDTTQEESSVKTKTVVPTQPGGS
VKPETIAPDQQKKHQIKTETTTSTTKQKGPKVTLMDGHVKQYYFARRGETSTHDTSLPPP
VKVLSGRSIPLKEIPFEATRNELVQIYLTSIDKLIKSNKLNSIPSQQIASHYLFLRSLAN
SETDGIKKNQILSLAKPLGTYLASKEPHVWKMINELIEKSEYPIIHYLKNNRAHSNFMLA
LIHEYHKEPLTKNQSAFVQKFRDSSVFLFPNPIYTAWLAHSYDEDSSFNPMFRERLSTNF
YHSTLTDNLLLRTEPKEVTLSSEHHYKKEKGPIDSSFRYQMSSDRLLRIQGRTLLFSTPQ
NDVVAVKVQKKGEPKSTLEEEFEMADYLLKHQRRLDVHSKLPQPLGQYSVKKSEILEISR
GSLDFERFKTLIDDSKDLEVYVYKAPQSYFTYLHDKNQDLEDLTASVKTNVHDLFVLLRE
GIVFPQLADIFHTHFGEDEREDKGRYQALVQLLNVLQFQLGRIDKWQKAVEYVNLRSSGL
ADLGDSLPITSLFTSSDFTKHYFSELLTGGYHPTFFDKSSGTANSLFTGKRRLFGNYLYL
NTIAEYLLVIQLTLGSYGDKVTRDMMDKPKKEAVWRELANVMFTSCAEAIHIMTGIPQSR
ALTLLKQRANIEKHFRQTQFWMTPDYSKLDEDTLQMEQYSIYSGEPEYEFTDKLVSGVGL
SVDGVHQDLGGYNRESPLRELEKLLYATVTLIEGTMQLDKEFFKQLEQVEKILSGEIKTD
ANSCFEAVAQLLDLARPGCHFQKRLVLSYYEEAKLKYPSAPTDAYDSRFQVVARTNAAIT
IQRFWREARKNLSEKSDIDSEKPESERTTDKRL

Sequence of entity 2 (C, D), FASTA

>6K4R_2 Calmodulin-1 (chains C, D)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	2

Water and common crystallization additives (PG4, CL) are not listed.

Primary citation

Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase. Gan, N., Zhen, X., Liu, Y. et al. Nature (2019) 572:387-391. DOI 10.1038/s41586-019-1439-1 · 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
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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