6K4L: Se-labelled SidJ complex with CaM

Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A. Determined by X-ray diffraction at 2.95 Å resolution. Released 24 Jul 2019.

Method: X-ray diffraction
Resolution: 2.95 Å
Organisms: Legionella pneumophila subsp. pneumophila str. Philadelphia 1, Homo sapiens
Chains: 4
Atoms: 12,597
Mol. weight: 235.92 kDa
Ligands: CA
Released: 24 Jul 2019

Explore 6K4L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K4L contains 90 α-helices and 56 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: 39 helices, 25 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	136-156	21
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	291-293	3	4
β-strand	298-300	3	4
α-helix	302-310	9
β-strand	316-320	5	1
β-strand	346-349	4	5
β-strand	353-356	4	5
β-strand	363-368	6	5
α-helix	375-390	16
α-helix	392-395	4
α-helix	400-402	3
β-strand	403-411	9	5
α-helix	412-417	6
β-strand	437-445	9	5
α-helix	447-450	4
β-strand	452	1	6
α-helix	460-479	20
β-strand	482-483	2	7
α-helix	510-512	3
β-strand	521	1	8
β-strand	523	1	9
α-helix	526-529	4
β-strand	535-536	2	6
β-strand	539-540	2	6
β-strand	547-548	2	7
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	3
β-strand	582-585	4	3
α-helix	587-592	6
α-helix	594-622	29
α-helix	628-654	27
α-helix	658-668	11
α-helix	671-681	11
α-helix	684-688	5
α-helix	691-701	11
α-helix	706-707	2
α-helix	712-714	3
β-strand	715	1	10
β-strand	719	1	10
β-strand	729	1	9
β-strand	735	1	8
α-helix	739-774	36
α-helix	781-793	13
α-helix	796	1
α-helix	800-816	17
α-helix	823-843	21

Chain B: 40 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	105	1	11
β-strand	108-109	2	12
α-helix	117-119	3
β-strand	121-124	4	13
β-strand	127-130	4	13
β-strand	131-133	3	14
α-helix	136-156	21
α-helix	160-162	3
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	15
β-strand	297-300	4	15
α-helix	302-310	9
α-helix	314-315	2
β-strand	316-317	2	12
β-strand	320	1	11
β-strand	346-349	4	16
β-strand	353-356	4	16
β-strand	363-368	6	16
α-helix	375-390	16
α-helix	392-395	4
α-helix	401-402	2
β-strand	403-408	6	16
α-helix	412-419	8
β-strand	440-445	6	16
α-helix	447-450	4
β-strand	452	1	17
α-helix	462-479	18
β-strand	482-483	2	18
β-strand	523	1	19
α-helix	526-529	4
β-strand	535	1	20
β-strand	536	1	17
β-strand	540	1	20
β-strand	547-548	2	18
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	14
β-strand	582-585	4	14
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	694-701	8
α-helix	706-707	2
α-helix	712-714	3
β-strand	715	1	21
β-strand	719	1	21
β-strand	729	1	19
α-helix	739-774	36
α-helix	781-793	13
α-helix	796	1
α-helix	800-816	17
α-helix	823-841	19

Chain C: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	24	1	1
β-strand	28	1	22
α-helix	30-38	9
β-strand	53	1	23
β-strand	56	1	23
β-strand	57	1	22
α-helix	59-70	12
α-helix	76-86	11
α-helix	97-100	4
α-helix	101-103	3

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-19	13
α-helix	33-38	6
α-helix	59-65	7
α-helix	77-82	6
α-helix	83-85	3

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

>6K4L_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

>6K4L_2 Calmodulin-1 (chains C, D)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Water and common crystallization additives (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
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

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