7MIS: SidJ-SdeC-CaM reaction intermediate complex

Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex. Determined by electron microscopy at 2.8 Å resolution. Released 18 Aug 2021.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 3
Atoms: 13,039
Mol. weight: 218.06 kDa
Ligands: ATP, MG, CA, AMP
Released: 18 Aug 2021

Explore 7MIS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MIS contains 90 α-helices and 55 β-strands across 3 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: 40 helices, 31 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	136-157	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	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
β-strand	316-320	5	1
α-helix	325-327	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	412-418	7
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	460-480	21
β-strand	482-483	2	8
β-strand	491	1	9
β-strand	505	1	9
α-helix	510-513	4
β-strand	521	1	10
β-strand	523	1	11
β-strand	524	1	9
α-helix	526-529	4
β-strand	535	1	12
β-strand	536	1	7
β-strand	540	1	12
β-strand	547-548	2	8
α-helix	550-553	4
α-helix	557-562	6
α-helix	565-568	4
α-helix	573-575	3
β-strand	576	1	3
β-strand	583-585	3	3
α-helix	588-592	5
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	691-701	11
α-helix	706-708	3
α-helix	712-714	3
β-strand	715	1	13
β-strand	719	1	13
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	801-816	16
α-helix	823-844	22

Chain B: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
β-strand	27-29	3	14
α-helix	33-39	7
α-helix	43-45	3
α-helix	46-57	12
β-strand	63-65	3	14
α-helix	66-76	11
α-helix	83-92	10
α-helix	103-112	10
α-helix	121-128	8
α-helix	139-142	4

Chain C: 41 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	238-247	10
α-helix	248-252	5
α-helix	284-307	24
α-helix	325-335	11
α-helix	358-374	17
α-helix	378-381	4
α-helix	386-397	12
α-helix	407-420	14
α-helix	421-423	3
α-helix	427-442	16
α-helix	444-460	17
β-strand	468	1	15
β-strand	481	1	16
β-strand	484	1	17
β-strand	489	1	17
β-strand	490	1	18
β-strand	492-493	2	19
α-helix	502-504	3
β-strand	509	1	18
β-strand	520-521	2	19
α-helix	522	1
β-strand	523	1	16
α-helix	524-527	4
α-helix	531-536	6
β-strand	544	1	15
α-helix	554-560	7
α-helix	563-583	21
α-helix	594-597	4
α-helix	599-613	15
α-helix	615-617	3
β-strand	618	1	20
β-strand	623-625	3	20
β-strand	628-630	3	20
α-helix	632-641	10
α-helix	644-650	7
α-helix	654-665	12
β-strand	669-670	2	21
β-strand	681-682	2	21
α-helix	683-686	4
α-helix	687-691	5
α-helix	698-710	13
α-helix	713-723	11
α-helix	732-752	21
α-helix	756-758	3
β-strand	760-765	6	22
α-helix	769-783	15
α-helix	795-804	10
α-helix	808-811	4
β-strand	816-819	4	22
α-helix	822-824	3
α-helix	825-829	5
β-strand	833-838	6	22
β-strand	847-848	2	22
α-helix	856-858	3
β-strand	859-862	4	22
β-strand	868-880	13	22
β-strand	886-896	11	22
α-helix	911-928	18
α-helix	1056-1068	13
α-helix	1069-1071	3
α-helix	1078-1083	6
α-helix	1104-1110	7
α-helix	1126-1136	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calmodulin-dependent glutamylase SidJ	A	protein	756	Legionella pneumophila	Q5ZTK6 (AlphaFold model)
Calmodulin	B	protein	150	Homo sapiens	P0DP24 (AlphaFold model)
SdeC	C	protein	997	Legionella pneumophila	Q5ZTK8

Sequence of entity 1 (A), FASTA

>7MIS_1 Calmodulin-dependent glutamylase SidJ (chains A)
SGHVKQYYFARRGETSTHDTSLPPPVKVLSGRSIPLKEIPFEATRNELVQIYLTSIDKLI
KSNKLNSIPSQQIASHYLFLRSLANSETDGIKKNQILSLAKPLGTYLASKEPHVWKMINE
LIEKSEYPIIHYLKNNRAHSNFMLALIHEYHKEPLTKNQSAFVQKFRDSSVFLFPNPIYT
AWLAHSYDEDSSFNPMFRERLSTNFYHSTLTDNLLLRTEPKEVTLSSEHHYKKEKGPIDS
SFRYQMSSDRLLRIQGRTLLFSTPQNDVVAVKVQKKGEPKSTLEEEFEMADYLLKHQRRL
DVHSKLPQPLGQYSVKKSEILEISRGSLDFERFKTLIDDSKDLEVYVYKAPQSYFTYLHD
KNQDLEDLTASVKTNVHDLFVLLREGIVFPQLADIFHTHFGEDEREDKGRYQALVQLLNV
LQFQLGRIDKWQKAVEYVNLRSSGLADLGDSLPITSLFTSSDFTKHYFSELLTGGYHPTF
FDKSSGTANSLFTGKRRLFGNYLYLNTIAEYLLVIQLTLGSYGDKVTRDMMDKPKKEAVW
RELANVMFTSCAEAIHIMTGIPQSRALTLLKQRANIEKHFRQTQFWMTPDYSKLDEDTLQ
MEQYSIYSGEPEYEFTDKLVSGVGLSVDGVHQDLGGYNRESPLRELEKLLYATVTLIEGT
MQLDKEFFKQLEQVEKILSGEIKTDANSCFEAVAQLLDLARPGCHFQKRLVLSYYEEAKL
KYPSAPTDAYDSRFQVVARTNAAITIQRFWREARKN

Sequence of entity 2 (B), FASTA

>7MIS_2 Calmodulin (chains B)
SMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD
GNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTD
EEVDEMIREADIDGDGQVNYEEFVQMMTAK

Sequence of entity 3 (C), FASTA

>7MIS_3 SdeC (chains C)
GAMGSSKLLENDDDVLDTIKYVHKEYLGKPYPGPLKNPKAPEEGRLPPNEGPDRGPHGLA
HTVRTMACAEVMIEEARKAQLRGETLGKAKNGQTLADVTPEELKKILIAQAFFVVGRDDE
RSGYDDVHKRNFYAEYHEKSEQAFRKYVEDNKLIGKIFKDQKEVDFYAAIILDKNHEWDA
TPAHILINQGHMVDLMRTKAPAEVALERTYNTLKGTVGSKGAEVVLKAHRDFFFATGAVV
PLVNPEAIDDPSRGGPYENPYSGEKFVIVDDKVPASKKDLPKAVNRDYKLKDNERFLTIK
EYYAFPDVQQTYPGYKTRLEASSYYFPTPFAGECEQNPAKCLGAIQKARSKLQTDAIKNG
FQSSSEKERRQPNMDEIAAARIIQQIMANPDCIHDDHVLINGQKLEEKFFRDLLAKCDMA
VVGSLLNDTDIKNIDTLMRHEKNTEFHSTDPKAVPVKIGDAWENRIRTKGGDVTQMKHDL
IFLMQNDAWYFSRVNAIAQNRDKGSNFKEVLFTTLMTPLTNKSLIDTSHVPAPKKLYRGL
NLPQEFTNKLINQSNAIIANTENTLFTDLSAEAFKQIKLNDFSQMSGKTCASTTKNMKLL
TDIWGSNVIFEMLDPDGLLHPKQVGTHMAGSEDEFSVYLPEDVALVPTKVTLEGKTDTGE
DRYIFTLVAVKSPDFIPRHESGYAVEPFMKMQKEKVTQALDAIEKDKDSYNIDEQLKSLR
TEMVRQAKLPLREGVFDRLSHRLSLETSDNKISPERRDFLNQHVIPVLQECHIALRANDM
DMMQKALAKFPTDKQWSAFKSGEAVRAKAQMDVLKQQIEKKIMLQTQIIPALTECGEALD
KQNVTEALQALNKLPAEKEIGKVKTIGQELRGQIVGVKQELTGNLEPLQRATTTPIVQDA
EKIKVRYETLLTDVTKRVTDFEKIKPANLDGYNKAIADLNNIQQELNLLRNEKIRMHTDK
DKAVDFSDIEALDKRLQDVQSKLPTQLLEQTSKDVAK

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
MG	Magnesium ion	Mg	2
CA	Calcium ion	Ca	1
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	1

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

Primary citation

Structural and mechanistic basis for protein glutamylation by the kinase fold. Osinski, A., Black, M.H., Pawlowski, K. et al. Mol Cell (2021) 81:4527. DOI 10.1016/j.molcel.2021.08.007 · 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
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

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