7MIR: SidJ-SdeA-CaM reaction intermediate complex

Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex. Determined by electron microscopy at 2.5 Å resolution. Released 18 Aug 2021.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 3
Atoms: 12,997
Mol. weight: 214.38 kDa
Ligands: CA, ATP, MG, AMP
Released: 18 Aug 2021

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

Secondary structure: helices and β-sheets

7MIR contains 94 α-helices and 56 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: 43 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	105-109	5	1
α-helix	117-119	3
β-strand	121-123	3	2
β-strand	128-130	3	2
β-strand	131-133	3	3
α-helix	136-157	22
α-helix	160-162	3
α-helix	165-181	17
α-helix	185-205	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
α-helix	314-315	2
β-strand	316-320	5	1
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	369	1
β-strand	370	1	6
α-helix	375-395	21
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	460-479	20
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
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	549-551	3
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	588-592	5
α-helix	594-621	28
α-helix	622-624	3
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	706-708	3
α-helix	713-714	2
β-strand	715	1	13
β-strand	719	1	13
β-strand	729	1	11
β-strand	735	1	10
α-helix	739-773	35
α-helix	781-793	13
α-helix	796	1
α-helix	801-816	16
α-helix	827-847	21

Chain B: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	27-29	3	14
α-helix	33-40	8
α-helix	46-56	11
β-strand	63-65	3	14
α-helix	66-77	12
α-helix	84-92	9
β-strand	100	1	15
α-helix	103-112	10
α-helix	122-128	7
β-strand	138	1	15
α-helix	139-145	7

Chain C: 43 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	238-247	10
α-helix	248-252	5
β-strand	265-267	3	16
β-strand	270-272	3	16
α-helix	279-301	23
α-helix	315-317	3
α-helix	320-330	11
α-helix	344-364	21
α-helix	366-369	4
α-helix	377-388	12
α-helix	398-409	12
α-helix	410-412	3
α-helix	418-430	13
α-helix	435-451	17
β-strand	459-460	2	17
β-strand	466	1	18
α-helix	467	1
β-strand	477	1	19
β-strand	478	1	20
β-strand	484	1	20
α-helix	485	1
β-strand	513	1	19
α-helix	514	1
β-strand	515	1	18
α-helix	516-520	5
α-helix	523-526	4
β-strand	535-536	2	17
α-helix	545-552	8
α-helix	555-562	8
α-helix	564-585	22
α-helix	588-590	3
α-helix	595-599	5
α-helix	600-614	15
α-helix	616-618	3
β-strand	619-620	2	21
β-strand	623-626	4	21
β-strand	629-631	3	21
α-helix	633-642	10
α-helix	645-650	6
α-helix	654-667	14
β-strand	670-671	2	22
β-strand	682-683	2	22
α-helix	684-695	12
α-helix	701-713	13
α-helix	716-726	11
α-helix	735-755	21
α-helix	759-761	3
β-strand	763-768	6	23
α-helix	772-787	16
α-helix	798-808	11
α-helix	811-813	3
β-strand	819-822	4	23
α-helix	825-831	7
β-strand	836-841	6	23
β-strand	850-851	2	23
α-helix	852-854	3
β-strand	862-865	4	23
β-strand	871-883	13	23
β-strand	889-899	11	23
α-helix	901-903	3
α-helix	907-908	2
α-helix	913-931	19
α-helix	1067-1074	8
α-helix	1079-1085	7
α-helix	1100-1117	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calmodulin-dependent glutamylase SidJ	A	protein	756	Legionella pneumophila	Q5ZTK6 (AlphaFold model)
Calmodulin-2	B	protein	150	Homo sapiens	P0DP24 (AlphaFold model)
Ubiquitinating/deubiquitinating enzyme SdeA	C	protein	965	Legionella pneumophila	Q5ZTK4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7MIR_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

>7MIR_2 Calmodulin-2 (chains B)
SMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD
GNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTD
EEVDEMIREADIDGDGQVNYEEFVQMMTAK

Sequence of entity 3 (C), FASTA

>7MIR_3 Ubiquitinating/deubiquitinating enzyme SdeA (chains C)
GAMGSGFSLYTDDTVKAAAQYAYDNYLGKPYTGSVESAPANFGGRMVYRQHHGLSHTLRT
MAYAELIVEEARKAKLRGETLGKFKDGRTIADVTPQELKKIMIAQAFFVAGRDDEASDAK
NYQKYHEQSRDAFLKYVKDNESTLIPDVFKDQEDVNFYARVIEDKSHDWESTPAHVLINQ
GHMVDLVRVKQPPESFLQRYFSSMQRWIGSQATEAVFGIQRQFFHATYEVVAGFDSDNKE
PHLVVSGLGRYVIGEDGQPIREAPKKGQKEGDLKVFPQTYKLKENERLMRVDEFLKLPEI
QNTFPGSGKHLQGGMPGMNEMDYWNRLNSLNRARCENDVDFCLKQLQTAHDKAKIEPIKQ
AFQSSKGKERRQPNVDEIAAARIIQQILANPDCIHDDHVLINGQKLEQQFFRDLLAKCEM
AVVGSLLNDTDIGNIDTLMRHEKDTEFHSTNPEAVPVKIGEYWINDQRINNSSGNITQKK
HDLIFLMQNDAWYFSRVNAIAQNRDKGSTFKEVLITTLMTPLTSKALVDTSQAKPPTRLF
RGLNLSEEFTKGLIDQANAMIANTTERLFTDHSPEAFKQIKLNDLSKMSGRTNASTTTEI
KLVKETWDSNVIFEMLDPDGLLHSKQVGRHGEGTESEFSVYLPEDVALVPVKVTLDGKTQ
KGENRYVFTFVAVKSPDFTPRHESGYAVEPFLRMQAAKLAEVKSSIEKAQRAPDLETIFN
LQNEVEAVQYSHLSTGYKNFLKNTVGPVLENSLSGLMESDTDTLSKALAAFPSDTQWSAF
NFEEARQAKRQMDAIKQMVGNKVVLDALTQCQDALEKQNIAGALDALKKIPSEKEMGTIR
RELREQIQSARQELESLQRAVVTPVVTDEKKVRERYDALIENTSKKITELETGKLPNLDA
VKKGISNLSNLKQEVTVLRNEKIRMHVGTDKVDFSDVEKLEQQIQVIDTKLADAYLLEVT
KQISA

Ligands and cofactors

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

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
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

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