7PQE: SidJ/CaM

Structure of SidJ/CaM bound to SdeA in post-catalysis state. Determined by electron microscopy at 3.7 Å resolution. Released 6 Oct 2021.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 3
Atoms: 10,746
Mol. weight: 221.83 kDa
Ligands: CA, MG
Released: 6 Oct 2021

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

Secondary structure: helices and β-sheets

7PQE contains 73 α-helices and 52 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: 23 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	240-247	8
α-helix	248-252	5
α-helix	255-256	2
α-helix	263-264	2
β-strand	265-267	3	1
β-strand	270-272	3	1
α-helix	279-302	24
α-helix	315-317	3
α-helix	320-331	12
α-helix	344-364	21
α-helix	366-368	3
α-helix	377-388	12
α-helix	398-409	12
α-helix	418-430	13
α-helix	435-451	17
α-helix	455-459	5
β-strand	460	1	2
β-strand	466	1	3
α-helix	467	1
β-strand	468-469	2	4
β-strand	474-475	2	4
β-strand	478	1	5
β-strand	484	1	5
β-strand	486	1	6
β-strand	497	1	6
α-helix	498-499	2
β-strand	500	1	4
β-strand	515	1	3
α-helix	516-520	5
β-strand	535	1	2
α-helix	545-552	8
α-helix	555-560	6
α-helix	564-586	23
β-strand	763	1	7
β-strand	765	1	8
β-strand	767-768	2	7
α-helix	772-786	15
α-helix	798-807	10
β-strand	822	1	8
α-helix	826-829	4
β-strand	836-841	6	7
β-strand	850-852	3	8
β-strand	862-864	3	8
β-strand	872-875	4	7
β-strand	879-883	5	7
β-strand	889-898	10	7

Chain B: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
β-strand	27-29	3	20
α-helix	33-38	6
α-helix	46-54	9
β-strand	63-65	3	20
α-helix	66-76	11
α-helix	83-90	8
α-helix	104-109	6
α-helix	119-128	10
α-helix	139-143	5

Chain C: 42 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	105-109	5	9
α-helix	117-119	3
β-strand	121-124	4	10
β-strand	127-130	4	10
β-strand	131-133	3	11
α-helix	136-157	22
α-helix	159-162	4
α-helix	165-181	17
α-helix	185-205	21
α-helix	207-217	11
α-helix	223-225	3
α-helix	237-244	8
α-helix	249-251	3
α-helix	252-260	9
α-helix	271-280	10
β-strand	291-292	2	12
β-strand	299-300	2	12
α-helix	302-310	9
α-helix	314-315	2
β-strand	316-320	5	9
α-helix	321	1
α-helix	332-334	3
α-helix	343-345	3
β-strand	346-350	5	13
β-strand	353-356	4	13
β-strand	363-368	6	13
β-strand	370	1	14
α-helix	375-390	16
α-helix	392-395	4
β-strand	403-411	9	13
α-helix	412-418	7
α-helix	425-431	7
β-strand	432	1	14
β-strand	437-445	9	13
α-helix	447-449	3
β-strand	452	1	15
α-helix	460-480	21
β-strand	482-483	2	16
α-helix	520	1
β-strand	521	1	17
α-helix	522	1
β-strand	523	1	18
α-helix	526-529	4
β-strand	535-536	2	15
β-strand	539-540	2	15
α-helix	543-545	3
β-strand	547-548	2	16
α-helix	550-553	4
α-helix	557-562	6
α-helix	564-567	4
β-strand	576-577	2	11
β-strand	582-585	4	11
α-helix	590-621	32
α-helix	628-654	27
α-helix	658-666	9
α-helix	671-681	11
α-helix	684-687	4
α-helix	691-702	12
α-helix	713-714	2
β-strand	715	1	19
β-strand	719	1	19
β-strand	729	1	18
β-strand	735	1	17
α-helix	739-773	35
α-helix	781-793	13
α-helix	796	1
α-helix	800-816	17
α-helix	823-825	3
α-helix	826-847	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitinating/deubiquitinating enzyme SdeA	A	protein	979	Legionella pneumophila	Q5ZTK4 (AlphaFold model)
Calmodulin-dependent glutamylase SidJ	C	protein	794	Legionella pneumophila	Q5ZTK6 (AlphaFold model)
Calmodulin	B	protein	168	Homo sapiens	P0DP24 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7PQE_1 Ubiquitinating/deubiquitinating enzyme SdeA (chains A)
HHHHHHSAGLEVLFQGPMVGFSLYTDDTVKAAAQYAYDNYLGKPYTGSVESAPANFGGRM
VYRQHHGLSHTLRTMAYAELIVEEARKAKLRGETLGKFKDGRTIADVTPQELKKIMIAQA
FFVAGRDDEASDAKNYQKYHEQSRDAFLKYVKDNESTLIPDVFKDQEDVNFYARVIEDKS
HDWESTPAHVLINQGHMVDLVRVKQPPESFLQRYFSSMQRWIGSQATEAVFGIQRQFFHA
TYEVVAGFDSDNKEPHLVVSGLGRYVIGEDGQPIREAPKKGQKEGDLKVFPQTYKLKENE
RLMRVDEFLKLPEIQNTFPGSGKHLQGGMPGMNEMDYWNRLNSLNRARCENDVDFCLKQL
QTAHDKAKIEPIKQAFQSSKGKERRQPNVDEIAAARIIQQILANPDCIHDDHVLINGQKL
EQQFFRDLLAKCEMAVVGSLLNDTDIGNIDTLMRHEKDTEFHSTNPEAVPVKIGEYWIND
QRINNSSGNITQKKHDLIFLMQNDAWYFSRVNAIAQNRDKGSTFKEVLITTLMTPLTSKA
LVDTSQAKPPTRLFRGLNLSEEFTKGLIDQANAMIANTTERLFTDHSPEAFKQIKLNDLS
KMSGRTNASTTTEIKLVKETWDSNVIFEMLDPDGLLHSKQVGRHGEGTESEFSVYLPEDV
ALVPVKVTLDGKTQKGENRYVFTFVAVKSPDFTPRHESGYAVEPFLRMQAAKLAEVKSSI
EKAQRAPDLETIFNLQNEVEAVQYSHLSTGYKNFLKNTVGPVLENSLSGLMESDTDTLSK
ALAAFPSDTQWSAFNFEEARQAKRQMDAIKQMVGNKVVLDALTQCQDALEKQNIAGALDA
LKKIPSEKEMGTIRRELREQIQSARQELESLQRAVVTPVVTDEKKVRERYDALIENTSKK
ITELETGKLPNLDAVKKGISNLSNLKQEVTVLRNEKIRMHVGTDKVDFSDVEKLEQQIQV
IDTKLADAYLLEVTKQISA

Sequence of entity 2 (C), FASTA

>7PQE_2 Calmodulin-dependent glutamylase SidJ (chains C)
HHHHHHSAGLEVLFQGPMVKQYYFARRGETSTHDTSLPPPVKVLSGRSIPLKEIPFETTR
NELVQIYLTSVDQLIKSNKLNSIPSQQIASHYLFLRSLANSETDGIKKNQILSLAKPLGI
YLASKEPHVWKTINELIEKSEYPIIHYLKNNRAHSNFMLALIHEYHKEPLTKNQSAFVQK
FRDSSVFLFPNPIYTAWLAHSYDEDSSFNPMFRERLSTNFYHSTLTDNLLLRTEPKEVTL
SSEHHYKKEKGPIDSSFRYQMSSDRLLRIQGRTLLFSTPQNDVVAVKVQKRGEPKSTLEE
EFQMADYLLKHQSRLDVYSKLPQPLGQYSVKKSEILEISRGSLDFERFKTLIGDSKDLEV
YVYKAPLTYFTYLHDKNQDLEDLTASVKTNVHDLFVLLREGIMFPQLADIFHTHFGEDER
EDKGRYQALVQLLNVLQFQLGRIDKWQKAVEYVNLRSSGLADLGDSLPITSLFTSSDFTK
HYFSALLTGGYHPTFFDKSSGTANSLFTGKRRLFGNYLYLNTIAEYLLVIQLTLGSYGDK
VTRDMMDKPKKEAVWRELANVMFTSCAEAIHIMTGIPQSRALTLLKQRANIEKHFRQTQF
WMTPDYSKLDEDTLQMEQYSIYSGEPEYEFTDKLVSGVGLSVDGTHQDLGGYNRESPLRE
LEKLLYATVTLIEGTMQLDKEFFKQLQQVEKILSGEIKTDANSCFEAVAQLLDLARPRCH
FQKRLVLSYYEEAKLKYPSAPTDAYDSRFQVVAKTNAAITIQRFWRETRKNLSENSDIES
EKPESERTTDKRLK

Sequence of entity 3 (B), FASTA

>7PQE_3 Calmodulin (chains B)
HHHHHHSSGLEVLFQGPHMMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLG
QNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYI
SAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
MG	Magnesium ion	Mg	1

Primary citation

Structural basis for protein glutamylation by the Legionella pseudokinase SidJ. Adams, M., Sharma, R., Colby, T. et al. Nat Commun (2021) 12:6174-6174. DOI 10.1038/s41467-021-26429-y · PubMed

Other PDB entries of the same protein (UniProt Q5ZTK4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5YSI 1.55 Å, SdeA mART-C domain EE/AA NCA complex
9R3T 1.98 Å, C-terminal domain of SdeA Legionella effector
5YSJ 2.06 Å, SdeA mART-C domain WT apo
6B7Q 2.2 Å, Crystal structure of Legionella effector protein sdeA (lpg2157) aa. 211-910
5YSK 2.4 Å, SdeA mART-C domain EE/AA apo
7MIR 2.5 Å, Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex
6WTG 2.63 Å, SdeA DUB Domain in complex with Ubiquitin
6G0C 2.8 Å, Crystal structure of SdeA catalytic core
8EFW 2.81 Å, Structure of SdeA DUB Domain disulfide crosslinked with Ubiquitin
7PPO 2.91 Å, Structure of SidJ/CaM bound to SdeA in pre-glutamylation state

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