5YIM: Legionella effector

Structure of a Legionella effector. Determined by X-ray diffraction at 3.39 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 3.39 Å
Organism: Legionella pneumophila
Chains: 2
Atoms: 14,128
Mol. weight: 217.55 kDa
Released: 30 May 2018

Explore 5YIM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YIM contains 102 α-helices and 50 β-strands across 2 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: 54 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	238-247	10
α-helix	248-252	5
α-helix	255-256	2
α-helix	264	1
β-strand	265-267	3	1
β-strand	270-272	3	1
α-helix	279-301	23
β-strand	308	1	2
β-strand	314	1	2
α-helix	315-317	3
α-helix	320-330	11
α-helix	347-363	17
α-helix	366-369	4
α-helix	377-388	12
α-helix	399-409	11
α-helix	418-433	16
α-helix	435-451	17
β-strand	466	1	3
α-helix	467	1
β-strand	475-476	2	4
β-strand	477-478	2	5
β-strand	479	1	6
β-strand	482	1	6
β-strand	485	1	7
α-helix	498-499	2
β-strand	500	1	7
α-helix	501	1
β-strand	502-503	2	4
β-strand	512-513	2	5
α-helix	514	1
β-strand	515	1	3
α-helix	516-520	5
α-helix	523-528	6
α-helix	530-532	3
α-helix	547-552	6
α-helix	555-562	8
α-helix	564-586	23
α-helix	596-598	3
α-helix	600-614	15
α-helix	616-618	3
β-strand	619	1	8
β-strand	624-626	3	8
β-strand	629-631	3	8
α-helix	633-642	10
α-helix	645-651	7
α-helix	654-666	13
β-strand	670-671	2	9
β-strand	682-683	2	9
α-helix	684-695	12
α-helix	701-713	13
α-helix	716-727	12
α-helix	735-748	14
β-strand	763-768	6	10
α-helix	772-787	16
α-helix	798-807	10
α-helix	812-814	3
β-strand	815	1	11
β-strand	819-822	4	10
β-strand	836-841	6	10
β-strand	850-851	2	10
β-strand	862-865	4	10
β-strand	867	1	11
β-strand	871-879	9	10
α-helix	888-890	3
β-strand	891-899	9	10
α-helix	901-903	3
α-helix	904-906	3
α-helix	913-934	22
α-helix	935-937	3
α-helix	941-952	12
α-helix	953-955	3
α-helix	960-965	6
α-helix	966-970	5
α-helix	971-982	12
α-helix	988-994	7
α-helix	996-998	3
α-helix	1010-1041	32
α-helix	1049-1053	5
α-helix	1066-1083	18
α-helix	1094-1115	22
α-helix	1125-1150	26
α-helix	1161-1183	23

Chain C: 48 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	238-250	13
α-helix	279-301	23
β-strand	308	1	12
β-strand	314	1	12
α-helix	315-317	3
α-helix	320-331	12
α-helix	349-358	10
α-helix	383-386	4
α-helix	398-410	13
α-helix	411-413	3
α-helix	418-432	15
α-helix	435-451	17
β-strand	459	1	13
β-strand	466	1	14
α-helix	467	1
β-strand	475-476	2	15
β-strand	487-488	2	15
β-strand	515	1	14
α-helix	516-520	5
α-helix	523-528	6
β-strand	536	1	13
α-helix	549-552	4
α-helix	554-562	9
α-helix	564-586	23
α-helix	596-598	3
α-helix	600-614	15
α-helix	616-618	3
β-strand	619	1	16
β-strand	624	1	16
β-strand	631	1	16
α-helix	633-642	10
α-helix	645-651	7
α-helix	654-666	13
α-helix	670-672	3
β-strand	673	1	17
β-strand	683	1	17
α-helix	686-695	10
α-helix	705-713	9
α-helix	716-726	11
α-helix	735-748	14
α-helix	749-751	3
α-helix	759-761	3
β-strand	763-768	6	18
α-helix	772-787	16
α-helix	798-807	10
β-strand	819-822	4	18
β-strand	836-841	6	18
β-strand	849-851	3	18
β-strand	862-865	4	18
β-strand	871-879	9	18
β-strand	883	1	19
α-helix	888	1
β-strand	889	1	19
α-helix	890	1
β-strand	891-899	9	18
α-helix	905-906	2
α-helix	913-934	22
α-helix	943-951	9
α-helix	953-955	3
α-helix	962-982	21
α-helix	987-994	8
α-helix	1011-1041	31
α-helix	1046-1054	9
α-helix	1056-1059	4
α-helix	1064-1083	20
α-helix	1091-1093	3
α-helix	1094-1114	21
α-helix	1122-1126	5
α-helix	1127-1150	24
α-helix	1161-1187	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SdeA	A, C	protein	960	Legionella pneumophila	Q6RCR0

Sequence of entity 1 (A, C), FASTA

>5YIM_1 SdeA (chains A, C)
MGFSLYTDDTVKAAAQYAYDNYLGKPYTGSVESAPANFGGRMVYRQHHGLSHTLRTMAYA
ELIVEEARKAKLRGETLGKFKDGRTIADVTPQELKKIMIAQAFFVAGRDDEASDAKNYQK
YHEQSRDAFLKYVKDNESTLIPDVFKDQEDVNFYARVIEDKSHDWESTPAHVLINQGHMV
DLVRVKQPPESFLQRYFSSMQRWIGSQATEAVFGIQRQFFHATYEVVAGFDSDNKEPHLV
VSGLGRYVIGEDGQPIREAPKKGQKEGDLKVFPQTYKLKENERLMRVDEFLKLPEIQNTF
PGSGKHLQGGMPGMNEMDYWNRLNSLNRARCENDVDFCLKQLQTAHDKAKIEPIKQAFQS
SKGKERRQPNVDEIAAARIIQQILANPDCIHDDHVLINGQKLEQQFFRDLLAKCEMAVVG
SLLNDTDIGNIDTLMRHEKDTEFHSTNPEAVPVKIGEYWINDQRINNSSGNITQKKHDLI
FLMQNDAWYFSRVNAIAQNRDKGSTFKEVLITTLMTPLTSKALVDTSQAKPPTRLFRGLN
LSEEFTKGLIDQANAMIANTTERLFTDHSPEAFKQIKLNDLSKMSGRTNASTTTEIKLVK
ETWDSNVIFEMLDPDGLLHSKQVGRHGEGTESEFSVYLPEDVALVPVKVTLDGKTQKGEN
RYVFTFVAVKSPDFTPRHESGYAVEPFLRMQAAKLAEVKSSIEKAQRAPDLETIFNLQNE
VEAVQYSHLSTGYKNFLKNTVGPVLENSLSGLMESDTDTLSKALAAFPSDTQWSAFNFEE
ARQAKRQMDAIKQMVGNKVVLDALTQCQDALEKQNIAGALDALKKIPSEKEMGTIRRELR
EQIQSARQELESLQRAVVTPVVTDEKKVRERYDALIENTSKKITELETGKLPNLDAVKKG
ISNLSNLKQEVTVLRNEKIRMHVGTDKVDFSDVEKLEQQIQVIDTKLADAYLLEVTKQIS

Primary citation

Structural basis of ubiquitin modification by the Legionella effector SdeA. Dong, Y., Mu, Y., Xie, Y. et al. Nature (2018) 557:674-678. DOI 10.1038/s41586-018-0146-7 · PubMed

Other PDB entries of the same protein (UniProt Q6RCR0), best resolution first:

5CRB 2.0 Å, Crystal Structure of SdeA DUB
5CRA 2.64 Å, Structure of the SdeA DUB Domain
5CRC 2.85 Å, Structure of the SdeA DUB Domain
5YIK 3.1 Å, Structure of a Legionella effector with its substrate
5YIJ 3.18 Å, Structure of a Legionella effector with substrates

Browse structure collections

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