5YIK: Legionella effector with its substrate

Structure of a Legionella effector with its substrate. Determined by X-ray diffraction at 3.1 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 4
Atoms: 9,381
Mol. weight: 136.19 kDa
Released: 30 May 2018

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

Secondary structure: helices and β-sheets

5YIK contains 61 α-helices and 46 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: 54 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	238-247	10
α-helix	248-252	5
α-helix	255-256	2
β-strand	265-267	3	1
β-strand	270-272	3	1
α-helix	279-301	23
α-helix	306-308	3
α-helix	315-317	3
α-helix	320-332	13
α-helix	344-364	21
α-helix	366-368	3
α-helix	369-373	5
α-helix	377-388	12
α-helix	398-408	11
α-helix	409-413	5
α-helix	418-430	13
α-helix	435-451	17
β-strand	459	1	2
β-strand	466	1	3
α-helix	467	1
β-strand	468-469	2	4
β-strand	474-476	3	4
β-strand	477-479	3	5
β-strand	483-484	2	5
β-strand	486	1	6
β-strand	497	1	6
β-strand	499-500	2	4
β-strand	512-513	2	5
α-helix	514	1
β-strand	515	1	3
α-helix	516-521	6
β-strand	536	1	2
α-helix	545-552	8
α-helix	555-562	8
α-helix	564-578	15
α-helix	581-586	6
α-helix	595-596	2
α-helix	600-614	15
α-helix	616-618	3
β-strand	619	1	7
β-strand	624-626	3	7
β-strand	629-631	3	7
α-helix	633-642	10
α-helix	645-649	5
α-helix	654-665	12
α-helix	669	1
β-strand	670-671	2	8
β-strand	682-683	2	8
α-helix	684-694	11
α-helix	701-714	14
α-helix	716-726	11
α-helix	735-755	21
β-strand	763-768	6	9
α-helix	772-787	16
α-helix	798-808	11
α-helix	811-814	4
β-strand	818-822	5	9
α-helix	825-826	2
α-helix	827-831	5
β-strand	836-841	6	9
β-strand	849-851	3	9
β-strand	859	1	10
β-strand	862-866	5	9
β-strand	871-883	13	9
β-strand	889-899	11	9
α-helix	905-906	2
α-helix	913-934	22
α-helix	941-952	12
α-helix	953-955	3
α-helix	960-964	5
α-helix	965-970	6
α-helix	971-982	12
α-helix	987-995	9
α-helix	997-998	2
α-helix	999-1003	5
α-helix	1010-1041	32
α-helix	1045-1053	9
β-strand	1058-1059	2	11
β-strand	1061	1	11
α-helix	1068-1081	14
α-helix	1094-1114	21
α-helix	1123-1149	27
α-helix	1160-1190	31

Chain C: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	12
β-strand	12-16	5	12
α-helix	23-33	11
β-strand	42-45	4	12
β-strand	48-49	2	12
β-strand	66-70	5	12

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	10
β-strand	12-16	5	10
α-helix	23-34	12
β-strand	41-45	5	10
β-strand	48-49	2	10
α-helix	50-51	2
β-strand	66-71	6	10

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	13
β-strand	12-17	6	13
β-strand	22	1	14
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	13
β-strand	48-49	2	13
α-helix	50-51	2
β-strand	55	1	14
α-helix	56-59	4
β-strand	66-71	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SdeA	A	protein	968	Legionella pneumophila	Q6RCR0
ubiquitin	C, D, F	protein	78	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YIK_1 SdeA (chains A)
GFSLYTDDTVKAAAQYAYDNYLGKPYTGSVESAPANFGGRMVYRQHHGLSHTLRTMAYAE
LIVEEARKAKLRGETLGKFKDGRTIADVTPQELKKIMIAQAFFVAGRDDEASDAKNYQKY
HEQSRDAFLKYVKDNESTLIPDVFKDQEDVNFYARVIEDKSHDWESTPAHVLINQGHMVD
LVRVKQPPESFLQRYFSSMQRWIGSQATEAVFGIQRQFFHATYEVVAGFDSDNKEPHLVV
SGLGRYVIGEDGQPIREAPKKGQKEGDLKVFPQTYKLKENERLMRVDEFLKLPEIQNTFP
GSGKHLQGGMPGMNEMDYWNRLNSLNRARCENDVDFCLKQLQTAHDKAKIEPIKQAFQSS
KGKERRQPNVDEIAAARIIQQILANPDCIHDDHVLINGQKLEQQFFRDLLAKCEMAVVGS
LLNDTDIGNIDTLMRHEKDTEFHSTNPEAVPVKIGEYWINDQRINNSSGNITQKKHDLIF
LMQNDAWYFSRVNAIAQNRDKGSTFKEVLITTLMTPLTSKALVDTSQAKPPTRLFRGLNL
SEEFTKGLIDQANAMIANTTERLFTDHSPEAFKQIKLNDLSKMSGRTNASTTTEIKLVKE
TWDSNVIFEMLDPDGLLHSKQVGRHGEGTESEFSVYLPEDVALVPVKVTLDGKTQKGENR
YVFTFVAVKSPDFTPRHESGYAVEPFLRMQAAKLAEVKSSIEKAQRAPDLETIFNLQNEV
EAVQYSHLSTGYKNFLKNTVGPVLENSLSGLMESDTDTLSKALAAFPSDTQWSAFNFEEA
RQAKRQMDAIKQMVGNKVVLDALTQCQDALEKQNIAGALDALKKIPSEKEMGTIRRELRE
QIQSARQELESLQRAVVTPVVTDEKKVRERYDALIENTSKKITELETGKLPNLDAVKKGI
SNLSNLKQEVTVLRNEKIRMHVGTDKVDFSDVEKLEQQIQVIDTKLADAYLLEVTKQISA
LEHHHHHH

Sequence of entity 2 (C, D, F), FASTA

>5YIK_2 ubiquitin (chains C, D, F)
SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD
YNIQKESTLHLVLRLRGG

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
5YIJ 3.18 Å, Structure of a Legionella effector with substrates
5YIM 3.39 Å, Structure of a Legionella effector

Browse structure collections

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