5YIJ: Legionella effector with substrates

Structure of a Legionella effector with substrates. Determined by X-ray diffraction at 3.18 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 3.18 Å
Organisms: Legionella pneumophila, Homo sapiens
Chains: 4
Atoms: 9,426
Mol. weight: 136.86 kDa
Ligands: NAI
Released: 30 May 2018

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

Secondary structure: helices and β-sheets

5YIJ contains 65 α-helices and 49 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: 56 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	234-236	3
α-helix	238-247	10
α-helix	248-252	5
α-helix	263-264	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	320-331	12
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	418-432	15
α-helix	435-451	17
β-strand	459-460	2	2
β-strand	466	1	3
α-helix	467	1
β-strand	469	1	4
β-strand	474	1	4
β-strand	475	1	5
β-strand	477-479	3	6
β-strand	484	1	6
β-strand	486	1	7
β-strand	497	1	7
β-strand	500	1	5
β-strand	511-513	3	6
α-helix	514	1
β-strand	515	1	3
α-helix	516-520	5
α-helix	523-526	4
β-strand	535-536	2	2
α-helix	545-552	8
α-helix	555-562	8
α-helix	564-577	14
α-helix	581-586	6
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	645-650	6
α-helix	654-666	13
β-strand	670-671	2	9
β-strand	682-683	2	9
α-helix	684-695	12
α-helix	701-712	12
α-helix	719-726	8
α-helix	735-755	21
α-helix	759-761	3
β-strand	763-768	6	10
α-helix	772-788	17
α-helix	798-808	11
α-helix	811-813	3
β-strand	819-822	4	10
α-helix	826	1
α-helix	827-831	5
β-strand	836-841	6	10
β-strand	850-852	3	10
β-strand	859	1	11
β-strand	862-865	4	10
β-strand	871-883	13	10
β-strand	889-899	11	10
α-helix	914-934	21
α-helix	941-952	12
α-helix	953-955	3
α-helix	962-964	3
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	1045-1052	8
α-helix	1058-1060	3
α-helix	1068-1081	14
α-helix	1094-1116	23
α-helix	1123-1149	27
α-helix	1156-1158	3
α-helix	1160-1190	31

Chain C: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	12-15	4	12
β-strand	22	1	13
α-helix	23-34	12
β-strand	42	1	14
β-strand	43-45	3	15
β-strand	48-50	3	15
α-helix	51	1
β-strand	55	1	13
β-strand	65-68	4	12
β-strand	70	1	14

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	11
β-strand	12-16	5	11
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	11
β-strand	48-49	2	11
α-helix	50-51	2
α-helix	56-59	4
β-strand	66-71	6	11

Chain G: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	16
β-strand	12-17	6	16
β-strand	22	1	17
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	16
β-strand	48-50	3	16
α-helix	51	1
β-strand	55	1	17
β-strand	66-71	6	16

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>5YIJ_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, G), FASTA

>5YIJ_2 Ubiquitin (chains C, D, G)
SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD
YNIQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
NAI	1,4-dihydronicotinamide adenine dinucleotide	C21 H29 N7 O14 P2	1

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
5YIM 3.39 Å, Structure of a Legionella effector

Browse structure collections

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