3SY2: Salmonella E3 ubiquitin ligase SopA

Crystal structure of the Salmonella E3 ubiquitin ligase SopA in complex with the human E2 UbcH7. Determined by X-ray diffraction at 3.27 Å resolution. Released 25 Jan 2012.

Method: X-ray diffraction
Resolution: 3.27 Å
Organisms: Salmonella enterica subsp. enterica serovar Typhimurium, Homo sapiens
Chains: 4
Atoms: 11,660
Mol. weight: 174.63 kDa
Released: 25 Jan 2012

Explore 3SY2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SY2 contains 85 α-helices and 60 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: 34 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	170-174	5
α-helix	181-184	4
β-strand	206	1	1
β-strand	223-224	2	2
β-strand	237	1	1
β-strand	242-244	3	2
β-strand	247	1	3
β-strand	252	1	4
β-strand	257	1	1
β-strand	262-264	3	2
β-strand	267	1	3
β-strand	272-273	2	4
β-strand	284	1	2
β-strand	289	1	3
β-strand	294-295	2	4
β-strand	300	1	2
α-helix	313-316	4
β-strand	323-326	4	4
β-strand	329-332	4	4
α-helix	333-334	2
α-helix	339-345	7
α-helix	356-361	6
α-helix	368-382	15
α-helix	389-392	4
α-helix	393-395	3
α-helix	396-403	8
α-helix	412-432	21
α-helix	443-448	6
α-helix	450-459	10
α-helix	463-466	4
α-helix	468-476	9
α-helix	486-501	16
α-helix	506-508	3
β-strand	531-534	4	5
α-helix	535	1
β-strand	541-545	5	5
α-helix	547-554	8
β-strand	566-569	4	5
β-strand	572-574	3	5
α-helix	581-587	7
α-helix	590-592	3
α-helix	593-596	4
α-helix	598-612	15
α-helix	620-627	8
α-helix	628-630	3
α-helix	642-651	10
α-helix	656-658	3
α-helix	662-672	11
α-helix	679-696	18
α-helix	710-726	17
α-helix	728-730	3
α-helix	734-744	11
α-helix	755-768	14
α-helix	770-773	4

Chain B: 37 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	170-185	16
α-helix	192-195	4
β-strand	196	1	6
β-strand	201	1	7
β-strand	206	1	8
α-helix	207-209	3
α-helix	213-216	4
β-strand	223-224	2	9
β-strand	227	1	6
β-strand	232	1	7
β-strand	237	1	8
β-strand	242-244	3	9
β-strand	247	1	6
β-strand	252	1	7
β-strand	257	1	8
β-strand	262-264	3	9
β-strand	267	1	6
β-strand	272-273	2	7
α-helix	282-283	2
β-strand	284-289	6	9
β-strand	294-295	2	7
β-strand	300-305	6	9
α-helix	312-315	4
β-strand	322-325	4	7
β-strand	330-333	4	7
α-helix	339-346	8
α-helix	356-360	5
α-helix	365-367	3
α-helix	368-384	17
α-helix	389-392	4
α-helix	393-395	3
α-helix	396-403	8
α-helix	412-430	19
α-helix	437-441	5
α-helix	443-444	2
α-helix	445-449	5
α-helix	450-459	10
α-helix	463-466	4
α-helix	468-480	13
α-helix	486-500	15
α-helix	506-508	3
β-strand	531-534	4	10
β-strand	541-545	5	10
α-helix	547-554	8
β-strand	566-569	4	10
β-strand	572-574	3	10
α-helix	581-588	8
α-helix	590-596	7
α-helix	598-612	15
α-helix	619-626	8
α-helix	641-651	11
α-helix	652-654	3
α-helix	662-671	10
α-helix	679-697	19
β-strand	704	1	11
β-strand	707	1	11
α-helix	710-726	17
α-helix	728-730	3
α-helix	734-744	11
α-helix	751-768	18
α-helix	770-773	4
α-helix	779-781	3

Chain C: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
β-strand	22-27	6	12
β-strand	34-39	6	12
β-strand	51-56	6	12
α-helix	57-58	2
β-strand	67-70	4	12
β-strand	84	1	12
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-130	8
α-helix	133-147	15
α-helix	149-152	4

Chain D: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
β-strand	22	1	13
β-strand	26-27	2	13
β-strand	34-39	6	13
β-strand	50	1	14
β-strand	51-56	6	13
α-helix	57-58	2
β-strand	67-70	4	13
β-strand	79	1	15
β-strand	84	1	13
β-strand	85	1	15
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15
β-strand	149	1	14
α-helix	150-152	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase SopA	A, B	protein	621	Salmonella enterica subsp. enterica serovar Typhimurium	Q8ZNR3 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	C, D	protein	156	Homo sapiens	P68036 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3SY2_1 E3 ubiquitin-protein ligase SopA (chains A, B)
SNASSPSSPADWAKKLTDAVLRQKAGETLTAADRDFSNADFRNITFSKILPPSFMERDGD
IIKGFNFSNSKFTYSDISHLHFDECRFTYSTLSDVVCSNTKFSNSDMNEVFLQYSITTQQ
QPSFIDTTLKNTLIRHKANLSGVILNEPDNSSPPSVSGGGNFIRLGDIWLQMPLLWTENA
VDGFLNHEHNNGKSILMTIDSLPDKYSQEKVQAMEDLVKSLRGGRLTEACIRPVESSLVS
VLAHPPYTQSALISEWLGPVQERFFAHQCQTYNDVPLPAPDTYYQQRILPVLLDSFDRNS
AAMTTHSGLFNQVILHCMTGVDCTDGTRQKAAALYEQYLAHPAVSPHIHNGLFGNYDGSP
DWTTRAADNFLLLSSQDSDTAMMLSTDTLLTMLNPTPDTAWDNFYLLRAGENVSTAQISP
VELFRHDFPVFLAAFNQQATQRRFGELIDIILSTEEHGELNQQFLAATNQKHSTVKLIDD
ASVSRLATIFDPLLPEGKLSPAHYQHILSAYHLTDATPQKQAETLFCLSTAFARYSSSAI
FGTEHDSPPALRGYAEALMQKAWELSPAIFPSSEQFTEWSDRFHGLHGAFTCTSVVADSM
QRHARKYFPSVLSSILPLAWA

Sequence of entity 2 (C, D), FASTA

>3SY2_2 Ubiquitin-conjugating enzyme E2 L3 (chains C, D)
GSMAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFP
AEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPE
HPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVD

Primary citation

Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions. Lin, D.Y., Diao, J., Chen, J. Proc Natl Acad Sci U S A (2012) 109:1925-1930. DOI 10.1073/pnas.1115025109 · PubMed

Other PDB entries of the same protein (UniProt Q8ZNR3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ST8 1.75 Å, Structure of E3 ligase SopA bound to ubiquitin
2QYU 2.1 Å, Crystal structure of Salmonella effector protein SopA
2QZA 2.8 Å, Crystal structure of Salmonella effector protein SopA
5JW7 2.85 Å, Crystal structure of SopA-Trim56 complex

Browse structure collections

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