3SQV: Secreted effector protein

Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7. Determined by X-ray diffraction at 3.3 Å resolution. Released 25 Jan 2012.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: Escherichia coli, Homo sapiens
Chains: 4
Atoms: 10,987
Mol. weight: 176.61 kDa
Released: 25 Jan 2012

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

Secondary structure: helices and β-sheets

3SQV contains 75 α-helices and 80 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: 32 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	178-190	13
α-helix	198-201	4
β-strand	202	1	1
β-strand	207	1	2
β-strand	212	1	3
β-strand	217	1	4
β-strand	222	1	1
β-strand	227	1	2
β-strand	232	1	3
β-strand	237	1	4
β-strand	242	1	1
β-strand	247	1	2
β-strand	252	1	3
β-strand	257	1	4
β-strand	262	1	1
β-strand	267	1	2
β-strand	271	1	3
β-strand	276	1	4
β-strand	281	1	1
β-strand	286	1	2
β-strand	291	1	3
β-strand	298	1	4
β-strand	303	1	1
β-strand	308-309	2	2
α-helix	310	1
β-strand	319	1	1
α-helix	321-323	3
β-strand	333-336	4	2
β-strand	339-342	4	2
α-helix	352-354	3
α-helix	364-368	5
α-helix	373-375	3
α-helix	376-387	12
α-helix	400-410	11
α-helix	419-439	21
α-helix	444-447	4
α-helix	450-462	13
α-helix	466-469	4
α-helix	471-483	13
α-helix	488-498	11
α-helix	505-508	4
β-strand	535-537	3	5
β-strand	544-547	4	5
α-helix	550-555	6
β-strand	569-572	4	5
β-strand	575-576	2	5
α-helix	579-581	3
α-helix	584-590	7
α-helix	596-605	10
α-helix	608-615	8
α-helix	619-625	7
α-helix	626-628	3
α-helix	644-651	8
β-strand	655-656	2	6
β-strand	659-660	2	6
α-helix	662-668	7
α-helix	679-696	18
α-helix	710-724	15
α-helix	728-730	3
α-helix	734-744	11
α-helix	754-768	15
α-helix	770-773	4
α-helix	779-781	3

Chain B: 33 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	178-190	13
α-helix	198-201	4
β-strand	202	1	7
β-strand	207	1	8
β-strand	212	1	9
β-strand	217	1	10
β-strand	222	1	7
β-strand	227	1	8
β-strand	232	1	9
β-strand	237	1	10
β-strand	242	1	7
β-strand	247	1	8
β-strand	252	1	9
β-strand	257	1	10
β-strand	262	1	7
β-strand	267	1	8
β-strand	271	1	9
β-strand	276	1	10
β-strand	281	1	7
β-strand	286	1	8
β-strand	291	1	9
β-strand	298	1	10
β-strand	303	1	7
β-strand	308-309	2	8
α-helix	310	1
β-strand	319	1	7
α-helix	321	1
α-helix	323	1
β-strand	333-336	4	8
β-strand	339-342	4	8
α-helix	352-354	3
α-helix	364-369	6
α-helix	373-375	3
α-helix	376-387	12
α-helix	400-410	11
α-helix	419-439	21
α-helix	444-447	4
α-helix	450-462	13
α-helix	466-469	4
α-helix	471-483	13
α-helix	488-498	11
α-helix	505-508	4
β-strand	534-537	4	11
β-strand	544-548	5	11
α-helix	550-555	6
β-strand	569-572	4	11
β-strand	575-576	2	11
α-helix	579-581	3
α-helix	584-590	7
α-helix	596-605	10
α-helix	608-615	8
α-helix	619-625	7
α-helix	626-628	3
α-helix	641-651	11
β-strand	655-656	2	12
β-strand	659-660	2	12
α-helix	662-668	7
α-helix	679-696	18
α-helix	710-724	15
α-helix	728-730	3
α-helix	734-744	11
α-helix	754-768	15
α-helix	770-773	4
α-helix	779-781	3

Chain C: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	1-16	16
β-strand	22-26	5	13
β-strand	34	1	14
β-strand	36-39	4	13
β-strand	53	1	15
β-strand	56	1	14
β-strand	67	1	14
β-strand	70	1	15
β-strand	79	1	16
β-strand	85	1	16
α-helix	102-110	9
α-helix	126-131	6
α-helix	134-137	4
α-helix	140-146	7

Chain D: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	1-16	16
β-strand	22-26	5	17
β-strand	34	1	18
β-strand	36-39	4	17
β-strand	51-53	3	17
β-strand	56	1	18
β-strand	67	1	18
β-strand	70	1	17
β-strand	79	1	19
β-strand	85	1	19
α-helix	102-110	9
α-helix	126-131	6
α-helix	134-137	4
α-helix	140-147	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
secreted effector protein	A, B	protein	616	Escherichia coli	A0A0H3JDV8 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	C, D	protein	156	Homo sapiens	P68036 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3SQV_1 secreted effector protein (chains A, B)
SNASQGRACLSKAELTADLIWLSANRTGEESAEELNYSGCDLSGLSLVGLNLSSVNFSGA
VLDDTDLRMSDLSQAVLENCSFKNSILNECNFCYANLSNCIIRALFENSNFSNSNLKNAS
FKGSSYIQYPPILNEADLTGAIIIPGMVLSGAILGDVKELFSEKSNTINLGGCYIDLSDI
QENILSVLDNYTKSNKSILLTMNTSDDKYNHDKVRAAEELIKKISLDELAAFRPYVKMSL
ADSFSIHPYLNNANIQQWLEPICDDFFDTIMSWFNNSIMMYMENGSLLQAGMYFERHPGA
MVSYNSSFIQIVMNGSRRDGMQERFRELYEVYLKNEKVYPVTQQSDFGLCDGSGKPDWDD
DSDLAYNWVLLSSQDDGMAMMCSLSHMVDMLSPNTSTNWMSFFLYKDGEVQNTFGYSLSN
LFSESFPIFSIPYHKAFSQNFVSGILDILISDNELKERFIEALNSNKSDYKMIADDQQRK
LACVWNPFLDGWELNAQHVDMIMGSHVLKDMPLRKQAEILFCLGGVFCKYSSSDMFGTEY
DSPEILRRYANGLIEQAYKTDPQVFGSVYYYNDILDRLQGRNNVFTCTAVLTDMLTEHAK
ESFPEIFSLYYPVAWR

Sequence of entity 2 (C, D), FASTA

>3SQV_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 A0A0H3JDV8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NB2 2.1 Å, Crystal structure of E. coli O157:H7 effector protein NleL
3NAW 2.5 Å, Crystal structure of E. coli O157:H7 effector protein NleL
8ST9 2.5 Å, Structure of E3 ligase NleL bound to ubiquitin

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