3NB2: E. coli O157:H7 effector protein NleL

Name: PDB 3NB2: Crystal structure of E. coli O157:H7 effector protein NleL
Published: 2010-10-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of E. coli O157:H7 effector protein NleL. Determined by X-ray diffraction at 2.1 Å resolution. Released 27 Oct 2010.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Escherichia coli
Chains: 4
Atoms: 20,830
Mol. weight: 283.2 kDa
Ligands: DTT
Released: 27 Oct 2010

Explore 3NB2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NB2 contains 136 α-helices and 120 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, 29 β-strands

Element	Residues	Length	Sheet
α-helix	178-190	13
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	247-252	6	3
β-strand	257	1	4
β-strand	262	1	1
β-strand	267-271	5	3
β-strand	276	1	4
β-strand	281	1	1
β-strand	286	1	3
β-strand	291	1	3
α-helix	296-297	2
β-strand	298	1	4
β-strand	303	1	1
β-strand	308-309	2	3
β-strand	319	1	1
β-strand	333-336	4	3
β-strand	339-342	4	3
α-helix	350-353	4
α-helix	360-362	3
α-helix	364-369	6
α-helix	373-375	3
α-helix	376-388	13
α-helix	400-410	11
α-helix	419-440	22
α-helix	444-447	4
α-helix	450-462	13
α-helix	466-469	4
α-helix	471-481	11
α-helix	488-499	12
α-helix	505-508	4
β-strand	534-537	4	5
β-strand	544-548	5	5
α-helix	550-557	8
β-strand	569-572	4	5
β-strand	575-576	2	5
α-helix	584-586	3
α-helix	587-591	5
α-helix	593-595	3
α-helix	596-604	9
α-helix	607-615	9
α-helix	619-628	10
α-helix	641-651	11
α-helix	652-654	3
β-strand	655-656	2	6
β-strand	659-660	2	6
α-helix	662-669	8
α-helix	679-697	19
α-helix	710-726	17
α-helix	728-731	4
α-helix	734-745	12
α-helix	755-768	14
α-helix	770-776	7
α-helix	779-781	3

Chain B: 36 helices, 33 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	8
β-strand	217	1	9
β-strand	222	1	7
β-strand	227	1	8
β-strand	232	1	8
β-strand	237	1	9
β-strand	242	1	7
β-strand	247-252	6	8
β-strand	257	1	9
β-strand	262	1	7
β-strand	267-271	5	8
β-strand	276	1	9
β-strand	281	1	7
β-strand	286	1	8
β-strand	291	1	8
α-helix	296-297	2
β-strand	298	1	9
β-strand	303	1	7
β-strand	308-309	2	8
β-strand	319	1	7
β-strand	333-336	4	8
β-strand	339-342	4	8
α-helix	350-353	4
α-helix	360-362	3
α-helix	364-369	6
α-helix	373-375	3
α-helix	376-388	13
α-helix	392-395	4
α-helix	400-410	11
α-helix	419-440	22
α-helix	444-447	4
α-helix	450-462	13
α-helix	466-469	4
α-helix	471-481	11
α-helix	488-498	11
α-helix	505-508	4
β-strand	513	1	10
β-strand	532	1	10
β-strand	534-537	4	11
α-helix	538	1
β-strand	544-548	5	11
α-helix	550-557	8
β-strand	569-572	4	11
β-strand	575-576	2	11
α-helix	584-586	3
α-helix	587-591	5
α-helix	593-595	3
α-helix	596-604	9
α-helix	607-615	9
α-helix	619-628	10
α-helix	641-651	11
α-helix	652-654	3
β-strand	655-656	2	12
β-strand	659-660	2	12
α-helix	662-669	8
α-helix	672-675	4
α-helix	679-696	18
β-strand	704	1	13
β-strand	707	1	13
α-helix	710-726	17
α-helix	728-731	4
α-helix	734-745	12
α-helix	755-768	14
α-helix	770-776	7
α-helix	779-781	3

Chain C: 33 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	178-190	13
α-helix	198-201	4
β-strand	202	1	14
β-strand	207	1	15
β-strand	212	1	15
β-strand	217	1	16
β-strand	222	1	14
β-strand	227	1	15
β-strand	232	1	15
β-strand	237	1	16
β-strand	242	1	14
β-strand	247-252	6	15
β-strand	257	1	16
β-strand	262	1	14
β-strand	267-271	5	15
β-strand	276	1	16
β-strand	281	1	14
β-strand	286	1	15
β-strand	291	1	15
α-helix	296-297	2
β-strand	298	1	16
β-strand	303	1	14
β-strand	308-309	2	15
β-strand	319	1	14
β-strand	333-336	4	15
β-strand	339-342	4	15
α-helix	350-353	4
α-helix	360-362	3
α-helix	364-370	7
α-helix	373-375	3
α-helix	376-387	12
α-helix	400-410	11
α-helix	415-417	3
α-helix	419-439	21
α-helix	444-447	4
α-helix	450-462	13
α-helix	466-469	4
α-helix	471-482	12
α-helix	488-499	12
α-helix	505-508	4
β-strand	534-537	4	17
β-strand	544-548	5	17
α-helix	550-557	8
β-strand	569-572	4	17
β-strand	575-576	2	17
α-helix	579-581	3
α-helix	584-590	7
α-helix	593-595	3
α-helix	596-615	20
α-helix	619-628	10
α-helix	641-651	11
α-helix	652-654	3
β-strand	655-656	2	18
β-strand	659-660	2	18
α-helix	662-669	8
α-helix	679-697	19
α-helix	710-726	17
α-helix	728-731	4
α-helix	734-745	12
α-helix	754-768	15
α-helix	770-776	7
α-helix	779-781	3

Chain D: 35 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	178-190	13
β-strand	202	1	19
β-strand	207	1	20
β-strand	212	1	20
β-strand	217	1	21
β-strand	222	1	19
β-strand	227	1	20
β-strand	232	1	20
β-strand	237	1	21
β-strand	242	1	19
β-strand	247-252	6	20
β-strand	257	1	21
β-strand	262	1	19
β-strand	267-271	5	20
β-strand	276	1	21
β-strand	281	1	19
β-strand	286	1	20
β-strand	291	1	20
α-helix	296-297	2
β-strand	298	1	21
β-strand	303	1	19
β-strand	308-309	2	20
β-strand	319	1	19
β-strand	333-336	4	20
β-strand	339-342	4	20
α-helix	350-353	4
α-helix	360-362	3
α-helix	364-370	7
α-helix	373-375	3
α-helix	376-387	12
α-helix	393-395	3
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	471-482	12
α-helix	488-499	12
α-helix	505-509	5
β-strand	534-537	4	22
α-helix	538	1
β-strand	544-548	5	22
α-helix	550-557	8
β-strand	569-572	4	22
β-strand	575-576	2	22
α-helix	579-581	3
α-helix	584-591	8
α-helix	593-595	3
α-helix	596-604	9
α-helix	607-615	9
α-helix	619-628	10
α-helix	641-651	11
α-helix	652-654	3
β-strand	655-656	2	23
β-strand	659-660	2	23
α-helix	662-669	8
α-helix	672-675	4
α-helix	679-697	19
α-helix	710-726	17
α-helix	728-731	4
α-helix	734-744	11
α-helix	754-768	15
α-helix	770-776	7
α-helix	779-781	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
secreted effector protein	A, B, C, D	protein	613	Escherichia coli	A0A0H3JDV8 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3NB2_1 secreted effector protein (chains A, B, C, D)
SQGRACLSKAELTADLIWLSANRTGEESAEELNYSGCDLSGLSLVGLNLSSVNFSGAVLD
DTDLRMSDLSQAVLENCSFKNSILNECNFCYANLSNCIIRALFENSNFSNSNLKNASFKG
SSYIQYPPILNEADLTGAIIIPGMVLSGAILGDVKELFSEKSNTINLGGCYIDLSDIQEN
ILSVLDNYTKSNKSILLTMNTSDDKYNHDKVRAAEELIKKISLDELAAFRPYVKMSLADS
FSIHPYLNNANIQQWLEPICDDFFDTIMSWFNNSIMMYMENGSLLQAGMYFERHPGAMVS
YNSSFIQIVMNGSRRDGMQERFRELYEVYLKNEKVYPVTQQSDFGLCDGSGKPDWDDDSD
LAYNWVLLSSQDDGMAMMCSLSHMVDMLSPNTSTNWMSFFLYKDGEVQNTFGYSLSNLFS
ESFPIFSIPYHKAFSQNFVSGILDILISDNELKERFIEALNSNKSDYKMIADDQQRKLAC
VWNPFLDGWELNAQHVDMIMGSHVLKDMPLRKQAEILFCLGGVFCKYSSSDMFGTEYDSP
EILRRYANGLIEQAYKTDPQVFGSVYYYNDILDRLQGRNNVFTCTAVLTDMLTEHAKESF
PEIFSLYYPVAWR

Ligands and cofactors

ID	Name	Formula	Copies
DTT	2,3-dihydroxy-1,4-dithiobutane	C4 H10 O2 S2	2

Water and common crystallization additives (GOL, MES, SO4) are not listed.

Primary citation

Biochemical and Structural Studies of a HECT-like Ubiquitin Ligase from Escherichia coli O157:H7. Lin, D.Y., Diao, J., Zhou, D. et al. J Biol Chem (2011) 286:441-449. DOI 10.1074/jbc.M110.167643 · PubMed

Other PDB entries of the same protein (UniProt A0A0H3JDV8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
3SQV 3.3 Å, Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7

Browse structure collections

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