4IP3: Complex structure of OspI and Ubc13

Complex structure of OspI and Ubc13. Determined by X-ray diffraction at 2.3 Å resolution. Released 20 Mar 2013.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Shigella flexneri, Homo sapiens
Chains: 2
Atoms: 2,837
Mol. weight: 42.81 kDa
Released: 20 Mar 2013

Explore 4IP3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IP3 contains 22 α-helices and 18 β-strands across 2 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: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	24-32	9
α-helix	38-53	16
α-helix	62-74	13
β-strand	79	1	1
α-helix	80-83	4
α-helix	84-86	3
α-helix	87-97	11
α-helix	99-102	4
β-strand	107-108	2	2
α-helix	109-110	2
β-strand	114	1	3
α-helix	115-127	13
β-strand	135-140	6	2
β-strand	145-151	7	2
β-strand	156-159	4	2
β-strand	160	1	4
β-strand	165	1	4
α-helix	174-176	3
β-strand	180	1	3
α-helix	181-182	2
β-strand	186-190	5	2
α-helix	194-202	9
α-helix	204-207	4
α-helix	210	1
β-strand	211	1	1

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
α-helix	19-20	2
β-strand	23-27	5	5
β-strand	34-40	7	5
α-helix	41-42	2
β-strand	51-57	7	5
α-helix	66-67	2
β-strand	68-71	4	5
β-strand	80	1	6
β-strand	85	1	5
β-strand	86	1	6
α-helix	89-91	3
α-helix	101-113	13
α-helix	124-131	8
α-helix	133-147	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ORF169b	A	protein	214	Shigella flexneri	Q8VSD5 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B	protein	172	Homo sapiens	P61088 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4IP3_1 ORF169b (chains A)
GSMINGVSLQGTAGYEAHTEEGNVNVKKLLESLNSKSLGDMDKDSELAATLQKMINPSGG
DGNASGCALHACMAMLGYGVREAPVPNEISEYMTGFFHRHLEQIDSEGIVSHPNETYSKF
RERIAENILQNTSKGSVVMISIEQATHWIAGFNDGEKIMFLDVQTGKGFNLYDPVEKSPD
AFVDENSSVQVIHVSDQEFDHYANSSSWKSKRLC

Sequence of entity 2 (B), FASTA

>4IP3_2 Ubiquitin-conjugating enzyme E2 N (chains B)
MGSSHHHHHHSSGLVPRGSHMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIA
GPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQ
IRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Primary citation

Structure Analysis of Ubc13 Inactivation. Fu, P., Jin, M., Zhang, X. et al. To be published.

Other PDB entries of the same protein (UniProt Q8VSD5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3B21 2.01 Å, Crystal structure of OspI from Shigella flexineri
4XZX 2.2 Å, Shigella flexneri effector OspI C62S mutant
3W31 2.96 Å, Structual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI
3W30 2.99 Å, Structual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI

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