5C7M: E3 ligase itch with a ub variant

Crystal structure of E3 ligase itch with a ub variant. Determined by X-ray diffraction at 3.03 Å resolution. Released 16 Mar 2016.

Method: X-ray diffraction
Resolution: 3.03 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,871
Mol. weight: 66.57 kDa
Released: 16 Mar 2016

Explore 5C7M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C7M contains 26 α-helices and 30 β-strands across 3 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: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	528-542	15
β-strand	547-551	5	1
α-helix	557-567	11
α-helix	570-573	4
β-strand	576-580	5	1
α-helix	593-604	12
α-helix	607-609	3
β-strand	612-613	2	2
β-strand	622	1	3
β-strand	623-624	2	2
α-helix	628-630	3
α-helix	634-651	18
β-strand	659	1	3
α-helix	661-667	7
α-helix	674-680	7
α-helix	682-693	12
α-helix	696-699	4
β-strand	704	1	4
β-strand	706-709	4	5
β-strand	716-719	4	5
α-helix	724-726	3
β-strand	728	1	4
α-helix	734-745	12
α-helix	751-764	14
α-helix	767-770	4
α-helix	775-783	9
α-helix	790-795	6
β-strand	797-800	4	6
α-helix	807-818	12
α-helix	821-832	12
α-helix	842-844	3
β-strand	846	1	7
β-strand	851	1	7
β-strand	854-858	5	6
α-helix	865-866	2
β-strand	867-869	3	6
β-strand	874-877	4	6
α-helix	883-896	14

Chain B: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
β-strand	41-44	4	8
β-strand	49	1	8
β-strand	55	1	9
β-strand	66-71	6	8

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	10
β-strand	12-16	5	10
β-strand	22	1	11
α-helix	23-33	11
β-strand	41-45	5	10
β-strand	48-49	2	10
α-helix	50-51	2
β-strand	55	1	11
α-helix	56-59	4
β-strand	66-71	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Itchy homolog	A	protein	394	Homo sapiens	Q96J02 (AlphaFold model)
Polyubiquitin-C	B, C	protein	84	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5C7M_1 E3 ubiquitin-protein ligase Itchy homolog (chains A)
MHHHHHHSSGRENLYFQGYVRDFKAKVQYFRFWCQQLAMPQHIKITVTRKTLFEDSFQQI
MSFSPQDLRRRLWVIFPGEEGLDYGGVAREWFFLLSHEVSNPMYCLFEYAGKDNYCLQIN
PASYINPDHLKYFRFIGRFIAMALFHGKFIDTGFSLPFYKRILNKPVGLKDLESIDPEFY
NSLIWVKENNIEECDLEMYFSVDKEILGEIKSHDLKPNGGNILVTEENKEEYIRMVAEWR
LSRGVEEQTQAFFEGFNEILPQQYLQYFDAKELEVLLCGMQEIDLNDWQRHAIYRRYART
SKQIMWFWQFVKEIDNEKRMRLLQFVTGTCRLPVGGFADLMGSNGPQKFCIEKVGKENWL
PRSHTCFNRLDLPPYKSYEQLKEKLLFAIEETEG

Sequence of entity 2 (B, C), FASTA

>5C7M_2 Polyubiquitin-C (chains B, C)
MHILVKTLRGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLLFGGNKLEDGRTLSDYN
IQKESNLYLLLRRLGSKFHHHHHH

Primary citation

System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes. Zhang, W., Wu, K.P., Sartori, M.A. et al. Mol Cell (2016) 62:121-136. DOI 10.1016/j.molcel.2016.02.005 · PubMed

Other PDB entries of the same protein (UniProt Q96J02 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CQ2 1.4 Å, Crystal Structure of tandem WW domains of ITCH in complex with TXNIP peptide
5DZD 1.57 Å, Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide
5DWS 1.65 Å, Crystal Structure of ITCH WW3 domain in complex with TXNIP peptide
5SXP 1.65 Å, Structural basis for the interaction between itch prr and beta-pix
2NQ3 1.8 Å, Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase
2P4R 2.0 Å, Structural basis for a novel interaction between AIP4 and beta-PIX
4ROF 2.03 Å, Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide
3TUG 2.27 Å, Crystal structure of the HECT domain of ITCH E3 ubiquitin ligase
2DMV Solution structure of the second ww domain of Itchy homolog E3 ubiquitin protein ligase…
2KYK The sandwich region between two LMP2A PY motif regulates the interaction between…
2YSF Solution structure of the fourth WW domain from the human E3 ubiquitin-protein ligase…

Browse structure collections

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