3ZNI: E3 ubiquitin-protein ligase cbl-B

Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex. Determined by X-ray diffraction at 2.21 Å resolution. Released 10 Jul 2013.

Method

X-ray diffraction

Resolution

2.21 Å

Organism

HOMO SAPIENS

Chains

16

Atoms

20,546

Mol. weight

291.87 kDa

Ligands

ZN, CA

Released

10 Jul 2013

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

Secondary structure: helices and β-sheets

3ZNI contains 136 α-helices and 127 β-strands across 16 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, 14 β-strands

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

>3ZNI_1 E3 UBIQUITIN-PROTEIN LIGASE CBL-B (chains A, E, I, M)
GSPKQAAADRRTVEKTWKLMDKVVRLCQNPKLQLKNSPPYILDILPDTYQHLRLILSKYD
DNQKLAQLSENEYFKIYIDSLMKKSKRAIRLFKEGKERMYEEQSQDRRNLTKLSLIFSHM
LAEIKAIFPNGQFQGDNFRITKADAAEFWRKFFGDKTIVPWKVFRQCLHEVHQISSGLEA
MALKSTIDLTCNDYISVFEFDIFTRLFQPWGSILRNWNFLAVTHPGYMAFLTYDEVKARL
QKYSTKPGSYIFRLSCTRLGQWAIGYVTGDGNILQTIPHNKPLFQALIDGSREGFYLYPD
GRSYNPDLTGLCEPTPHDHIKVTQEQFELYCEMGSTFQLCKICAENDKDVKIEPCGHLMC
TSCLTAWQESDGQGCPFCRCEIKGTEPIIVDPFD

>3ZNI_2 TYROSINE-PROTEIN KINASE ZAP-70 (chains B, F, J, N)
TLNSDGYTPEPA

>3ZNI_3 UBIQUITIN-CONJUGATING ENZYME E2 D2 (chains C, G, K, O)
ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYP
FKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVP
EIARIYKTDREKYNRIAREWTQKYAM

>3ZNI_4 POLYUBIQUITIN-C (chains D, H, L, P)
GSGGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRT
LSDYNIQKESTLHLVLRLRGG

Ligands and cofactors

Water and common crystallization additives (EDO) are not listed.

Primary citation

Essentiality of a Non-Ring Element in Priming Donor Ubiquitin for Catalysis by a Monomeric E3. Dou, H., Buetow, L., Sibbet, G.J. et al. Nat Struct Mol Biol (2013) 20:982. DOI 10.1038/NSMB.2621 · PubMed

Related structures

Other PDB entries of the same protein (UniProt Q13191 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 8QTG 1.42 Å, Crystal structure of CBL-b in complex with an allosteric inhibitor (compound 9)
• 8QTJ 1.52 Å, Crystal structure of Cbl-b in complex with an allosteric inhibitor (compound 30)
• 2OOA 1.56 Å, crystal structure of the UBA domain from Cbl-b ubiquitin ligase
• 9FQJ 1.56 Å, E3 ligase Cbl-b in complex with a carbamate scaffold inhibitor (compound 12)
• 9XZD 1.65 Å, E3 ubiquitin-protein ligase CBL-B in complex with compound 8
• 9I0B 1.66 Å, E3 ubiquitin ligase CBL-B in complex with inhibitor
• 2J6F 1.7 Å, N-terminal SH3 domain of cms (CD2AP human homolog) bound to cbl-B peptide
• 9XZB 1.75 Å, E3 ubiquitin-protein ligase CBL-B in complex with compound 2
• 8VW5 1.76 Å, Crystal structure of Cbl-b TKB bound to compound 2
• 10ZJ 1.77 Å, Structure of Cbl-B bound to compound 8
• 9FQH 1.79 Å, E3 ligase Cbl-b in complex with a triazolone core inhibitor (compound 1)
• 9XZC 1.8 Å, E3 ubiquitin-protein ligase CBL-B in complex with compound 6

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