4A4B: E3 ubiquitin-protein ligase cbl

Structure of modified phosphoTyr371-c-Cbl-UbcH5B-ZAP-70 complex. Determined by X-ray diffraction at 2.79 Å resolution. Released 25 Jan 2012.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 4,284
Mol. weight: 63.41 kDa
Ligands: ZN, CA
Released: 25 Jan 2012

Explore 4A4B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4A4B contains 30 α-helices and 22 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: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	53-70	18
α-helix	84-101	18
α-helix	106-110	5
α-helix	113-136	24
α-helix	137-141	5
α-helix	146-168	23
α-helix	176-178	3
α-helix	184-194	11
β-strand	199-201	3	1
α-helix	202-212	11
α-helix	218-228	11
β-strand	235-237	3	1
α-helix	238-248	11
α-helix	251-253	3
α-helix	254-258	5
α-helix	259-263	5
β-strand	268	1	2
α-helix	274-282	9
β-strand	290-295	6	2
β-strand	303-308	6	2
β-strand	314-317	4	2
α-helix	324-333	10
β-strand	339-340	2	2
α-helix	350-353	4
α-helix	355-358	4
β-strand	360	1	3
α-helix	365-374	10
β-strand	380	1	4
β-strand	388	1	4
β-strand	391-394	4	5
β-strand	399-400	2	5
α-helix	402-409	8
β-strand	425-428	4	5
β-strand	430	1	3

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	2
α-helix	9-11	3

Chain C: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	17-18	2
β-strand	21-26	6	6
β-strand	29-38	10	6
α-helix	39-40	2
β-strand	49-55	7	6
α-helix	64-65	2
β-strand	66-69	4	6
β-strand	78	1	7
β-strand	83	1	6
β-strand	84	1	7
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-141	11
α-helix	142-146	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase cbl	A	protein	391	HOMO SAPIENS	P22681 (AlphaFold model)
Tyrosine-protein kinase zap-70	B	protein	12	HOMO SAPIENS	P43403 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D2	C	protein	147	HOMO SAPIENS	P62837 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4A4B_1 E3 UBIQUITIN-PROTEIN LIGASE CBL (chains A)
GSPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEG
KMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAE
LKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMAL
KSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKF
IHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRN
QNPDLTGLCEPTPQDHIKVTQEQFELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSC
LTSWQESEGQGCPFCRCEIKGTEPIVVDPFD

Sequence of entity 2 (B), FASTA

>4A4B_2 TYROSINE-PROTEIN KINASE ZAP-70 (chains B)
TLNSDGYTPEPA

Sequence of entity 3 (C), FASTA

>4A4B_3 UBIQUITIN-CONJUGATING ENZYME E2 D2 (chains C)
MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLV
PEIARIYKTDREKYNRIAREWTQKYAM

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CA	Calcium ion	Ca	1

Primary citation

Structural Basis for Autoinhibition and Phosphorylation-Dependent Activation of C-Cbl. Dou, H., Buetow, L., Hock, A. et al. Nat Struct Mol Biol (2012) 19:184. DOI 10.1038/NSMB.2231 · PubMed

Other PDB entries of the same protein (UniProt P22681 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BUX 1.35 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in c-Met
3BUW 1.45 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk
7SIY 1.48 Å, cCBL TKB domain in complex with pZAP70 peptide
5HKY 1.8 Å, Crystal structure of c-Cbl TKBD domain in complex with SPRY2 peptide (36-60, pY55)…
5HKZ 1.8 Å, Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (36-60, pY55) Refined to…
5HKX 1.85 Å, Crystal Structure of c-Cbl TKBD-RING domains (Y371E mutant) Refined to 1.85 A Resolution
3PLF 1.92 Å, Reverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain
2Y1N 2.0 Å, Structure of c-Cbl-ZAP-70 peptide complex
3BUM 2.0 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty2
3BUN 2.0 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Sprouty4
9ERZ 2.02 Å, Structure of CBL-TKBD bound to Ubiquitin-fused CBLock peptide
1YVH 2.05 Å, Crystal Structure of the c-Cbl TKB Domain in Complex with the APS pTyr-618 Phosphopeptide

Browse structure collections

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