2Y1N: C-Cbl-ZAP-70 peptide complex

Structure of c-Cbl-ZAP-70 peptide complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 18 Jan 2012.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 6,623
Mol. weight: 92.89 kDa
Ligands: CA, ZN
Released: 18 Jan 2012

Explore 2Y1N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Y1N contains 47 α-helices and 32 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: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	54-70	17
α-helix	84-101	18
α-helix	106-111	6
α-helix	113-136	24
α-helix	137-141	5
α-helix	146-168	23
α-helix	170-172	3
α-helix	176-178	3
α-helix	184-194	11
β-strand	199-201	3	1
α-helix	202-210	9
α-helix	218-228	11
β-strand	235-237	3	1
α-helix	238-247	10
α-helix	251-253	3
α-helix	254-258	5
α-helix	259-263	5
β-strand	268	1	2
α-helix	274-281	8
α-helix	282-284	3
β-strand	290-295	6	2
β-strand	300	1	3
β-strand	302	1	3
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	345-347	3
α-helix	365-371	7
α-helix	372-376	5
β-strand	380	1	4
β-strand	388	1	4
β-strand	391-394	4	5
β-strand	399-400	2	5
α-helix	402-411	10
β-strand	415	1	6
β-strand	422	1	6
β-strand	425-428	4	5

Chains B and D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7	1
β-strand	8	1	2
α-helix	9-11	3

Chain C: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	53-71	19
α-helix	80	1
α-helix	84-101	18
α-helix	106-111	6
α-helix	113-136	24
α-helix	137-141	5
α-helix	146-168	23
α-helix	170-172	3
α-helix	184-194	11
β-strand	199-201	3	7
α-helix	202-210	9
α-helix	218-228	11
β-strand	235-237	3	7
α-helix	238-247	10
α-helix	251-253	3
α-helix	254-258	5
α-helix	259-263	5
β-strand	268	1	8
α-helix	274-280	7
β-strand	290-295	6	8
β-strand	303-308	6	8
β-strand	314-317	4	8
α-helix	324-333	10
β-strand	339-340	2	8
α-helix	345-348	4
α-helix	365-371	7
α-helix	372-376	5
β-strand	380	1	9
β-strand	388	1	9
β-strand	391-394	4	10
β-strand	399-400	2	10
α-helix	402-411	10
β-strand	415	1	11
β-strand	422	1	11
β-strand	425-428	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase	A, C	protein	389	HOMO SAPIENS	P22681 (AlphaFold model)
Tyrosine-protein kinase zap-70 zap-70,70 kda zeta-associated protein, syk-related tyrosine kinase	B, D	protein	12	HOMO SAPIENS	P43403 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2Y1N_1 E3 UBIQUITIN-PROTEIN LIGASE (chains A, C)
PPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKM
ETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELK
GIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKS
TIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIH
KPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQN
PDLTGLCEPTPQDHIKVTQEQYELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLT
SWQESEGQGCPFCRCEIKGTEPIVVDPFD

Sequence of entity 2 (B, D), FASTA

>2Y1N_2 TYROSINE-PROTEIN KINASE ZAP-70 ZAP-70,70 KDA ZETA-ASSOCIATED PROTEIN, SYK-RELATED TYROSINE KINASE (chains B, D)
TLNSDGYTPEPA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
ZN	Zinc ion	Zn	4

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
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
2CBL 2.1 Å, N-terminal domain of cbl in complex with its binding site on zap-70

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