5O76: PhosphoY371 c-CBL

Name: PDB 5O76: Structure of phosphoY371 c-CBL in complex with ZAP70-peptide and UbV.pCBL ubiquitin variant
Published: 2017-11-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of phosphoY371 c-CBL in complex with ZAP70-peptide and UbV.pCBL ubiquitin variant. Determined by X-ray diffraction at 2.47 Å resolution. Released 1 Nov 2017.

Method: X-ray diffraction
Resolution: 2.47 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,879
Mol. weight: 111.58 kDa
Ligands: ZN, CA
Released: 1 Nov 2017

Explore 5O76 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O76 contains 50 α-helices and 47 β-strands across 5 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	53-70	18
α-helix	84-101	18
α-helix	106-110	5
α-helix	113-134	22
α-helix	138-140	3
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	202-212	11
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	268-271	4	2
α-helix	274-281	8
α-helix	282-284	3
β-strand	290-295	6	2
β-strand	303-307	5	2
β-strand	315-317	3	2
α-helix	324-333	10
β-strand	339-340	2	2
α-helix	357-358	2
β-strand	359-362	4	3
α-helix	363-364	2
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	402-410	9
β-strand	415	1	6
β-strand	422	1	6
β-strand	425-428	4	5
β-strand	429-432	4	3

Chain C: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	53-70	18
α-helix	73-75	3
α-helix	84-101	18
α-helix	106-111	6
α-helix	113-136	24
α-helix	146-168	23
α-helix	184-193	10
β-strand	199-201	3	7
α-helix	202-212	11
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	268-269	2	8
α-helix	274-281	8
β-strand	290-295	6	8
β-strand	303-307	5	8
β-strand	315-317	3	8
α-helix	324-334	11
β-strand	339-340	2	8
α-helix	345-347	3
α-helix	350-352	3
α-helix	357-358	2
β-strand	359-362	4	9
α-helix	363-364	2
α-helix	365-373	9
β-strand	380	1	10
β-strand	388	1	10
β-strand	391-394	4	11
β-strand	399-400	2	11
α-helix	402-411	10
β-strand	415	1	12
β-strand	422	1	12
β-strand	425-428	4	11
β-strand	429-432	4	9

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7-8	2	8

Chain E: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	13
α-helix	12	1
β-strand	13-17	5	13
β-strand	22	1	14
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	13
β-strand	48-49	2	13
α-helix	50-51	2
β-strand	55	1	14
α-helix	57-59	3
β-strand	66-71	6	13

Chain F: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	15
β-strand	13-17	5	15
β-strand	22	1	16
α-helix	23-34	12
β-strand	41-45	5	15
β-strand	48-49	2	15
α-helix	50-51	2
β-strand	55	1	16
β-strand	66-71	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase CBL	A, C	protein	391	Homo sapiens	P22681 (AlphaFold model)
Tyrosine protein kinase ZAP70 peptide	B, D	protein	12	Homo sapiens	P43403 (AlphaFold model)
UbV.pCBL ubiquitin variant	E, F	protein	82	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>5O76_1 E3 ubiquitin-protein ligase CBL (chains A, C)
GSPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEG
KMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAE
LKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMAL
KSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKF
IHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRN
QNPDLTGLCEPTPQDHIKVTQEQFELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSC
LTSWQESEGQGCPFCRCEIKGTEPIVVDPFD

Sequence of entity 2 (B, D), FASTA

>5O76_2 Tyrosine protein kinase ZAP70 peptide (chains B, D)
TLNSDGYTPEPA

Sequence of entity 3 (E, F), FASTA

>5O76_3 UbV.pCBL ubiquitin variant (chains E, F)
GSGGSMHIFVKTGIGPIISLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFVGKQLEDGRT
LSDYNIRKASYLYLVLRLHRSS

Ligands and cofactors

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

Primary citation

A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants. Gabrielsen, M., Buetow, L., Nakasone, M.A. et al. Mol Cell (2017) 68:456-470.e10. DOI 10.1016/j.molcel.2017.09.027 · 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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