3PLF: Reverse Binding Mode of MetRD peptide

Reverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain. Determined by X-ray diffraction at 1.92 Å resolution. Released 1 Dec 2010.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,612
Mol. weight: 79.36 kDa
Ligands: CA
Released: 1 Dec 2010

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

Secondary structure: helices and β-sheets

3PLF contains 36 α-helices and 14 β-strands across 2 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 B: 17 helices, 7 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	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	274-282	9
β-strand	290-295	6	2
β-strand	303-308	6	2
β-strand	314-317	4	2
α-helix	324-334	11
β-strand	339-340	2	2

Chain D: 19 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	53-70	18
α-helix	73-75	3
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	170-172	3
α-helix	176-178	3
α-helix	184-194	11
β-strand	199-201	3	3
α-helix	202-210	9
α-helix	218-228	11
β-strand	235-237	3	3
α-helix	238-247	10
α-helix	251-253	3
α-helix	254-258	5
α-helix	259-263	5
β-strand	268	1	4
α-helix	274-281	8
α-helix	282-284	3
β-strand	290-295	6	4
β-strand	303-308	6	4
β-strand	314-317	4	4
α-helix	324-334	11
β-strand	339-340	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MetRD peptide	A, C	protein	11
E3 ubiquitin-protein ligase CBL	B, D	protein	329	Homo sapiens	P22681 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3PLF_1 MetRD peptide (chains A, C)
NESVRYDATFP

Sequence of entity 2 (B, D), FASTA

>3PLF_2 E3 ubiquitin-protein ligase CBL (chains B, D)
GSLIGLMKDAFQPHHHHHHHLSPHPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPP
YILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYE
ENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPW
KSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLA
VTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNK
PLFQALIDGFREGFYLFPDGRNQNPDLTG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

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

Primary citation

An adjacent arginine, and the phosphorylated tyrosine in the c-Met receptor target sequence, dictates the orientation of c-Cbl binding. Sun, Q., Ng, C., Guy, G.R. et al. FEBS Lett (2011) 585:281-285. DOI 10.1016/j.febslet.2010.11.060 · 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
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
2CBL 2.1 Å, N-terminal domain of cbl in complex with its binding site on zap-70

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