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- PDB-3plf: Reverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain -

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Basic information

Entry
Database: PDB / ID: 3plf
TitleReverse Binding Mode of MetRD peptide complexed with c-Cbl TKB domain
Components
  • E3 ubiquitin-protein ligase CBL
  • MetRD peptide
KeywordsPROTEIN BINDING/LIGASE / c-Cbl TKB domain / Met / reverse binding / PROTEIN BINDING-LIGASE complex
Function / homology
Function and homology information


regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to starvation ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / Interleukin-6 signaling / response to starvation / negative regulation of epidermal growth factor receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / response to testosterone / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / protein autoubiquitination / FLT3 signaling by CBL mutants / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ephrin receptor binding / phosphotyrosine residue binding / cellular response to nerve growth factor stimulus / InlB-mediated entry of Listeria monocytogenes into host cell / response to activity / response to gamma radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / EGFR downregulation / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Constitutive Signaling by EGFRvIII / Spry regulation of FGF signaling / RING-type E3 ubiquitin transferase / Negative regulation of MET activity / cilium / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / positive regulation of receptor-mediated endocytosis / SH3 domain binding / protein polyubiquitination / ubiquitin-protein transferase activity / Signaling by CSF1 (M-CSF) in myeloid cells / male gonad development / ubiquitin protein ligase activity / Cargo recognition for clathrin-mediated endocytosis / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / cellular response to hypoxia / growth cone / ubiquitin-dependent protein catabolic process / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cadherin binding / symbiont entry into host cell / membrane raft / focal adhesion / calcium ion binding / DNA damage response / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / plasma membrane / cytosol
Similarity search - Function
Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. ...Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal helical / Adaptor protein Cbl, EF hand-like / Adaptor protein Cbl, SH2-like domain / Adaptor protein Cbl, PTB domain / Adaptor protein Cbl / CBL proto-oncogene N-terminal domain 1 / CBL proto-oncogene N-terminus, EF hand-like domain / CBL proto-oncogene N-terminus, SH2-like domain / Cbl-type phosphotyrosine-binding (Cbl-PTB) domain profile. / Adaptor protein Cbl, N-terminal domain superfamily / Transcription Elongation Factor S-II; Chain A / UBA/TS-N domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / SH2 domain / SHC Adaptor Protein / UBA-like superfamily / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CBL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsSun, Q. / Sivaraman, J.
CitationJournal: Febs Lett. / Year: 2011
Title: An adjacent arginine, and the phosphorylated tyrosine in the c-Met receptor target sequence, dictates the orientation of c-Cbl binding
Authors: Sun, Q. / Ng, C. / Guy, G.R. / Sivaraman, J.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MetRD peptide
B: E3 ubiquitin-protein ligase CBL
C: MetRD peptide
D: E3 ubiquitin-protein ligase CBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,36510
Polymers79,1434
Non-polymers2226
Water10,521584
1
A: MetRD peptide
B: E3 ubiquitin-protein ligase CBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7186
Polymers39,5712
Non-polymers1464
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-5 kcal/mol
Surface area14760 Å2
MethodPISA
2
C: MetRD peptide
D: E3 ubiquitin-protein ligase CBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6474
Polymers39,5712
Non-polymers762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-5 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.743, 104.483, 60.548
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12A
22C

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUBB49 - 34927 - 327
21GLYGLYLEULEUDD49 - 34927 - 327
12ARGARGALAALAAA1002 - 10055 - 8
22ARGARGALAALACC1002 - 10055 - 8

NCS ensembles :
ID
1
2

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Components

#1: Protein/peptide MetRD peptide


Mass: 1379.345 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This is a designed peptide (two residues switched position) based on human Met protein sequence.
#2: Protein E3 ubiquitin-protein ligase CBL / Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / Signal ...Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / Signal transduction protein CBL


Mass: 38192.090 Da / Num. of mol.: 2 / Fragment: TKB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: c-Cbl / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P22681, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.65 % / Mosaicity: 0.673 °
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: 100mM Bis-tris propane, 50mM ammonium sulfate, pH 6.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker AXIOM 200 / Detector: CCD / Date: Jun 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 48545 / Num. obs: 48545 / % possible obs: 97.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Χ2: 0.4 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.92-1.992.90.20345750.273192.5
1.99-2.073.10.16446640.325194.2
2.07-2.163.20.13347830.354195.7
2.16-2.283.40.11247910.376196.7
2.28-2.423.50.09148650.393198
2.42-2.613.70.07649020.359199.4
2.61-2.8740.0749770.368199.8
2.87-3.284.50.06349510.4221100
3.28-4.145.20.0649880.4741100
4.14-505.90.05750490.475199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BUX

3bux


Resolution: 1.92→47.08 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1889 / WRfactor Rwork: 0.1681 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9004 / SU B: 5.31 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1097 / SU Rfree: 0.1242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1802 2462 5.1 %RANDOM
Rwork0.1591 ---
all0.1602 ---
obs0.1602 46063 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.64 Å2 / Biso mean: 26.9618 Å2 / Biso min: 8.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0.24 Å2
2---0.83 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.92→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 6 584 5612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225152
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9616954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.515606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05723.279244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76515930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5011536
X-RAY DIFFRACTIONr_chiral_restr0.1510.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213878
X-RAY DIFFRACTIONr_mcbond_it2.1511.53042
X-RAY DIFFRACTIONr_mcangle_it3.26224916
X-RAY DIFFRACTIONr_scbond_it5.05832110
X-RAY DIFFRACTIONr_scangle_it7.1144.52038
X-RAY DIFFRACTIONr_rigid_bond_restr3.22935152
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2471LOOSE POSITIONAL0.315
1B2471LOOSE THERMAL2.7910
2A40LOOSE POSITIONAL0.35
2A40LOOSE THERMAL1.8610
LS refinement shellResolution: 1.923→1.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 147 -
Rwork0.188 3138 -
all-3285 -
obs--88.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1077-0.02240.00530.0714-0.03160.0806-0.00170.01040.00520.00210.0014-0.0025-0.00250.00140.00030.00040.0004-0.00060.0203-0.00190.010614.58461.00590.7374
20.02-0.0109-0.00260.0607-0.00120.00060.00130.0073-0.00170.002-0.0017-0.0084000.00050.00210.0002-0.00020.01780.00140.011411.5538-0.328330.2172
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B49 - 349
2X-RAY DIFFRACTION2D49 - 349

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