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- PDB-4a49: Structure of phosphoTyr371-c-Cbl-UbcH5B complex -

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Basic information

Entry
Database: PDB / ID: 4a49
TitleStructure of phosphoTyr371-c-Cbl-UbcH5B complex
Components
  • E3 ubiquitin-protein ligase CBL
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE
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 / entry of bacterium into host cell / (E3-independent) E2 ubiquitin-conjugating enzyme / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / E2 ubiquitin-conjugating enzyme / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling ...regulation of platelet-derived growth factor receptor-alpha signaling pathway / ubiquitin-dependent endocytosis / regulation of Rap protein signal transduction / entry of bacterium into host cell / (E3-independent) E2 ubiquitin-conjugating enzyme / flotillin complex / phosphatidylinositol 3-kinase regulatory subunit binding / E2 ubiquitin-conjugating enzyme / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / mast cell degranulation / response to testosterone / Interleukin-6 signaling / negative regulation of epidermal growth factor receptor signaling pathway / response to starvation / cellular response to platelet-derived growth factor stimulus / ubiquitin conjugating enzyme activity / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / FLT3 signaling by CBL mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / phosphotyrosine residue binding / ephrin receptor binding / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / cellular response to nerve growth factor stimulus / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / response to activity / Negative regulators of DDX58/IFIH1 signaling / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Peroxisomal protein import / response to gamma radiation / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / EGFR downregulation / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / protein modification process / RING-type E3 ubiquitin transferase / Constitutive Signaling by EGFRvIII / cilium / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of MET activity / receptor tyrosine kinase binding / CLEC7A (Dectin-1) signaling / SH3 domain binding / FCERI mediated NF-kB activation / protein polyubiquitination / positive regulation of receptor-mediated endocytosis / cytokine-mediated signaling pathway / ubiquitin-protein transferase activity / male gonad development / Signaling by CSF1 (M-CSF) in myeloid cells / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Cargo recognition for clathrin-mediated endocytosis / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / Neddylation / growth cone / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / response to ethanol / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / cadherin binding / membrane raft / focal adhesion / DNA damage response / ubiquitin protein ligase binding / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Prokaryotic RING finger family 4 / 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. ...Prokaryotic RING finger family 4 / 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 / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / UBA-like superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain superfamily / EF-hand domain pair / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase CBL / Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.214 Å
AuthorsDou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2012
Title: Structural basis for autoinhibition and phosphorylation-dependent activation of c-Cbl.
Authors: Dou, H. / Buetow, L. / Hock, A. / Sibbet, G.J. / Vousden, K.H. / Huang, D.T.
History
DepositionOct 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 2.0Nov 21, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / entity_name_com / entity_src_gen / entity_src_nat / exptl_crystal_grow / pdbx_struct_mod_residue / struct_ref
Item: _atom_site.occupancy / _citation.journal_abbrev ..._atom_site.occupancy / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_mutation / _entity.src_method / _entity_name_com.name / _exptl_crystal_grow.temp / _pdbx_struct_mod_residue.details / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CBL
B: Ubiquitin-conjugating enzyme E2 D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4345
Polymers26,2642
Non-polymers1703
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7.1 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.877, 115.877, 52.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-1148-

K

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Components

#1: Protein E3 ubiquitin-protein ligase CBL / Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / RING- ...Casitas B-lineage lymphoma proto-oncogene / Proto-oncogene c-Cbl / RING finger protein 55 / RING-type E3 ubiquitin transferase CBL / Signal transduction protein CBL


Mass: 9508.621 Da / Num. of mol.: 1 / Fragment: C-CBL RESIDUES 354-435 / Mutation: Y368F
Source method: isolated from a genetically manipulated source
Details: TYR371 IS PHOSPHORYLATED / Source: (gene. exp.) Homo sapiens (human) / Gene: CBL, CBL2, RNF55 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P22681, RING-type E3 ubiquitin transferase
#2: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 16755.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 368 TO PHE
Sequence detailsY368 IS MUTATED TO PHE. Y371 IS PHOSPHORYLATED. N-TERMINAL GS IS RESULTED FROM CLONING AND TEV CLEAVAGE.

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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: 3.8 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growTemperature: 291 K
Details: 20% (W/V) PEG 3350 AND 0.2 M POTASSIUM THIOCYANATE AT 18 DEGREES CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.21→40 Å / Num. obs: 20424 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 44.92 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6
Reflection shellResolution: 2.21→2.27 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2ESK AND 1FBV

2esk

1fbv


Resolution: 2.214→36.297 Å / SU ML: 0.57 / σ(F): 1.35 / Phase error: 19.67 / Stereochemistry target values: ML
Details: CHAIN A RESIDUE 354-358 AND CHAIN B RESIDUE 1 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2055 1045 5.1 %
Rwork0.1681 --
obs0.1699 20424 99.55 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.77 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.4777 Å20 Å20 Å2
2--3.4777 Å20 Å2
3----6.9554 Å2
Refinement stepCycle: LAST / Resolution: 2.214→36.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 3 132 1911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081876
X-RAY DIFFRACTIONf_angle_d1.1852559
X-RAY DIFFRACTIONf_dihedral_angle_d13.764718
X-RAY DIFFRACTIONf_chiral_restr0.095273
X-RAY DIFFRACTIONf_plane_restr0.007336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2141-2.33090.30271660.24832748X-RAY DIFFRACTION100
2.3309-2.47690.28571640.22972727X-RAY DIFFRACTION100
2.4769-2.66810.22071310.2052754X-RAY DIFFRACTION100
2.6681-2.93640.23171480.18862766X-RAY DIFFRACTION100
2.9364-3.36110.23461470.17772773X-RAY DIFFRACTION100
3.3611-4.23360.17661520.14622797X-RAY DIFFRACTION100
4.2336-36.30220.17451370.14722814X-RAY DIFFRACTION97
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)
12.3917-0.66961.53873.3741-3.32133.61180.14810.868-0.0517-0.7214-0.0541-0.47890.57610.32150.05040.5910.08880.10.8916-0.32820.848241.1821-50.1133-28.6102
26.8057-0.2329-1.9293.02772.15346.9377-0.1460.2623-1.16890.2013-0.15660.45360.7178-0.21050.27860.3138-0.0028-0.01860.4473-0.02940.713939.2836-52.8763-15.3071
33.28040.6288-0.22945.7584-0.7344.6355-0.05760.7977-0.52-0.4089-0.01380.02450.06920.36120.03380.2929-0.04220.00220.5521-0.08050.344635.7505-40.9603-21.3664
43.8192-0.0478-0.02181.81720.63660.7694-0.49830.4828-0.012-0.18370.4412-0.4096-0.26850.70010.06990.3217-0.08960.0470.71170.02710.460943.7655-36.7188-23.443
57.67224.78582.82644.81483.99523.7658-0.30741.04650.79-1.20130.38230.3509-1.10020.8083-0.19150.6278-0.1513-0.02840.63360.12860.392435.7007-27.8773-24.4576
66.362-1.9638-1.33955.97650.38026.680.28-0.18321.2508-0.52870.1491-0.6665-0.70171.7075-0.40150.4636-0.27770.06420.8496-0.04830.493845.0416-27.3027-20.9851
72.3663-3.45662.75617.8556-1.24935.9466-0.19291.2987-0.6551-1.31650.2740.02290.4358-0.08920.00920.4826-0.10990.08030.8613-0.19460.475238.881-45.7955-28.6155
82.95140.3043-0.65385.45140.30094.8614-0.0599-0.226-0.05620.234-0.0814-0.39630.20310.46210.12520.2807-0.0679-0.05820.4325-0.00450.357330.2163-38.7265-4.7373
93.75950.00035.34134.1320.63847.71090.1956-0.8114-0.22770.3266-0.33750.15640.0823-0.46620.12370.293-0.09410.00130.3523-0.01140.411827.8672-31.2185-0.102
104.99410.46972.63843.2592-1.17667.52580.0786-0.6226-0.44780.4902-0.1506-0.0890.03090.2070.05050.3762-0.203-0.02290.4179-0.00420.428238.5591-29.75418.5432
114.28931.55142.27862.0430.9053.8197-0.1231-0.1890.7475-0.1168-0.09630.1621-0.67480.21130.3420.2815-0.0889-0.00350.3281-0.01640.355933.3934-24.5606-3.3945
124.38342.83640.2083.65421.1115.41350.0347-0.14540.97770.19610.1726-0.0669-0.70730.312-0.18680.3842-0.0903-0.03310.3764-0.0630.53839.7996-18.62554.9878
134.6182-0.73050.6041.43070.51219.6612-0.24530.57680.1145-0.71630.1543-0.789-1.06410.61970.11380.3333-0.1303-0.00190.51510.02510.382441.3748-25.7887-9.001
144.89231.98682.13665.09651.85222.6368-0.01470.1995-0.1092-0.00550.1168-1.0009-0.19640.3175-0.09410.3308-0.1023-0.03240.42410.00930.453345.1213-26.041.3107
153.15291.21080.04342.5032-1.1943.15430.7522-1.27420.19580.8745-0.6022-0.1974-0.37490.2715-0.11360.5029-0.2532-0.08610.7138-0.03960.448547.3122-20.317615.5586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 359:364)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 365:373)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 374:394)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 395:401)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 402:410)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 411:424)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 425:435)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 2:28)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 29:38)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 39:55)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 56:74)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 75:84)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 85:98)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 99:120)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 121:147)

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