Structure of phosphoTyr363-Cbl-b - UbcH5B-Ub - ZAP-70 peptide complex
Components
E3 UBIQUITIN-PROTEIN LIGASE CBL-B
POLYUBIQUITIN-C
TYROSINE-PROTEIN KINASE ZAP-70
UBIQUITIN-CONJUGATING ENZYME E2 D2
Keywords
LIGASE / LIGASES / DEGRADATION
Function / homology
Function and homology information
T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell migration / T cell anergy / positive regulation of T cell anergy / positive regulation of alpha-beta T cell proliferation / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of CD4-positive, alpha-beta T cell proliferation ...T cell aggregation / regulation of platelet-derived growth factor receptor-alpha signaling pathway / T cell migration / T cell anergy / positive regulation of T cell anergy / positive regulation of alpha-beta T cell proliferation / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / (E3-independent) E2 ubiquitin-conjugating enzyme / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive thymic T cell selection / beta selection / positive regulation of alpha-beta T cell differentiation / positive regulation of T cell differentiation / T cell receptor complex / negative regulation of T cell receptor signaling pathway / E2 ubiquitin-conjugating enzyme / NLS-bearing protein import into nucleus / B cell activation / Translocation of ZAP-70 to Immunological synapse / ubiquitin conjugating enzyme activity / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / Nuclear events stimulated by ALK signaling in cancer / protein autoubiquitination / protein K48-linked ubiquitination / positive regulation of calcium-mediated signaling / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / extrinsic component of cytoplasmic side of plasma membrane / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / T cell activation / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / phosphotyrosine residue binding / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation Similarity search - Function
Prokaryotic RING finger family 4 / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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 ...Prokaryotic RING finger family 4 / E3 ubiquitin-protein ligase CBL-B, RING finger, HC subclass / 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 / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 domain / Transcription Elongation Factor S-II; Chain A / 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. / SH2 domain / SHC Adaptor Protein / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / EF-hand / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Recoverin; domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / SH2 domain / Ubiquitin domain signature. / Ubiquitin conserved site / Src homology 2 (SH2) domain profile. / Ubiquitin domain / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / EF-hand domain pair / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
E3UBIQUITIN-PROTEINLIGASECBL-B / CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE B / RING FINGER PROTEIN 56 / SH3-BINDING PROTEIN CBL-B / ...CASITAS B-LINEAGE LYMPHOMA PROTO-ONCOGENE B / RING FINGER PROTEIN 56 / SH3-BINDING PROTEIN CBL-B / SIGNAL TRANSDUCTION PROTEIN CBL-B
Mass: 45748.281 Da / Num. of mol.: 4 / Fragment: RESIDUES 36-427 / Mutation: YES Source method: isolated from a genetically manipulated source Details: Y363 IS PHOSPHORYLATED. GS AT THE N-TERMINUS OF PROTEIN RESULTED FROM CLONING. Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13191, ubiquitin-protein ligase
Mass: 16720.186 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-147 / Mutation: YES Source method: isolated from a genetically manipulated source Details: K85 SIDECHAIN IN CHIANS C, G, K AND O FORMS AN ISOPEPTIDE LINKAGE WITH THE CARBONYL CARBON OF G76 IN CHAINS D, H, L AND P, RESPECTIVELY. Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62837, ubiquitin-protein ligase
#4: Protein
POLYUBIQUITIN-C / UBIQUITIN
Mass: 8922.141 Da / Num. of mol.: 4 / Fragment: RESIDUES 77-152 Source method: isolated from a genetically manipulated source Details: CARBONYL CARBON OF G76 IN CHIANS D, H, L AND P FORMS AN ISOPEPTIDE LINKAGE WITH THE SIDECHAIN OF K85 IN CHAINS C, G, K AND O, RESPECTIVELY. GSGGS LINKER AT THE N- TERMINUS OF PROTEIN RESULTED FROM CLONING Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0CG48
Mass: 1344.275 Da / Num. of mol.: 4 / Fragment: RESIDUES 286-297 / Source method: obtained synthetically Details: Y292 IS PHOSPHORYLATED. IN THE STRUCTURE Y292 IS NUMBERED AS 7. Source: (synth.) HOMO SAPIENS (human) References: UniProt: P43403, non-specific protein-tyrosine kinase
Resolution: 2.21→30.54 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML Details: FINAL MODEL CONTAINS FOLLOWING RESIDUES. CHAINS A, E, M RESIDUES 38 TO 427 AND CHAIN I RESIDUES 41 TO 426. CHAINS B AND N RESIDUES 4 TO 12 AND CHAINS F AND J RESIDUES 5 TO 12. CHAINS C, G, K ...Details: FINAL MODEL CONTAINS FOLLOWING RESIDUES. CHAINS A, E, M RESIDUES 38 TO 427 AND CHAIN I RESIDUES 41 TO 426. CHAINS B AND N RESIDUES 4 TO 12 AND CHAINS F AND J RESIDUES 5 TO 12. CHAINS C, G, K AND O RESIDUES 2 TO 147. CHAINS D, H, L AND P RESIDUES 1 TO 76. ATOMS FROM RESIDUES WITH DISORDER SIDECHAIN ELECTRON DENSITY WERE OMITTED.
Rfactor
Num. reflection
% reflection
Rfree
0.2114
7484
5 %
Rwork
0.1748
-
-
obs
0.1767
149230
99.58 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL