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- PDB-2lvp: gp78CUE domain bound to the distal ubiquitin of K48-linked diubiquitin -

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Basic information

Entry
Database: PDB / ID: 2lvp
Titlegp78CUE domain bound to the distal ubiquitin of K48-linked diubiquitin
Components
  • E3 ubiquitin-protein ligase AMFR
  • Ubiquitin
KeywordsSIGNALING PROTEIN/LIGASE / CUE domain / SIGNALING PROTEIN-LIGASE complex
Function / homology
Function and homology information


regulation of SREBP signaling pathway / RING-type E3 ubiquitin transferase (cysteine targeting) / endoplasmic reticulum mannose trimming / protein K27-linked ubiquitination / endoplasmic reticulum quality control compartment / BAT3 complex binding / Derlin-1 retrotranslocation complex / non-canonical NF-kappaB signal transduction / ubiquitin-ubiquitin ligase activity / ubiquitin-specific protease binding ...regulation of SREBP signaling pathway / RING-type E3 ubiquitin transferase (cysteine targeting) / endoplasmic reticulum mannose trimming / protein K27-linked ubiquitination / endoplasmic reticulum quality control compartment / BAT3 complex binding / Derlin-1 retrotranslocation complex / non-canonical NF-kappaB signal transduction / ubiquitin-ubiquitin ligase activity / ubiquitin-specific protease binding / ubiquitin ligase complex / protein K48-linked ubiquitination / endoplasmic reticulum unfolded protein response / protein autoubiquitination / ERAD pathway / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / ubiquitin binding / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53
Similarity search - Function
E3 ubiquitin-protein ligase AMFR, Ube2g2-binding region / E3 gp78 Ube2g2-binding region (G2BR) / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ring finger domain / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...E3 ubiquitin-protein ligase AMFR, Ube2g2-binding region / E3 gp78 Ube2g2-binding region (G2BR) / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ring finger domain / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / E3 ubiquitin-protein ligase AMFR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLiu, S. / Chen, Y. / Huang, T. / Tarasov, S.G. / King, A. / Li, J. / Weissman, A.M. / Byrd, R.A. / Das, R.
CitationJournal: Structure / Year: 2012
Title: Promiscuous Interactions of gp78 E3 Ligase CUE Domain with Polyubiquitin Chains.
Authors: Liu, S. / Chen, Y. / Li, J. / Huang, T. / Tarasov, S. / King, A. / Weissman, A.M. / Byrd, R.A. / Das, R.
History
DepositionJul 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: E3 ubiquitin-protein ligase AMFR


Theoretical massNumber of molelcules
Total (without water)23,1203
Polymers23,1203
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein E3 ubiquitin-protein ligase AMFR / Autocrine motility factor receptor / isoform 2 / AMF receptor / isoform 2 / RING finger protein 45 / gp78


Mass: 5966.752 Da / Num. of mol.: 1 / Fragment: CUE domain residues 453-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMFR, RNF45 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UKV5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Amide shifts of gp78CUE and distal Ubiquitin in the gp78CUE/K48-Ub2 complex
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D C(CO)NH
1613D H(CCO)NH
1713D HN(CA)CB
1812D 1H-13C HSQC aromatic
1913D 1H-15N NOESY

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Sample preparation

DetailsContents: 50 mM TRIS, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMTRIS-11
50 mMsodium chloride-21
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker INOVABrukerINOVA6001
Bruker INOVABrukerINOVA7002
Varian INOVAVarianINOVA6003
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSAlexandre Bonvinstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: FINAL STEP IN WATER
NMR constraintsNOE constraints total: 43 / NOE long range total count: 43
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 8 Å
NMR ensemble rmsDistance rms dev: 0 Å

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