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- PDB-2lxp: NMR structure of two domains in ubiquitin ligase gp78, RING and G... -

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Basic information

Entry
Database: PDB / ID: 2lxp
TitleNMR structure of two domains in ubiquitin ligase gp78, RING and G2BR, bound to its conjugating enzyme Ube2g
Components
  • (E3 ubiquitin-protein ligase AMFR) x 2
  • Ubiquitin-conjugating enzyme E2 G2
KeywordsLIGASE / RING domain / ubiquitin
Function / homology
Function and homology information


regulation of SREBP signaling pathway / negative regulation of retrograde protein transport, ER to cytosol / 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 ...regulation of SREBP signaling pathway / negative regulation of retrograde protein transport, ER to cytosol / 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 / E2 ubiquitin-conjugating enzyme / ubiquitin-specific protease binding / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / protein K48-linked ubiquitination / endoplasmic reticulum unfolded protein response / cellular response to interferon-beta / protein autoubiquitination / ERAD pathway / ER Quality Control Compartment (ERQC) / lipid droplet / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / protein-folding chaperone binding / growth cone / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / learning or memory / neuronal cell body / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / signal transduction / protein-containing complex / zinc ion binding / ATP binding / identical protein binding / membrane / cytosol
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 Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...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 Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 G2 / E3 ubiquitin-protein ligase AMFR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsDas, R. / Linag, Y. / Mariano, J. / Li, J. / Huang, T. / King, A. / Weissman, A. / Ji, X. / Byrd, R.
CitationJournal: Embo J. / Year: 2013
Title: Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine.
Authors: Das, R. / Liang, Y.H. / Mariano, J. / Li, J. / Huang, T. / King, A. / Tarasov, S.G. / Weissman, A.M. / Ji, X. / Byrd, R.A.
History
DepositionAug 30, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_nmr_data / _pdbx_nmr_software.name / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 G2
B: E3 ubiquitin-protein ligase AMFR
C: E3 ubiquitin-protein ligase AMFR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4215
Polymers28,2903
Non-polymers1312
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 / 200Lowest Haddock Scores
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 G2 / Ubiquitin carrier protein G2 / Ubiquitin-protein ligase G2


Mass: 18451.062 Da / Num. of mol.: 1 / Fragment: UNP residues 2-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2G2 / Production host: Escherichia coli (E. coli) / References: UniProt: P60604, ubiquitin-protein ligase
#2: Protein/peptide E3 ubiquitin-protein ligase AMFR / Autocrine motility factor receptor / isoform 2 / AMF receptor / isoform 2 / RING finger protein 45 / gp78


Mass: 3365.910 Da / Num. of mol.: 1 / Fragment: UNP residues 574-600
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)
#3: Protein E3 ubiquitin-protein ligase AMFR / Autocrine motility factor receptor / isoform 2 / AMF receptor / isoform 2 / RING finger protein 45 / gp78


Mass: 6473.361 Da / Num. of mol.: 1 / Fragment: UNP residues 327-384
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)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D C(CO)NH
1613D H(CCO)NH
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1913D HNCO
11013D 1H-13C NOESY
11113D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.7-1 mM [U-100% 13C; U-100% 15N] gp78RING, 50 mM TRIS, 2 mM TCEP, 0.2 mM sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMgp78RING-1[U-100% 13C; U-100% 15N]0.7-11
50 mMTRIS-21
2 mMTCEP-31
0.2 mMsodium azide-41
Sample conditionsIonic strength: 0 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSAlexandre Bonvinstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 26 / NOE long range total count: 26
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Lowest Haddock Scores / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 4 Å / Maximum upper distance constraint violation: 6 Å

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