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- PDB-2jz3: SOCS box elonginBC ternary complex -

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Basic information

Entry
Database: PDB / ID: 2jz3
TitleSOCS box elonginBC ternary complex
Components
  • Suppressor of cytokine signaling 3
  • Transcription elongation factor B polypeptide 1
  • Transcription elongation factor B polypeptide 2
KeywordsTRANSCRIPTION INHIBITOR/TRANSCRIPTION / socs proteins / elongins / cytokine signaling / Growth regulation / Phosphoprotein / SH2 domain / Signal transduction inhibitor / Ubl conjugation pathway / Nucleus / Transcription / Transcription regulation / signaling protein / TRANSCRIPTION INHIBITOR-TRANSCRIPTION COMPLEX
Function / homology
Function and homology information


TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Regulation of IFNG signaling / PTK6 Activates STAT3 / RNA Polymerase II Pre-transcription Events / Interferon gamma signaling / Interleukin-6 signaling / Interferon alpha/beta signaling / Inactivation of CSF3 (G-CSF) signaling ...TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Regulation of IFNG signaling / PTK6 Activates STAT3 / RNA Polymerase II Pre-transcription Events / Interferon gamma signaling / Interleukin-6 signaling / Interferon alpha/beta signaling / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / negative regulation of tyrosine phosphorylation of STAT protein / branching involved in labyrinthine layer morphogenesis / cellular response to interleukin-17 / placenta blood vessel development / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / 1-phosphatidylinositol-3-kinase regulator activity / protein tyrosine kinase inhibitor activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / Cul5-RING ubiquitin ligase complex / miRNA binding / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / phosphatidylinositol phosphate biosynthetic process / cell surface receptor signaling pathway via JAK-STAT / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of insulin receptor signaling pathway / RNA Polymerase II Pre-transcription Events / phosphotyrosine residue binding / transcription corepressor binding / cellular response to leukemia inhibitory factor / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / regulation of protein phosphorylation / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / negative regulation of inflammatory response / Regulation of expression of SLITs and ROBOs / cytoplasmic side of plasma membrane / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / cell differentiation / intracellular signal transduction / protein ubiquitination / ubiquitin protein ligase binding / protein-containing complex binding / signal transduction / nucleoplasm / cytosol
Similarity search - Function
Suppressor of cytokine signalling 3 / SOCS3, SH2 domain / suppressors of cytokine signalling / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A ...Suppressor of cytokine signalling 3 / SOCS3, SH2 domain / suppressors of cytokine signalling / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Suppressor of cytokine signaling 3 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBabon, J.J. / Sabo, J. / Soetopo, A. / Yao, S. / Bailey, M.F. / Zhang, J. / Nicola, N.A. / Norton, R.S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The SOCS box domain of SOCS3: structure and interaction with the elonginBC-cullin5 ubiquitin ligase
Authors: Babon, J.J. / Sabo, J.K. / Soetopo, A. / Yao, S. / Bailey, M.F. / Zhang, J.-G. / Nicola, N.A. / Norton, R.S.
History
DepositionDec 27, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Suppressor of cytokine signaling 3
B: Transcription elongation factor B polypeptide 2
C: Transcription elongation factor B polypeptide 1


Theoretical massNumber of molelcules
Total (without water)28,5643
Polymers28,5643
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Suppressor of cytokine signaling 3 / SOCS-3 / Cytokine-inducible SH2 protein 3 / CIS-3 / Protein EF-10


Mass: 4573.189 Da / Num. of mol.: 1 / Fragment: SOCS box, UNP residues 186-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: O35718
#2: Protein Transcription elongation factor B polypeptide 2 / elonginB / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Elongin-B / EloB / ...elonginB / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Elongin-B / EloB / Elongin 18 kDa subunit


Mass: 13147.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#3: Protein Transcription elongation factor B polypeptide 1 / elonginC / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Elongin-C / EloC / ...elonginC / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Elongin-C / EloC / Elongin 15 kDa subunit / Stromal membrane-associated protein SMAP1B homolog


Mass: 10843.420 Da / Num. of mol.: 1 / Fragment: UNP residues 17-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P83940

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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 HNCO
1513D HNCA
1613D HN(CO)CA
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D (H)CCH-TOCSY
11012D 1H-1H NOESY

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] socs box; 1mM elonginB; 1mM elonginC; 50mM potassium chloride; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMsocs box[U-100% 13C; U-100% 15N]1
1 mMelonginB1
1 mMelonginC1
50 mMpotassium chloride1
Sample conditionsIonic strength: 0.05 / pH: 6.7 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxstructure solution
TALOSCornilescu, Delaglio and Baxrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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