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- PDB-6i4x: Crystal structure of SOCS2:Elongin C:Elongin B in complex with er... -

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Basic information

Entry
Database: PDB / ID: 6i4x
TitleCrystal structure of SOCS2:Elongin C:Elongin B in complex with erythropoietin receptor peptide
Components
  • Elongin-B
  • Elongin-C
  • Erythropoietin receptor
  • Suppressor of cytokine signaling 2
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


negative regulation of growth hormone receptor signaling pathway / JAK pathway signal transduction adaptor activity / phosphorylation-dependent protein binding / cytokine receptor binding / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / VCB complex / elongin complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex ...negative regulation of growth hormone receptor signaling pathway / JAK pathway signal transduction adaptor activity / phosphorylation-dependent protein binding / cytokine receptor binding / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / VCB complex / elongin complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex / growth hormone receptor signaling pathway / Cul2-RING ubiquitin ligase complex / negative regulation of multicellular organism growth / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / mammary gland alveolus development / cell surface receptor signaling pathway via JAK-STAT / regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / negative regulation of signal transduction / Formation of HIV elongation complex in the absence of HIV Tat / Growth hormone receptor signaling / cellular response to hormone stimulus / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / insulin-like growth factor receptor binding / lactation / RNA Polymerase II Pre-transcription Events / Negative regulation of FLT3 / Interleukin-7 signaling / positive regulation of neuron differentiation / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / regulation of cell growth / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / cytokine-mediated signaling pathway / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Regulation of expression of SLITs and ROBOs / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / response to estradiol / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular signal transduction / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
SOCS box / Suppressor of cytokine signalling 2 / SOCS2, SH2 domain / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin C; Chain C, domain 1 ...SOCS box / Suppressor of cytokine signalling 2 / SOCS2, SH2 domain / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin C; Chain C, domain 1 / Elongin-C / Elongin B / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Suppressor of cytokine signaling 2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKung, W.W. / Ramachandran, S. / Makukhin, N. / Bruno, E. / Ciulli, A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460 DrugE3CRLs United Kingdom
University of Dundee, PhD Scholarship United Kingdom
Wellcome Trust100476/Z/12/Z United Kingdom
Wellcome Trust094090/Z/10/Z United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase.
Authors: Kung, W.W. / Ramachandran, S. / Makukhin, N. / Bruno, E. / Ciulli, A.
History
DepositionNov 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Structure summary / Category: audit_author / struct
Item: _audit_author.identifier_ORCID / _audit_author.name / _struct.title
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Elongin-B
C: Elongin-C
A: Suppressor of cytokine signaling 2
D: Erythropoietin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4595
Polymers43,3534
Non-polymers1061
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, ITC, peptide alanine scan by SPR and NMR,
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-49 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.287, 56.327, 203.392
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

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Components

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Protein , 3 types, 3 molecules BCA

#1: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11852.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370
#2: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#3: Protein Suppressor of cytokine signaling 2 / SOCS-2 / Cytokine-inducible SH2 protein 2 / CIS-2 / STAT-induced STAT inhibitor 2 / SSI-2


Mass: 19203.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOCS2, CIS2, SSI2, STATI2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14508

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Erythropoietin receptor


Mass: 1322.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 12 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Sodium cacodylate, ethanol, HEPES, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.69→29.36 Å / Num. obs: 12273 / % possible obs: 93.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.6
Reflection shellResolution: 2.69→2.82 Å / Rmerge(I) obs: 0.514

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→29.36 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.21
RfactorNum. reflection% reflection
Rfree0.2351 640 5.22 %
Rwork0.1964 --
obs0.1986 12266 93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.69→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 7 11 2782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022828
X-RAY DIFFRACTIONf_angle_d0.4513834
X-RAY DIFFRACTIONf_dihedral_angle_d8.5041710
X-RAY DIFFRACTIONf_chiral_restr0.038445
X-RAY DIFFRACTIONf_plane_restr0.003480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.688-2.89540.4004790.2951751X-RAY DIFFRACTION70
2.8954-3.18650.30641370.26332449X-RAY DIFFRACTION98
3.1865-3.64680.23381430.20712433X-RAY DIFFRACTION99
3.6468-4.59180.21891440.16842484X-RAY DIFFRACTION99
4.5918-29.36290.19611370.16912509X-RAY DIFFRACTION98

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