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- PDB-7m6t: Crystal structure of SOCS2/ElonginB/ElonginC bound to a non-canon... -

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Basic information

Entry
Database: PDB / ID: 7m6t
TitleCrystal structure of SOCS2/ElonginB/ElonginC bound to a non-canonical peptide that enhances phospho-peptide binding
Components
  • Elongin-B
  • Elongin-C
  • Non-canonical peptide F3
  • Suppressor of cytokine signaling 2
KeywordsSIGNALING PROTEIN / SH2 / E3 Ligase
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 / elongin complex / growth hormone receptor binding / VCB complex / 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 / elongin complex / growth hormone receptor binding / VCB complex / Cul5-RING ubiquitin ligase complex / growth hormone receptor signaling pathway / negative regulation of multicellular organism growth / Cul2-RING ubiquitin ligase complex / 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 / regulation of signal transduction / cell surface receptor signaling pathway via JAK-STAT / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Growth hormone receptor signaling / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / 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 / positive regulation of neuron differentiation / Negative regulation of FLT3 / Interleukin-7 signaling / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / regulation of cell growth / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / cytokine-mediated signaling pathway / 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 / cytoplasm / cytosol
Similarity search - Function
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 / Elongin B ...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 / Elongin B / 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 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Suppressor of cytokine signaling 2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.194 Å
AuthorsKershaw, N.J. / Li, K. / Linossi, E.M. / Nicholson, S.E.
CitationJournal: Nat Commun / Year: 2021
Title: Discovery of an exosite on the SOCS2-SH2 domain that enhances SH2 binding to phosphorylated ligands.
Authors: Linossi, E.M. / Li, K. / Veggiani, G. / Tan, C. / Dehkhoda, F. / Hockings, C. / Calleja, D.J. / Keating, N. / Feltham, R. / Brooks, A.J. / Li, S.S. / Sidhu, S.S. / Babon, J.J. / Kershaw, N.J. / Nicholson, S.E.
History
DepositionMar 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Suppressor of cytokine signaling 2
B: Elongin-B
C: Elongin-C
D: Non-canonical peptide F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0105
Polymers44,9144
Non-polymers961
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: 1:1:1:1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-71 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.749, 110.612, 139.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Suppressor of cytokine signaling 2 / SOCS-2 / Cytokine-inducible SH2 protein 2 / CIS-2 / STAT-induced STAT inhibitor 2 / SSI-2


Mass: 19342.121 Da / Num. of mol.: 1 / Mutation: K115A, K117A, Q118A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOCS2, CIS2, SSI2, STATI2 / Production host: Escherichia coli (E. coli) / References: UniProt: O14508
#2: 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: 13251.764 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) / Strain (production host): BL21(DE3) / References: UniProt: Q15370
#3: 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: 10843.420 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 (E. coli) / References: UniProt: Q15369

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Non-canonical peptide F3


Mass: 1476.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 2M ammonium sulphate Bis-Tris pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 3.194→43.383 Å / Num. obs: 8106 / % possible obs: 99.29 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 14.2
Reflection shellResolution: 3.194→3.308 Å / Num. unique obs: 780 / CC1/2: 0.782 / % possible all: 98.86

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C9W

2c9w


Resolution: 3.194→43.383 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 807 9.99 %
Rwork0.2273 7270 -
obs0.2313 8077 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 218.73 Å2 / Biso mean: 110.4021 Å2 / Biso min: 75.03 Å2
Refinement stepCycle: final / Resolution: 3.194→43.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 5 1 2670
Biso mean--113.08 100.27 -
Num. residues----350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.194-3.39370.49531200.3696115797
3.3937-3.65560.31841340.28751197100
3.6556-4.02320.24531330.22631198100
4.0232-4.60480.24751360.20591209100
4.6048-5.79940.26261390.21221228100
5.7994-43.3830.24371450.21161281100

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