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- PDB-6i5j: Crystal structure of SOCS2:Elongin C:Elongin B in complex with gr... -

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Basic information

Entry
Database: PDB / ID: 6i5j
TitleCrystal structure of SOCS2:Elongin C:Elongin B in complex with growth hormone receptor peptide
Components
  • (Suppressor of cytokine signaling ...) x 2
  • Elongin-B
  • Elongin-C
  • Growth hormone receptor peptide
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


JAK pathway signal transduction adaptor activity / negative regulation of receptor signaling pathway via JAK-STAT / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...JAK pathway signal transduction adaptor activity / negative regulation of receptor signaling pathway via JAK-STAT / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / growth hormone receptor binding / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / growth hormone receptor signaling pathway / negative regulation of multicellular organism growth / cell surface receptor signaling pathway via JAK-STAT / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / phosphatidylinositol phosphate biosynthetic process / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / regulation of signal transduction / mammary gland alveolus development / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Growth hormone receptor signaling / cellular response to hormone stimulus / Negative regulation of FLT3 / RNA Polymerase II Pre-transcription Events / insulin-like growth factor receptor binding / positive regulation of neuron differentiation / lactation / Interleukin-7 signaling / transcription corepressor binding / regulation of cell growth / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Regulation of expression of SLITs and ROBOs / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / response to estradiol / Neddylation / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / protein ubiquitination / intracellular signal transduction / 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 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-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Suppressor of cytokine signaling 2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Wellcome Trust100476/Z/12/Z United Kingdom
Wellcome Trust094090/Z/10/Z United Kingdom
University of Dundee, PhD scholarship 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 13, 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 1.3Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Suppressor of cytokine signaling 2
B: Elongin-B
C: Elongin-C
D: Suppressor of cytokine signaling 2
E: Elongin-B
F: Elongin-C
I: Growth hormone receptor peptide
J: Growth hormone receptor peptide
K: Growth hormone receptor peptide
L: Growth hormone receptor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,91212
Polymers89,79410
Non-polymers1182
Water59433
1
A: Suppressor of cytokine signaling 2
B: Elongin-B
C: Elongin-C
I: Growth hormone receptor peptide
K: Growth hormone receptor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0086
Polymers44,9495
Non-polymers591
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-85 kcal/mol
Surface area19340 Å2
MethodPISA
2
D: Suppressor of cytokine signaling 2
E: Elongin-B
F: Elongin-C
J: Growth hormone receptor peptide
L: Growth hormone receptor peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9046
Polymers44,8455
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-84 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.835, 113.707, 156.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Suppressor of cytokine signaling ... , 2 types, 2 molecules AD

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


Mass: 19481.232 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
#4: Protein Suppressor of cytokine signaling 2 / SOCS-2 / Cytokine-inducible SH2 protein 2 / CIS-2 / STAT-induced STAT inhibitor 2 / SSI-2


Mass: 19377.250 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 , 2 types, 4 molecules BECF

#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: 11852.389 Da / Num. of mol.: 2
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
#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: 10974.616 Da / Num. of mol.: 2
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

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Protein/peptide , 1 types, 4 molecules IJKL

#5: Protein/peptide
Growth hormone receptor peptide


Mass: 1320.407 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 35 molecules

#6: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, cobalt chloride, MES, ammonium sulphate

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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: 2.8→92.08 Å / Num. obs: 26321 / % possible obs: 100 % / Redundancy: 7.8 % / Net I/σ(I): 7.3
Reflection shellResolution: 2.8→2.95 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
AutoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→64.585 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 1305 4.97 %
Rwork0.2096 --
obs0.2123 26267 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→64.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6089 0 2 33 6124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026235
X-RAY DIFFRACTIONf_angle_d0.4128463
X-RAY DIFFRACTIONf_dihedral_angle_d8.0444070
X-RAY DIFFRACTIONf_chiral_restr0.036968
X-RAY DIFFRACTIONf_plane_restr0.0031072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.91220.30781400.26932733X-RAY DIFFRACTION100
2.9122-3.04470.37351400.26892741X-RAY DIFFRACTION100
3.0447-3.20520.28451420.25542719X-RAY DIFFRACTION100
3.2052-3.4060.32391530.23132726X-RAY DIFFRACTION100
3.406-3.6690.25231380.21682747X-RAY DIFFRACTION100
3.669-4.03820.23931400.18382752X-RAY DIFFRACTION100
4.0382-4.62240.20851370.16362791X-RAY DIFFRACTION100
4.6224-5.82310.25651540.18912813X-RAY DIFFRACTION100
5.8231-64.60210.25241610.21572940X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 79.9436 Å / Origin y: 27.3959 Å / Origin z: 28.3844 Å
111213212223313233
T0.2419 Å2-0.0091 Å2-0.0313 Å2-0.25 Å2-0.0038 Å2--0.2452 Å2
L0.5339 °20.0481 °2-0.1707 °2-0.1398 °2-0.0896 °2--0.2453 °2
S0.0015 Å °0.0366 Å °-0.007 Å °-0.0404 Å °0.0239 Å °0.0265 Å °0.0669 Å °0.0131 Å °-0.0163 Å °
Refinement TLS groupSelection details: all

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