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- PDB-4jgh: Structure of the SOCS2-Elongin BC complex bound to an N-terminal ... -

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Basic information

Entry
Database: PDB / ID: 4jgh
TitleStructure of the SOCS2-Elongin BC complex bound to an N-terminal fragment of Cullin5
Components
  • Cullin-5
  • Suppressor of cytokine signaling 2
  • Transcription elongation factor B polypeptide 1
  • Transcription elongation factor B polypeptide 2
KeywordsLIGASE / Cullin-RING E3 ubiquitin ligases / Ubiquitination / Cytosol
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 / RNA Polymerase II Pre-transcription Events / JAK pathway signal transduction adaptor activity / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ERBB2 signaling pathway / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation ...TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / JAK pathway signal transduction adaptor activity / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ERBB2 signaling pathway / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / 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 / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / growth hormone receptor signaling pathway / negative regulation of multicellular organism growth / site of DNA damage / cell surface receptor signaling pathway via JAK-STAT / phosphatidylinositol phosphate biosynthetic process / regulation of signal transduction / mammary gland alveolus development / Growth hormone receptor signaling / cellular response to hormone stimulus / Negative regulation of FLT3 / insulin-like growth factor receptor binding / positive regulation of neuron differentiation / lactation / Interleukin-7 signaling / intrinsic apoptotic signaling pathway / transcription corepressor binding / regulation of cell growth / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / Vif-mediated degradation of APOBEC3G / G1/S transition of mitotic cell cycle / calcium channel activity / Inactivation of CSF3 (G-CSF) signaling / Downregulation of ERBB2 signaling / ubiquitin-protein transferase activity / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / response to estradiol / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / transcription regulator complex / transcription coactivator activity / protein ubiquitination / intracellular signal transduction / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / nucleus / cytosol / cytoplasm
Similarity search - Function
SOCS box / Suppressor of cytokine signalling 2 / SOCS2, SH2 domain / Cullin Repeats / suppressors of cytokine signalling / 5 helical Cullin repeat like / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. ...SOCS box / Suppressor of cytokine signalling 2 / SOCS2, SH2 domain / Cullin Repeats / suppressors of cytokine signalling / 5 helical Cullin repeat like / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / Elongin C; Chain C, domain 1 / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Elongin B / Cullin / Elongin-C / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SH2 domain / SHC Adaptor Protein / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Suppressor of cytokine signaling 2 / Elongin-B / Elongin-C / Cullin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKim, Y.K. / Kwak, M.J. / Ku, B. / Suh, H.Y. / Joo, K. / Lee, J. / Jung, J.U. / Oh, B.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural basis of intersubunit recognition in elongin BC-cullin 5-SOCS box ubiquitin-protein ligase complexes.
Authors: Kim, Y.K. / Kwak, M.J. / Ku, B. / Suh, H.Y. / Joo, K. / Lee, J. / Jung, J.U. / Oh, B.H.
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Suppressor of cytokine signaling 2
B: Transcription elongation factor B polypeptide 2
C: Transcription elongation factor B polypeptide 1
D: Cullin-5


Theoretical massNumber of molelcules
Total (without water)87,8784
Polymers87,8784
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-48 kcal/mol
Surface area35930 Å2
MethodPISA
2
D: Cullin-5

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


Theoretical massNumber of molelcules
Total (without water)87,8784
Polymers87,8784
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation7_544-x+1/2,y-1/2,-z-1/21
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-49 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.849, 141.456, 182.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 19812.828 Da / Num. of mol.: 1 / Fragment: unp residues 32-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIS2, Homo sapiens, SOCS2, SSI2, STATI2 / Plasmid: pProEx HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14508
#2: Protein Transcription elongation factor B polypeptide 2 / Elongin 18 kDa subunit / Elongin-B / EloB / RNA polymerase II transcription factor SIII subunit B / SIII p18


Mass: 13185.833 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mus musculus, Tceb2 / Plasmid: pRSFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62869
#3: Protein Transcription elongation factor B polypeptide 1 / Elongin 15 kDa subunit / Elongin-C / EloC / RNA polymerase II transcription factor SIII subunit C / ...Elongin 15 kDa subunit / Elongin-C / EloC / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Stromal membrane-associated protein SMAP1B homolog


Mass: 10869.457 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) / Gene: Mus musculus, Tceb1 / Plasmid: pRSFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P83940
#4: Protein Cullin-5 / / CUL-5 / Vasopressin-activated calcium-mobilizing receptor 1 / VACM-1


Mass: 44010.363 Da / Num. of mol.: 1 / Fragment: unp residues 10-386 / Mutation: V341R, L345D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL5, Homo sapiens, VACM1 / Plasmid: pET22b-CPD10H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q93034
Sequence detailsTHIS DISCREPANCY ARISES FROM THE TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 (MUS MUSCULUS) OF NP_080581

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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: 5.08 Å3/Da / Density % sol: 75.81 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.25 M sodium citrate and 18 % (w/v) PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 18, 2011
RadiationMonochromator: K-B mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 35501 / Num. obs: 34527 / % possible obs: 97.3 % / Observed criterion σ(F): 12.8 / Observed criterion σ(I): 165.9 / Redundancy: 9 % / Net I/σ(I): 23

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C9W (for SOCS2-Elongin BC) and 2WZK (for Cul5)

2c9w

2wzk


Resolution: 3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 3405 5% Random
Rwork0.225 --
all0.225 34151 -
obs0.225 30746 -
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5902 0 0 0 5902
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d1.1
LS refinement shellHighest resolution: 3 Å

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