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- PDB-2c9w: CRYSTAL STRUCTURE OF SOCS-2 IN COMPLEX WITH ELONGIN-B AND ELONGIN... -

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Entry
Database: PDB / ID: 2c9w
TitleCRYSTAL STRUCTURE OF SOCS-2 IN COMPLEX WITH ELONGIN-B AND ELONGIN-C AT 1.9A RESOLUTION
Components
  • (TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ...) x 2
  • SUPPRESSOR OF CYTOKINE SIGNALING 2
KeywordsTRANSCRIPTION REGULATION / GROWTH REGULATION / SH2 DOMAIN / SIGNAL TRANSDUCTION INHIBITOR / NUCLEAR PROTEIN / TRANSCRIPTION / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


JAK pathway signal transduction adaptor activity / negative regulation of growth hormone receptor signaling pathway / 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 / growth hormone receptor signaling pathway ...JAK pathway signal transduction adaptor activity / negative regulation of growth hormone receptor signaling pathway / 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 / growth hormone receptor signaling pathway / negative regulation of multicellular organism growth / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / mammary gland alveolus development / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / regulation of signal transduction / cell surface receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / 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 / lactation / insulin-like growth factor receptor binding / 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 / regulation of cell growth / transcription elongation by RNA polymerase II / 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 / response to estradiol / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-containing complex assembly / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / 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
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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Elongin-C / Elongin B / SH2 domain / SHC Adaptor Protein / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ domain superfamily / 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
NICKEL (II) ION / Suppressor of cytokine signaling 2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDebreczeni, J.E. / Bullock, A. / Amos, A. / Savitsky, P. / Barr, A. / Burgess, N. / Sundstrom, M. / Weigelt, J. / Arrowsmith, C. / Edwards, A. / Knapp, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2006
Title: Crystal structure of the SOCS2-elongin C-elongin B complex defines a prototypical SOCS box ubiquitin ligase.
Authors: Bullock, A.N. / Debreczeni, J.E. / Edwards, A.M. / Sundstrom, M. / Knapp, S.
History
DepositionDec 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Oct 9, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
C: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8609
Polymers43,3963
Non-polymers4646
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.290, 105.290, 70.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SUPPRESSOR OF CYTOKINE SIGNALING 2 / HUMAN SOCS2 / SOCS-2 / CYTOKINE-INDUCIBLE SH2 PROTEIN 2 / CIS-2 / STAT-INDUCED STAT INHIBITOR 2 / SSI-2


Mass: 19273.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: O14508

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TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ... , 2 types, 2 molecules BC

#2: Protein TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 / HUMAN ELONGIN B / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B / SIII P18 / ELONGIN B / ...HUMAN ELONGIN B / 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 BL21(DE3) (bacteria) / References: UniProt: Q15370
#3: Protein TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 / HUMAN ELONGIN C / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C / SIII P15 / ELONGIN C / ...HUMAN ELONGIN C / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C / SIII P15 / ELONGIN C / ELOC / ELONGIN 15 KDA SUBUNIT


Mass: 10974.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369

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Non-polymers , 3 types, 178 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsSOCS FAMILY PROTEINS PARTICIPATE AT THE CLASSICAL NEGATIVE FEEDBACK SYSTEM THAT REGULATES CYTOKINE ...SOCS FAMILY PROTEINS PARTICIPATE AT THE CLASSICAL NEGATIVE FEEDBACK SYSTEM THAT REGULATES CYTOKINE SIGNAL TRANSDUCTION. ELONGIN IS A GENERAL TRANSCRIPTION ELONGATION FACTOR

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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: 2.7 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 2M AMSO4 0.2M NACL, 0.1M CACODYLATE PH 6.5 300 NL SITTING DROPS AT 4 DEGREES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.90008
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90008 Å / Relative weight: 1
ReflectionResolution: 1.9→38.25 Å / Num. obs: 395240 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 11.6 % / Rmerge(I) obs: 0.0726 / Net I/σ(I): 28.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 11.19 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.29 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1O4H, 1LM8

1o4h

1lm8


Resolution: 1.9→91.29 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.738 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1762 5 %RANDOM
Rwork0.185 ---
obs0.187 33443 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.27 Å20 Å2
2--0.55 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 18 172 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222689
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9833648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31423.491106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71215454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1951514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021976
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.21155
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21846
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2196
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.14431734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.09452712
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0271091
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.81411936
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 130
Rwork0.253 2485
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4081-0.9939-0.31872.43241.67873.70560.0509-0.07210.0687-0.07550.0757-0.36320.02040.3356-0.1267-0.082-0.00580.0215-0.19330.0009-0.12560.35222.2114.612
20.6972-1.12851.03753.1554-2.75984.22050.09190.18790.35180.0585-0.2304-0.1896-0.26830.21430.1385-0.07590.0638-0.0061-0.08380.0733-0.04-12.35954.421-4.421
32.3959-1.08941.79253.8513-2.23345.2003-0.0283-0.05490.03660.23330.19950.3324-0.0998-0.4512-0.1711-0.09830.01870.0245-0.26070.0274-0.1692-15.71344.77710.746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 198
2X-RAY DIFFRACTION2B2 - 104
3X-RAY DIFFRACTION3C17 - 112

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