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- PDB-2izv: CRYSTAL STRUCTURE OF SOCS-4 IN COMPLEX WITH ELONGIN-B AND ELONGIN... -

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Basic information

Entry
Database: PDB / ID: 2izv
TitleCRYSTAL STRUCTURE OF SOCS-4 IN COMPLEX WITH ELONGIN-B AND ELONGIN-C AT 2.55A RESOLUTION
Components
  • (TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ...) x 2
  • SUPPRESSOR OF CYTOKINE SIGNALING 4
KeywordsTRANSCRIPTION / SIGNAL TRANSDUCTION INHIBITOR / GROWTH REGULATION / SIGNAL TRANSDUCTION / SH2 DOMAIN / NUCLEAR PROTEIN / UBL CONJUGATION PATHWAY / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


negative regulation of epidermal growth factor-activated receptor activity / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / regulation of growth / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...negative regulation of epidermal growth factor-activated receptor activity / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / 1-phosphatidylinositol-3-kinase regulator activity / target-directed miRNA degradation / elongin complex / VCB complex / phosphatidylinositol 3-kinase complex / regulation of growth / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / phosphatidylinositol phosphate biosynthetic process / 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 / Tat-mediated elongation of the HIV-1 transcript / 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 / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / Evasion by RSV of host interferon responses / 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 / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / 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 / nucleoplasm / cytosol
Similarity search - Function
Suppressor of cytokine signalling 4 / SOCS4, SH2 domain / SOCS4, SOCS box domain / SOCS4/SOCS5 domain / Suppressor of cytokine signalling / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. ...Suppressor of cytokine signalling 4 / SOCS4, SH2 domain / SOCS4, SOCS box domain / SOCS4/SOCS5 domain / Suppressor of cytokine signalling / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / 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 / 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 domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Elongin-C / Elongin-B / Suppressor of cytokine signaling 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsDebreczeni, J.E. / Bullock, A. / Papagrigoriou, E. / Turnbull, A. / Pike, A.C.W. / Gorrec, F. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. ...Debreczeni, J.E. / Bullock, A. / Papagrigoriou, E. / Turnbull, A. / Pike, A.C.W. / Gorrec, F. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Knapp, S.
CitationJournal: Structure / Year: 2007
Title: Structure of the SOCS4-ElonginB/C complex reveals a distinct SOCS box interface and the molecular basis for SOCS-dependent EGFR degradation.
Authors: Bullock, A.N. / Rodriguez, M.C. / Debreczeni, J.E. / Songyang, Z. / Knapp, S.
History
DepositionJul 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._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 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 4
B: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
C: TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9806
Polymers45,8593
Non-polymers1213
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)154.770, 154.770, 67.909
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SUPPRESSOR OF CYTOKINE SIGNALING 4 / SOCS-4 ELONGIN B / C COMPLEX / SOCS-4 / SOCS-7 / SUPPRESSOR OF CYTOKINE SIGNALING 7


Mass: 21736.711 Da / Num. of mol.: 1 / Fragment: RESIDUES 274-437
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: Q8WXH5

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

#2: Protein TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 / 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) / Variant (production host): R3 / References: UniProt: Q15370
#3: Protein TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 / 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 / Fragment: RESIDUES 17-112
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: Q15369

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Non-polymers , 4 types, 116 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.98 Å3/Da / Density % sol: 69 %
Crystal growMethod: vapor diffusion, sitting drop / Details: 150 UL SITTING DROP 2M NACL 10% PEK6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8984
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 16, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8984 Å / Relative weight: 1
ReflectionResolution: 2.55→44.68 Å / Num. obs: 19724 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 2.71 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.14
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 1.72 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.98 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9W

2c9w


Resolution: 2.55→77.38 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.503 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1000 5.1 %RANDOM
Rwork0.172 ---
obs0.175 18723 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0.61 Å20 Å2
2---1.22 Å20 Å2
3---1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.55→77.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 6 113 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222882
X-RAY DIFFRACTIONr_bond_other_d0.0010.021966
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9713910
X-RAY DIFFRACTIONr_angle_other_deg1.00634791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78523.465127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15515476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0921516
X-RAY DIFFRACTIONr_chiral_restr0.1440.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02596
X-RAY DIFFRACTIONr_nbd_refined0.20.2535
X-RAY DIFFRACTIONr_nbd_other0.190.21935
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21397
X-RAY DIFFRACTIONr_nbtor_other0.0890.21487
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.51851774
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.29572881
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.00291131
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.759111029
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: 2.55→2.62 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 69
Rwork0.274 1358
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)
10.90310.81460.10392.67570.03031.03060.0394-0.2001-0.10570.2938-0.0036-0.01990.0146-0.0199-0.0358-0.01270.0407-0.0385-0.00860.0516-0.05358.5008-16.113861.5944
20.5906-0.203-0.97013.75990.66111.62250.1165-0.19750.124-0.20940.011-0.3413-0.10420.0249-0.1274-0.04570.0241-0.0087-0.0571-0.02490.013821.2349-6.527547.1676
32.309-1.6996-1.69513.0441.94041.86460.05120.1284-0.1869-0.2321-0.16230.0169-0.0674-0.10620.1111-0.08540.02750.0156-0.09740.0214-0.040335.1863-29.759127.7502
42.5625-0.4579-0.24971.87080.15852.22590.10760.08540.1179-0.3384-0.11580.0085-0.0863-0.08930.0082-0.03230.0621-0.0006-0.11560.0204-0.049223.639-16.859132.2935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A267 - 383
2X-RAY DIFFRACTION1A422 - 429
3X-RAY DIFFRACTION2A384 - 421
4X-RAY DIFFRACTION3B2 - 104
5X-RAY DIFFRACTION4C17 - 112

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