[English] 日本語
Yorodumi
- PDB-6i5j: Crystal structure of SOCS2:Elongin C:Elongin B in complex with gr... -

+
Open data


ID or keywords:

Loading...

-
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 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 / growth hormone receptor signaling pathway / VCB complex ...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 / growth hormone receptor signaling pathway / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / negative regulation of DNA-templated DNA replication / 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 / regulation of signal transduction / negative regulation of signal transduction / Growth hormone receptor signaling / 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 / cell surface receptor signaling pathway via JAK-STAT / cellular response to hormone stimulus / ubiquitin-like ligase-substrate adaptor activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / insulin-like growth factor receptor binding / ribosome-associated ubiquitin-dependent protein catabolic process / RNA Polymerase II Pre-transcription Events / Negative regulation of FLT3 / Interleukin-7 signaling / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / regulation of cell growth / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Inactivation of CSF3 (G-CSF) signaling / Vif-mediated degradation of APOBEC3G / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cytokine-mediated signaling pathway / Regulation of expression of SLITs and ROBOs / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / response to estradiol / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / intracellular signal transduction / protein ubiquitination / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / 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 / Elongin C; Chain C, domain 1 / SOCS box domain / SOCS box domain profile. / SOCS_box ...SOCS box / Suppressor of cytokine signalling 2 / SOCS2, SH2 domain / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / Elongin C; Chain C, domain 1 / SOCS box domain / SOCS box domain profile. / SOCS_box / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Elongin-C / Elongin B / 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
: / 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
Revision 1.5Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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)

-
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


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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more