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- PDB-2yho: The IDOL-UBE2D complex mediates sterol-dependent degradation of t... -

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Basic information

Entry
Database: PDB / ID: 2yho
TitleThe IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor
Components
  • E3 UBIQUITIN-PROTEIN LIGASE MYLIP
  • UBIQUITIN-CONJUGATING ENZYME E2 D1
KeywordsLIGASE / E2 LIGASE-E3 LIGASE COMPLEX / RING ZINC-FINGER / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / negative regulation of low-density lipoprotein particle clearance / Aberrant regulation of mitotic exit in cancer due to RB1 defects / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / Phosphorylation of the APC/C / Signaling by BMP ...regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / negative regulation of low-density lipoprotein particle clearance / Aberrant regulation of mitotic exit in cancer due to RB1 defects / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / Phosphorylation of the APC/C / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin conjugating enzyme activity / Transcriptional Regulation by VENTX / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / ubiquitin ligase complex / negative regulation of TORC1 signaling / cytoskeletal protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / cholesterol homeostasis / positive regulation of protein ubiquitination / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Negative regulators of DDX58/IFIH1 signaling / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Peroxisomal protein import / Regulation of TNFR1 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Inactivation of CSF3 (G-CSF) signaling / protein destabilization / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / positive regulation of protein catabolic process / Separation of Sister Chromatids / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Ovarian tumor domain proteases / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / nervous system development / Neddylation / negative regulation of neuron projection development / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
MYLIP, FERM domain C-lobe / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / FERM central domain ...MYLIP, FERM domain C-lobe / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / FERM central domain / Zinc finger, C3HC4 type (RING finger) / FERM/acyl-CoA-binding protein superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / FERM central domain / Ubiquitin-conjugating enzyme/RWD-like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Zinc finger RING-type profile. / Zinc finger, RING-type / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Ubiquitin-conjugating enzyme E2 D1 / E3 ubiquitin-protein ligase MYLIP
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsFairall, L. / Goult, B.T. / Millard, C.J. / Tontonoz, P. / Schwabe, J.W.R.
CitationJournal: Genes Dev. / Year: 2011
Title: The Idol-Ube2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor.
Authors: Zhang, L. / Fairall, L. / Goult, B.T. / Calkin, A.C. / Hong, C. / Millard, C.J. / Tontonoz, P. / Schwabe, J.W.
History
DepositionMay 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 20, 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 / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
B: UBIQUITIN-CONJUGATING ENZYME E2 D1
C: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
D: UBIQUITIN-CONJUGATING ENZYME E2 D1
E: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
F: UBIQUITIN-CONJUGATING ENZYME E2 D1
G: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
H: UBIQUITIN-CONJUGATING ENZYME E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,50125
Polymers102,4468
Non-polymers1,05517
Water7,314406
1
A: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
B: UBIQUITIN-CONJUGATING ENZYME E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9798
Polymers25,6122
Non-polymers3676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
D: UBIQUITIN-CONJUGATING ENZYME E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7424
Polymers25,6122
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
F: UBIQUITIN-CONJUGATING ENZYME E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8015
Polymers25,6122
Non-polymers1903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: E3 UBIQUITIN-PROTEIN LIGASE MYLIP
H: UBIQUITIN-CONJUGATING ENZYME E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9798
Polymers25,6122
Non-polymers3676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.690, 137.870, 63.750
Angle α, β, γ (deg.)90.00, 106.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
E3 UBIQUITIN-PROTEIN LIGASE MYLIP / INDUCIBLE DEGRADER OF THE LDL-RECEPTOR / IDOL / MYOSIN REGULATORY LIGHT CHAIN INTERACTING PROTEIN / MIR


Mass: 8861.413 Da / Num. of mol.: 4 / Fragment: RING, RESIDUES 369-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA
References: UniProt: Q8WY64, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein
UBIQUITIN-CONJUGATING ENZYME E2 D1 / STIMULATOR OF FE TRANSPORT / SFT / UBC4/5 HOMOLOG / UBCH5 / UBIQUITIN CARRIER PROTEIN D1 / ...STIMULATOR OF FE TRANSPORT / SFT / UBC4/5 HOMOLOG / UBCH5 / UBIQUITIN CARRIER PROTEIN D1 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 1 / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 1 / UBIQUITIN-PROTEIN LIGASE D1 / UBE2D1


Mass: 16750.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: P51668, ubiquitin-protein ligase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.35 Å3/Da / Density % sol: 47.69 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→55.91 Å / Num. obs: 53163 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 23.87 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRIES 3EB6, 2YHN

3eb6

2yhn


Resolution: 2.1→55.906 Å / SU ML: 0.27 / σ(F): 0.01 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 2696 5.1 %
Rwork0.1856 --
obs0.1881 53163 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.236 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 31.37 Å2
Baniso -1Baniso -2Baniso -3
1-13.1919 Å20 Å20.0484 Å2
2---3.5725 Å20 Å2
3----9.6193 Å2
Refinement stepCycle: LAST / Resolution: 2.1→55.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6758 0 44 406 7208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096996
X-RAY DIFFRACTIONf_angle_d1.1539514
X-RAY DIFFRACTIONf_dihedral_angle_d15.0822571
X-RAY DIFFRACTIONf_chiral_restr0.0721052
X-RAY DIFFRACTIONf_plane_restr0.0051228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.25592350.18794738X-RAY DIFFRACTION90
2.1751-2.26220.27222590.20934887X-RAY DIFFRACTION92
2.2622-2.36510.2682510.19894872X-RAY DIFFRACTION93
2.3651-2.48980.26112490.1884971X-RAY DIFFRACTION94
2.4898-2.64580.25522590.19585056X-RAY DIFFRACTION96
2.6458-2.85010.26932650.19435050X-RAY DIFFRACTION96
2.8501-3.13690.24862660.19165169X-RAY DIFFRACTION98
3.1369-3.59070.23912970.1785207X-RAY DIFFRACTION98
3.5907-4.52360.19283020.15925238X-RAY DIFFRACTION100
4.5236-55.92540.20763130.18535279X-RAY DIFFRACTION99

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