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- PDB-6qlz: IDOL F3ab subdomain -

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Basic information

Entry
Database: PDB / ID: 6qlz
TitleIDOL F3ab subdomain
ComponentsE3 ubiquitin-protein ligase MYLIP
KeywordsLIGASE / E3 LIGASE CHOLESTEROL METABOLISM LDLR degradation
Function / homology
Function and homology information


regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of low-density lipoprotein particle clearance / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / cytoskeletal protein binding / VLDLR internalisation and degradation / cholesterol homeostasis / protein destabilization / RING-type E3 ubiquitin transferase / positive regulation of protein catabolic process / ubiquitin-protein transferase activity ...regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of low-density lipoprotein particle clearance / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / cytoskeletal protein binding / VLDLR internalisation and degradation / cholesterol homeostasis / protein destabilization / RING-type E3 ubiquitin transferase / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of neuron projection development / nervous system development / ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / metal ion binding / plasma membrane / cytosol
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 / FERM central domain / Zinc finger, C3HC4 type (RING finger) / FERM/acyl-CoA-binding protein superfamily ...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 / FERM central domain / Zinc finger, C3HC4 type (RING finger) / FERM/acyl-CoA-binding protein superfamily / FERM central domain / 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase MYLIP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.343 Å
AuthorsMartinelli, L. / Johansson, P. / Wan, P.T. / Gunnarsson, J. / Guo, H. / Boyd, H.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural analysis of the LDL receptor-interacting FERM domain in the E3 ubiquitin ligase IDOL reveals an obscured substrate-binding site.
Authors: Martinelli, L. / Adamopoulos, A. / Johansson, P. / Wan, P.T. / Gunnarsson, J. / Guo, H. / Boyd, H. / Zelcer, N. / Sixma, T.K.
History
DepositionFeb 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: E3 ubiquitin-protein ligase MYLIP
C: E3 ubiquitin-protein ligase MYLIP


Theoretical massNumber of molelcules
Total (without water)33,3893
Polymers33,3893
Non-polymers00
Water19811
1
A: E3 ubiquitin-protein ligase MYLIP


Theoretical massNumber of molelcules
Total (without water)11,1301
Polymers11,1301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase MYLIP


Theoretical massNumber of molelcules
Total (without water)11,1301
Polymers11,1301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase MYLIP


Theoretical massNumber of molelcules
Total (without water)11,1301
Polymers11,1301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.365, 69.536, 74.318
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / ...Inducible degrader of the LDL-receptor / Idol / Myosin regulatory light chain interacting protein / MIR / RING-type E3 ubiquitin transferase MYLIP


Mass: 11129.610 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYLIP, BZF1, IDOL, BM-023, PP5242 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): T1R
References: UniProt: Q8WY64, RING-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100mM Hepes pH 7.0 10% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.343→74.318 Å / Num. obs: 12704 / % possible obs: 99.3 % / Redundancy: 4.6 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.108 / Rsym value: 0.084 / Net I/av σ(I): 7.7 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.343-2.474.41.1470.717570.7111.5061.14797.2
2.47-2.624.80.768117350.4470.9810.768100
2.62-2.84.60.4961.516330.30.6480.49699.8
2.8-3.024.70.2922.615250.1730.3780.29299.8
3.02-3.314.70.1564.814320.0910.1980.15699.9
3.31-3.74.60.0818.812620.0470.1030.08199.2
3.7-4.284.60.05512.611490.0310.0690.05599.9
4.28-5.244.40.03616.99800.0210.0460.03699.7
5.24-7.414.30.0415.37650.0230.050.0498.7
7.41-74.31840.02718.44660.0160.0340.02798.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
BUSTERrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HE7

2he7


Resolution: 2.343→50 Å / Cross valid method: THROUGHOUT /
Num. reflection% reflection
obs12627 99.3 %
Displacement parametersBiso max: 141.86 Å2 / Biso mean: 63.5 Å2 / Biso min: 31.11 Å2
Refinement stepCycle: LAST / Resolution: 2.343→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 0 11 2213

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