[English] 日本語
Yorodumi
- PDB-6qly: IDOL FERM domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qly
TitleIDOL FERM domain
ComponentsE3 ubiquitin-protein ligase MYLIP
KeywordsLIGASE / FERM domain / Ubiquitin 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: 2.5 Å
AuthorsMartinelli, L. / Sixma, T.K.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase MYLIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1614
Polymers38,9411
Non-polymers2203
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-15 kcal/mol
Surface area20040 Å2
2
A: E3 ubiquitin-protein ligase MYLIP
hetero molecules

A: E3 ubiquitin-protein ligase MYLIP
hetero molecules

A: E3 ubiquitin-protein ligase MYLIP
hetero molecules

A: E3 ubiquitin-protein ligase MYLIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,64316
Polymers155,7624
Non-polymers88112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_455-x-1,-y,z1
crystal symmetry operation16_445-y-1/2,-x-1/2,-z+1/21
Buried area17360 Å2
ΔGint-162 kcal/mol
Surface area65170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.490, 159.490, 76.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

-
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: 38940.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYLIP, BZF1, IDOL, BM-023, PP5242 / Plasmid: pETNKI-hisSUMO3-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): T1R
References: UniProt: Q8WY64, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.47 % / Description: Pyramidal-like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Tris pH 8.5, 20mM MgSO4, 4% (w/v) ethylene glycol, 12% (w/v) 2-Methyl-2,4-pentanediol (MPD)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.4→56.39 Å / Num. obs: 19675 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.03 / Rrim(I) all: 0.083 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.466.76.80514000.0462.7937.37897.7
10.72-56.396.10.02126610.0090.02399.3

-
Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qij

3qij


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.338 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.338 / SU Rfree Blow DPI: 0.238 / SU Rfree Cruickshank DPI: 0.241
RfactorNum. reflection% reflectionSelection details
Rfree0.247 841 4.83 %RANDOM
Rwork0.216 ---
obs0.217 17399 99.9 %-
Displacement parametersBiso max: 218.69 Å2 / Biso mean: 113 Å2 / Biso min: 56.54 Å2
Baniso -1Baniso -2Baniso -3
1--8.9239 Å20 Å20 Å2
2---8.9239 Å20 Å2
3---17.8479 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 13 38 2662
Biso mean--141.49 83.96 -
Num. residues----330
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d951SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes450HARMONIC5
X-RAY DIFFRACTIONt_it2667HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion343SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2844SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2667HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3594HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion20.84
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2395 130 4.7 %
Rwork0.2182 2636 -
all0.2192 2766 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: -47.6755 Å / Origin y: -5.0946 Å / Origin z: 9.7951 Å
111213212223313233
T0.0179 Å2-0.0695 Å2-0.0101 Å2-0.0025 Å20.1946 Å2---0.146 Å2
L2.6685 °2-1.0844 °20.201 °2-0.2789 °2-0.0973 °2--0.2999 °2
S0.0438 Å °0.7422 Å °0.6873 Å °0.0607 Å °-0.2015 Å °-0.0966 Å °-0.1881 Å °0.0946 Å °0.1577 Å °
Refinement TLS groupSelection details: { A|* }

+
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://pdbjlc1.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