[English] 日本語
Yorodumi
- PDB-13sr: PanDDA analysis group deposition -- IDOL RING domain in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 13sr
TitlePanDDA analysis group deposition -- IDOL RING domain in complex with Z48852953
ComponentsE3 ubiquitin-protein ligase MYLIP
KeywordsLIGASE / Diamond I04-1 fragment screening / PanDDA / XChemExplorer / E3 / ubiquitin / Zinc finger / RING
Function / homology
Function and homology information


regulation of low-density lipoprotein particle receptor catabolic process / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / negative regulation of low-density lipoprotein particle clearance / cytoskeletal protein binding / cholesterol homeostasis / VLDLR internalisation and degradation / RING-type E3 ubiquitin transferase / protein destabilization / ubiquitin-protein transferase activity / positive regulation of protein catabolic process ...regulation of low-density lipoprotein particle receptor catabolic process / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / negative regulation of low-density lipoprotein particle clearance / cytoskeletal protein binding / cholesterol homeostasis / VLDLR internalisation and degradation / RING-type E3 ubiquitin transferase / protein destabilization / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / nervous system development / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of neuron projection development / ubiquitin-dependent protein catabolic process / cytoskeleton / protein ubiquitination / zinc 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 / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.65 Å
AuthorsBradshaw, W.J. / Guenther, F. / Murphy, E.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Alzheimers Research UK (ARUK)ARUK2018DDI-OX United Kingdom
Alzheimers Research UK (ARUK)520909 United Kingdom
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Bradshaw, W.J. / Guenther, F. / Murphy, E.J.
History
DepositionOct 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,27915
Polymers35,2814
Non-polymers99811
Water2,972165
1
A: E3 ubiquitin-protein ligase MYLIP
B: E3 ubiquitin-protein ligase MYLIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1017
Polymers17,6412
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-21 kcal/mol
Surface area9380 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase MYLIP
D: E3 ubiquitin-protein ligase MYLIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1798
Polymers17,6412
Non-polymers5386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-17 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.640, 47.730, 69.940
Angle α, β, γ (deg.)90.000, 90.780, 90.000
Int Tables number4
Space group name H-MP1211

-
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: 8820.361 Da / Num. of mol.: 4
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)
References: UniProt: Q8WY64, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1CYD / 4-methyl-N-{[(2S)-oxolan-2-yl]methyl}-1,3-thiazol-2-amine


Mass: 198.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.75 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92204 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92204 Å / Relative weight: 1
ReflectionResolution: 1.65→37.86 Å / Num. obs: 35621 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.054 / Rrim(I) all: 0.141 / Net I/σ(I): 9.5 / Num. measured all: 241972 / Scaling rejects: 172
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.696.92.3792621181370.3010.9712.5730.8100
7.38-37.865.70.04843024370.9940.0220.05335.898.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
BUSTER2.10.4 (23-JAN-2024)refinement
Aimless0.8.2data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 9SA2

9sa2


Resolution: 1.65→22.32 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 1747 4.91 %RANDOM
Rwork0.202 ---
obs0.2033 35591 99.9 %-
Displacement parametersBiso max: 73.23 Å2 / Biso mean: 36.07 Å2 / Biso min: 17.85 Å2
Baniso -1Baniso -2Baniso -3
1-5.1585 Å20 Å2-0.7932 Å2
2--0.856 Å20 Å2
3----6.0145 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.65→22.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 38 165 2458
Biso mean--41.39 45.37 -
Num. residues----290
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d995SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes463HARMONIC5
X-RAY DIFFRACTIONt_it2526HARMONIC10
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_contact2126SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2526HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3452HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion15.94
LS refinement shellResolution: 1.65→1.66 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3249 35 4.92 %
Rwork0.351 677 -
all-712 -
obs--99.71 %
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)
10.7750.3489-1.29580.6158-0.53012.0402-0.00230.14430.14490.08770.00280.09540.0391-0.3231-0.0005-0.05830.01570.00180.00620.01250.0156-24.08737.899115.3152
20.748-0.06330.68940.09880.03630.93180.00680.17060.08310.0619-0.01990.0133-0.02420.05660.01310.0072-0.00460.02570.0050.0084-0.0183-10.084711.319814.081
30.83540.0220.77710.10440.11551.67240.00840.0645-0.23690.06580.0172-0.0403-0.01110.1792-0.0256-0.0390.01280.0071-0.0403-0.03270.05221.2915-8.042517.2895
40.4717-0.6494-0.60110.73870.63770.1228-0.07330.1621-0.11540.10770.0588-0.0198-0.0433-0.12320.0144-0.0022-0.01910.0133-0.0072-0.0148-0.0085-12.4063-11.656116.5773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A368 - 436
2X-RAY DIFFRACTION2{ B|* }B368 - 444
3X-RAY DIFFRACTION3{ C|* }C368 - 437
4X-RAY DIFFRACTION4{ D|* }D368 - 441

+
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