[English] 日本語
Yorodumi
- PDB-7u3e: GID4 in complex with compound 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u3e
TitleGID4 in complex with compound 1
ComponentsGlucose-induced degradation protein 4 homolog
KeywordsPEPTIDE BINDING PROTEIN/INHIBITOR / Complex / Inhibitor / Protein degradation / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-INHIBITOR complex
Function / homologyVacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / Regulation of pyruvate metabolism / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cytosol / Chem-L4O / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.852 Å
AuthorsChana, C.K. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-143277 Canada
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery and Structural Characterization of Small Molecule Binders of the Human CTLH E3 Ligase Subunit GID4.
Authors: Chana, C.K. / Maisonneuve, P. / Posternak, G. / Grinberg, N.G.A. / Poirson, J. / Ona, S.M. / Ceccarelli, D.F. / Mader, P. / St-Cyr, D.J. / Pau, V. / Kurinov, I. / Tang, X. / Deng, D. / Cui, ...Authors: Chana, C.K. / Maisonneuve, P. / Posternak, G. / Grinberg, N.G.A. / Poirson, J. / Ona, S.M. / Ceccarelli, D.F. / Mader, P. / St-Cyr, D.J. / Pau, V. / Kurinov, I. / Tang, X. / Deng, D. / Cui, W. / Su, W. / Kuai, L. / Soll, R. / Tyers, M. / Rost, H.L. / Batey, R.A. / Taipale, M. / Gingras, A.C. / Sicheri, F.
History
DepositionFeb 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucose-induced degradation protein 4 homolog
B: Glucose-induced degradation protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6064
Polymers39,2102
Non-polymers3972
Water1,45981
1
A: Glucose-induced degradation protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8032
Polymers19,6051
Non-polymers1981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose-induced degradation protein 4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8032
Polymers19,6051
Non-polymers1981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.115, 39.785, 66.722
Angle α, β, γ (deg.)90.000, 94.910, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 126 through 127 and (name N...
21(chain B and ((resid 126 through 127 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYS(chain A and ((resid 126 through 127 and (name N...AA126 - 1274 - 5
12VALVAL(chain A and ((resid 126 through 127 and (name N...AA126 - 2894 - 167
13VALVAL(chain A and ((resid 126 through 127 and (name N...AA126 - 2894 - 167
14VALVAL(chain A and ((resid 126 through 127 and (name N...AA126 - 2894 - 167
15VALVAL(chain A and ((resid 126 through 127 and (name N...AA126 - 2894 - 167
21LYSLYS(chain B and ((resid 126 through 127 and (name N...BB126 - 1274 - 5
22VALVAL(chain B and ((resid 126 through 127 and (name N...BB124 - 2892 - 167
23VALVAL(chain B and ((resid 126 through 127 and (name N...BB124 - 2892 - 167
24VALVAL(chain B and ((resid 126 through 127 and (name N...BB124 - 2892 - 167

-
Components

#1: Protein Glucose-induced degradation protein 4 homolog / Vacuolar import and degradation protein 24 homolog


Mass: 19604.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Plasmid: PET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: Q8IVV7
#2: Chemical ChemComp-L4O / tert-butyl (1S,4S)-2,5-diazabicyclo[2.2.1]heptane-2-carboxylate


Mass: 198.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17% PEG3350, 0.1 M Bis-tris, 0.2 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→66.48 Å / Num. obs: 23568 / % possible obs: 96.7 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.037 / Rrim(I) all: 0.084 / Net I/σ(I): 11 / Num. measured all: 111545
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.893.20.866334910520.5480.531.0271.171.2
9.07-66.484.60.03910852360.9980.0190.04432.899.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.85 Å66.48 Å
Translation1.85 Å66.48 Å

-
Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDS20190315data reduction
Aimless0.5.32data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CCR

6ccr


Resolution: 1.852→66.478 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2341 1145 4.86 %
Rwork0.204 22394 -
obs0.2055 23539 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.48 Å2 / Biso mean: 38.8345 Å2 / Biso min: 20.26 Å2
Refinement stepCycle: final / Resolution: 1.852→66.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 28 81 2609
Biso mean--31.38 40.05 -
Num. residues----317
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1315X-RAY DIFFRACTION11.6TORSIONAL
12B1315X-RAY DIFFRACTION11.6TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.852-1.93610.30151260.2957223178
1.9361-2.03820.31111390.2597280297
2.0382-2.16590.27011640.23252860100
2.1659-2.33320.2571410.2131288099
2.3332-2.5680.24961340.2173285999
2.568-2.93960.24431590.20942867100
2.9396-3.70350.22171280.1956292199
3.7035-66.4780.211540.1841297499
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)
14.44782.59091.72623.82321.79361.93290.04670.01940.28860.1058-0.12430.22140.04360.00550.10110.3138-0.00180.0240.1930.01460.2122-11.79255.0601-32.2149
23.12310.43090.24453.64340.90413.3817-0.0827-0.3593-0.04480.41240.1041-0.47930.1230.1411-0.06050.4015-0.0188-0.03350.2237-0.01670.2784-2.00710.8305-24.3976
34.2584-0.9957-1.65681.80190.99232.8179-0.0791-0.0426-0.09270.2422-0.02160.14680.3664-0.07290.0890.3598-0.033-0.0060.23610.00670.273-10.39520.6575-27.5153
43.56971.1182-0.20056.8578-0.72882.3950.2310.2685-0.4127-0.0598-0.2168-0.9794-0.01260.5198-0.05130.3211-0.06730.0350.34030.02880.2292-5.8639-6.482-67.9718
53.48720.032-0.14953.36020.32942.474-0.14570.02220.03740.08410.0011-0.1788-0.05450.29540.13510.295-0.0117-0.01320.25630.06150.1913-10.3492-6.2465-57.0027
64.47593.4003-0.79535.4417-1.63642.93420.1475-0.3247-0.69920.4859-0.24320.5375-0.6614-0.3140.16290.27260.03420.06060.30220.02740.3711-27.4274-0.2719-60.0852
73.925-0.48290.96422.798-0.06272.39340.0551-0.05190.0865-0.0534-0.0581-0.2209-0.31780.270.02260.2913-0.03440.01670.26640.02880.199-11.2871-3.7662-61.1821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 127 through 162 )A127 - 162
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 229 )A163 - 229
3X-RAY DIFFRACTION3chain 'A' and (resid 230 through 289 )A230 - 289
4X-RAY DIFFRACTION4chain 'B' and (resid 124 through 149 )B124 - 149
5X-RAY DIFFRACTION5chain 'B' and (resid 150 through 204 )B150 - 204
6X-RAY DIFFRACTION6chain 'B' and (resid 205 through 221 )B205 - 221
7X-RAY DIFFRACTION7chain 'B' and (resid 222 through 289 )B222 - 289

+
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