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- PDB-7q50: human Gid4 bound to a Phe/N-peptide -

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Basic information

Entry
Database: PDB / ID: 7q50
Titlehuman Gid4 bound to a Phe/N-peptide
Components
  • FDVSWFMG peptide
  • Glucose-induced degradation protein 4 homolog
KeywordsLIGASE / GID / CTLH / ubiquitin / E3 ligase
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 / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsChrustowicz, J. / Sherpa, D. / Loke, M.S. / Prabu, J.R. / Schulman, B.A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035 Germany
German Research Foundation (DFG)SCHU 3196/1 Germany
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Multifaceted N-Degron Recognition and Ubiquitylation by GID/CTLH E3 Ligases.
Authors: Chrustowicz, J. / Sherpa, D. / Teyra, J. / Loke, M.S. / Popowicz, G.M. / Basquin, J. / Sattler, M. / Prabu, J.R. / Sidhu, S.S. / Schulman, B.A.
History
DepositionNov 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-induced degradation protein 4 homolog
B: FDVSWFMG peptide


Theoretical massNumber of molelcules
Total (without water)20,9652
Polymers20,9652
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.307, 131.307, 131.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

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


Mass: 20034.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GID4, C17orf39, VID24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IVV7
#2: Protein/peptide FDVSWFMG peptide


Mass: 931.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.41 Å3/Da / Density % sol: 72.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.1 M Sodium malonate, 0.3% Jeffamine ED-2001 pH 7, 0.1 M HEPES pH 7

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.16→46.42 Å / Num. obs: 12581 / % possible obs: 99.6 % / Redundancy: 20.6 % / CC1/2: 0.994 / Net I/σ(I): 9.1
Reflection shellResolution: 3.16→3.35 Å / Num. unique obs: 1981 / CC1/2: 0.206

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q4Y

7q4y


Resolution: 3.16→46.42 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2927 680 5.42 %
Rwork0.2363 --
obs0.2393 12549 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.16→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 0 9 1403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051443
X-RAY DIFFRACTIONf_angle_d0.761963
X-RAY DIFFRACTIONf_dihedral_angle_d19.261193
X-RAY DIFFRACTIONf_chiral_restr0.047197
X-RAY DIFFRACTIONf_plane_restr0.005249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.40.39671480.35962318X-RAY DIFFRACTION98
3.4-3.740.3061400.28212380X-RAY DIFFRACTION100
3.74-4.280.31171230.24252396X-RAY DIFFRACTION100
4.28-5.390.25711410.20492380X-RAY DIFFRACTION100
5.4-46.420.27941280.21592395X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.7202 Å / Origin y: 14.9345 Å / Origin z: 24.3194 Å
111213212223313233
T0.6233 Å20.0943 Å20.1341 Å2-0.7984 Å20.3579 Å2--0.8228 Å2
L7.1409 °2-1.0765 °21.2854 °2-8.6209 °2-0.019 °2--5.4805 °2
S-0.2504 Å °-1.2142 Å °-1.2059 Å °0.2253 Å °0.6316 Å °1.2816 Å °0.3784 Å °-0.9202 Å °-0.1675 Å °
Refinement TLS groupSelection details: all

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