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- PDB-8v1p: CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH UBF9092 -

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Basic information

Entry
Database: PDB / ID: 8v1p
TitleCRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH UBF9092
ComponentsGlucose-induced degradation protein 4 homolog
KeywordsPEPTIDE BINDING PROTEIN / UBIQUITIN / PRO/N-DEGRON / PROTEIN DEGRADATION / STRUCTURAL GENOMICS CONSORTIUM / SGC
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 / N,N~2~-bis[(4-methoxyphenyl)methyl]glycinamide / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsDong, C. / Dong, A. / Calabrese, M. / Wang, F. / Owen, D. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF GID4 IN COMPLEX WITH UBF9092
Authors: Dong, C. / Dong, A. / Calabrese, M. / Wang, F. / Owen, D. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionNov 21, 2023Deposition site: RCSB / Processing site: RCSB
SupersessionDec 6, 2023ID: 7S12
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,8622
Polymers19,5481
Non-polymers3141
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.099, 40.099, 201.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 19547.725 Da / Num. of mol.: 1 / Fragment: Residues 124-289
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 (E. coli) / References: UniProt: Q8IVV7
#2: Chemical ChemComp-98C / N,N~2~-bis[(4-methoxyphenyl)methyl]glycinamide


Mass: 314.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl 8.5, 30% PEG3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 8994 / % possible obs: 99.5 % / Redundancy: 9.8 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.018 / Rrim(I) all: 0.057 / Χ2: 1.112 / Net I/σ(I): 12.2 / Num. measured all: 88354
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.21-2.255.90.6884360.7570.9280.2890.750.85499.5
2.25-2.297.20.6384180.7670.9320.2460.6870.81599.5
2.29-2.338.50.514420.9160.9780.180.5430.84599.8
2.33-2.389.70.4484390.9150.9780.1490.4740.85299.8
2.38-2.4310.30.4254230.9480.9860.1370.4470.841100
2.43-2.4910.90.3654490.9570.9890.1130.3820.916100
2.49-2.5511.40.2824250.9660.9910.0870.2950.897100
2.55-2.6211.40.2374290.9820.9960.0730.2480.939100
2.62-2.711.10.1854630.9860.9960.0580.1941.011100
2.7-2.7811.40.1554210.9920.9980.0480.1631.02100
2.78-2.88110.1274610.9940.9990.040.1331.05299.8
2.88-3110.14290.9950.9990.0310.1051.111100
3-3.1410.30.084540.9970.9990.0260.0841.26399.6
3.14-3.39.30.0684480.99810.0240.0721.338100
3.3-3.5110.10.0584420.9980.9990.0190.0611.453100
3.51-3.789.90.0514630.99910.0170.0541.42799.4
3.78-4.1610.50.0474530.9980.9990.0150.0491.40999.3
4.16-4.769.70.0414690.99910.0140.0441.39998.3
4.76-69.10.0394820.99910.0130.0421.31398.4
6-508.30.0365480.99910.0130.0391.26198.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
REFMACphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→39.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.92 / SU B: 20.391 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27817 895 10 %RANDOM
Rwork0.216 ---
obs0.22208 8016 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.576 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---1.2 Å20 Å2
3---2.41 Å2
Refinement stepCycle: 1 / Resolution: 2.21→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 23 6 1327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121366
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171105
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.6411854
X-RAY DIFFRACTIONr_angle_other_deg1.2421.5642543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8995165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.10923.12564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95715182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.213153
X-RAY DIFFRACTIONr_chiral_restr0.0620.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021578
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02337
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2793.918662
X-RAY DIFFRACTIONr_mcbond_other2.2673.915661
X-RAY DIFFRACTIONr_mcangle_it3.3595.865826
X-RAY DIFFRACTIONr_mcangle_other3.3645.868827
X-RAY DIFFRACTIONr_scbond_it2.2684.004704
X-RAY DIFFRACTIONr_scbond_other2.2664.003705
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3335.9681029
X-RAY DIFFRACTIONr_long_range_B_refined4.88643.4461506
X-RAY DIFFRACTIONr_long_range_B_other4.88443.4341507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.211→2.269 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 66 -
Rwork0.299 572 -
obs--99.07 %
Refinement TLS params.Method: refined / Origin x: -11.7185 Å / Origin y: 14.1425 Å / Origin z: -13.5238 Å
111213212223313233
T0.0403 Å2-0.0682 Å2-0.0314 Å2-0.2913 Å20.0992 Å2--0.0798 Å2
L4.0538 °2-0.9609 °2-1.0435 °2-3.187 °20.6301 °2--5.0504 °2
S0.0663 Å °0.2329 Å °0.304 Å °0.258 Å °-0.2776 Å °-0.3366 Å °0.0126 Å °0.0335 Å °0.2113 Å °

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