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- PDB-6cct: Fragment of GID4 in complex with a short peptide -

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Basic information

Entry
Database: PDB / ID: 6cct
TitleFragment of GID4 in complex with a short peptide
Components
  • Glucose-induced degradation protein 4 homolog
  • Tetrapeptide
KeywordsPEPTIDE BINDING PROTEIN / Structural Genomics / 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 / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDong, C. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Molecular basis of GID4-mediated recognition of degrons for the Pro/N-end rule pathway.
Authors: Dong, C. / Zhang, H. / Li, L. / Tempel, W. / Loppnau, P. / Min, J.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: 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

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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: Tetrapeptide


Theoretical massNumber of molelcules
Total (without water)20,0332
Polymers20,0332
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-4 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.140, 40.140, 203.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 19604.777 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IVV7
#2: Protein/peptide Tetrapeptide


Mass: 428.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.05 Å3/Da / Density % sol: 40 % / Mosaicity: 0.23 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 2% Tacsimate pH 7.0 and 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→101.67 Å / Num. obs: 10614 / % possible obs: 100 % / Redundancy: 11.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.016 / Rrim(I) all: 0.053 / Net I/σ(I): 22.4 / Num. measured all: 125391 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.16111.0591108278270.9210.3261.1021.8100
8.91-101.678.60.0417452040.9980.0130.04250.299.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: early version of model from PDB entry 6CCR

6ccr


Resolution: 2.4→39.3 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.935 / SU B: 18.466 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.52 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The rotamer of peptide residue T2 was not clearly resolved by electron density, but chosen so as to enable plausible interactions with surrounding atoms of the model.
RfactorNum. reflection% reflection
Rfree0.2596 717 10 %
Rwork0.2177 --
obs0.2219 6457 99.94 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.05 Å2 / Biso mean: 60.158 Å2 / Biso min: 38.87 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.4→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 0 0 1270
Num. residues----167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191312
X-RAY DIFFRACTIONr_bond_other_d0.0020.021038
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.8951783
X-RAY DIFFRACTIONr_angle_other_deg0.98432386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2965164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35823.7162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59715167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.484152
X-RAY DIFFRACTIONr_chiral_restr0.0920.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
X-RAY DIFFRACTIONr_mcbond_it1.9174.259658
X-RAY DIFFRACTIONr_mcbond_other1.9154.266659
X-RAY DIFFRACTIONr_mcangle_it2.9776.375819
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 50 -
Rwork0.261 449 -
all-499 -
obs--100 %
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)
15.6809-1.0051-0.57933.99541.27095.10590.0188-0.11660.27040.2624-0.0331-0.28060.06370.14020.01420.0221-0.0161-0.01710.16050.01660.0314-12.691814.1277-14.8245
200000000000000-00.2039000.203900.2039000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A124 - 289
2X-RAY DIFFRACTION2A0

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