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- PDB-6ccu: Complex between a GID4 fragment and a short peptide -

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Basic information

Entry
Database: PDB / ID: 6ccu
TitleComplex between a GID4 fragment and a short peptide
Components
  • Glucose-induced degradation protein 4 homolog
  • Short peptide
KeywordsPROTEIN BINDING / Structural Genomics / Structural Genomics Consortium / SGC
Function / homologyVacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / ubiquitin ligase complex / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / Glucose-induced degradation protein 4 homolog
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 / _citation_author.name
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: Short peptide


Theoretical massNumber of molelcules
Total (without water)22,2497
Polymers22,2492
Non-polymers05
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.045, 43.669, 99.984
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21739.176 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 (E. coli) / References: UniProt: Q8IVV7
#2: Protein/peptide Short peptide


Mass: 509.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 5 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.18 Å3/Da / Density % sol: 37.39 % / Mosaicity: 0.14 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 and 0.03M Citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.7→43.67 Å / Num. obs: 20007 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Rrim(I) all: 0.078 / Net I/σ(I): 14.7 / Num. measured all: 128263 / 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
1.7-1.736.51.7886820104410440.6710.7511.9421.199.2
9-43.675.40.0299451760.9990.0140.03349.299.6

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Processing

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

6ccr


Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.827 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflection
Rfree0.2359 908 5 %
Rwork0.1909 --
obs0.193 17417 99.89 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.7 Å2 / Biso mean: 31.715 Å2 / Biso min: 19.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å2-0 Å2
2--2.02 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 5 47 1411
Biso mean--34.15 34.46 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191417
X-RAY DIFFRACTIONr_bond_other_d0.0020.021190
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9141922
X-RAY DIFFRACTIONr_angle_other_deg0.94632757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69323.94471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.921152
X-RAY DIFFRACTIONr_chiral_restr0.0940.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_mcbond_it1.0571.915673
X-RAY DIFFRACTIONr_mcbond_other1.0571.914672
X-RAY DIFFRACTIONr_mcangle_it1.6732.86837
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 57 -
Rwork0.312 1257 -
all-1314 -
obs--99.85 %
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)
12.9050.14950.50651.5070.43532.8580.0268-0.24480.0732-0.052-0.0330.0441-0.057-0.13660.00620.02070.0084-0.00130.13790.00910.0053-8.1403-9.30812.2368
20.59410.397-1.38947.1877-0.81357.70430.0373-0.09680.03860.2761-0.05720.1892-0.133-0.02060.01990.1494-0.0054-0.00760.1908-0.03180.1285-14.8328-4.264823.8725
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 289
2X-RAY DIFFRACTION2B1 - 4

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