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- PDB-7q9r: Cocrystal structure of PDE6D bound to NRAS peptide -

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Basic information

Entry
Database: PDB / ID: 7q9r
TitleCocrystal structure of PDE6D bound to NRAS peptide
ComponentsRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsTRANSPORT PROTEIN / Complex
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cilium / intracellular membrane-bounded organelle ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / visual perception / cytoplasmic vesicle membrane / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cilium / intracellular membrane-bounded organelle / cytoplasm / cytosol
Similarity search - Function
Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Immunoglobulin E-set
Similarity search - Domain/homology
FARNESYL / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYelland, T. / Ismail, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.
Authors: Yelland, T. / Garcia, E. / Parry, C. / Kowalczyk, D. / Wojnowska, M. / Gohlke, A. / Zalar, M. / Cameron, K. / Goodwin, G. / Yu, Q. / Zhu, P.C. / ElMaghloob, Y. / Pugliese, A. / Archibald, L. ...Authors: Yelland, T. / Garcia, E. / Parry, C. / Kowalczyk, D. / Wojnowska, M. / Gohlke, A. / Zalar, M. / Cameron, K. / Goodwin, G. / Yu, Q. / Zhu, P.C. / ElMaghloob, Y. / Pugliese, A. / Archibald, L. / Jamieson, A. / Chen, Y.X. / McArthur, D. / Bower, J. / Ismail, S.
History
DepositionNov 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 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 / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BBB: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1849
Polymers17,4411
Non-polymers7438
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.788, 55.788, 114.842
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta / GMP-PDE delta / Protein p17


Mass: 17440.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED / Production host: Escherichia coli (E. coli) / References: UniProt: O43924
#2: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid pH 4.0 and 3.2 M AmSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.5→114.87 Å / Num. obs: 7634 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.995 / Net I/σ(I): 10.5
Reflection shellResolution: 2.5→2.56 Å / Num. unique obs: 547 / CC1/2: 0.859

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TB5

5tb5


Resolution: 2.5→48.36 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.878 / SU B: 10.312 / SU ML: 0.228 / Cross valid method: FREE R-VALUE / ESU R: 0.483 / ESU R Free: 0.299
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2759 346 4.551 %
Rwork0.2335 7256 -
all0.235 --
obs-7602 99.974 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.585 Å2
Baniso -1Baniso -2Baniso -3
1-0.731 Å20.366 Å20 Å2
2--0.731 Å20 Å2
3----2.373 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1197 0 46 59 1302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0131278
X-RAY DIFFRACTIONr_bond_other_d00.0171226
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.6491714
X-RAY DIFFRACTIONr_angle_other_deg0.9971.5762832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14521.11172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16515232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7891510
X-RAY DIFFRACTIONr_chiral_restr0.0190.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02285
X-RAY DIFFRACTIONr_nbd_refined0.2010.2213
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2230.21096
X-RAY DIFFRACTIONr_nbtor_refined0.160.2541
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.2617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0810.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.211
X-RAY DIFFRACTIONr_nbd_other0.2850.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0960.210
X-RAY DIFFRACTIONr_mcbond_it0.6183.018593
X-RAY DIFFRACTIONr_mcbond_other0.6183.019592
X-RAY DIFFRACTIONr_mcangle_it1.1694.517740
X-RAY DIFFRACTIONr_mcangle_other1.1684.516741
X-RAY DIFFRACTIONr_scbond_it0.3273.105685
X-RAY DIFFRACTIONr_scbond_other0.3253.075674
X-RAY DIFFRACTIONr_scangle_it0.6684.629973
X-RAY DIFFRACTIONr_scangle_other0.6684.581956
X-RAY DIFFRACTIONr_lrange_it2.69633.2091323
X-RAY DIFFRACTIONr_lrange_other2.68733.2031321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.306290.287518X-RAY DIFFRACTION100
2.565-2.6350.341190.282525X-RAY DIFFRACTION100
2.635-2.7110.341210.273491X-RAY DIFFRACTION100
2.711-2.7950.267170.255480X-RAY DIFFRACTION99.5992
2.795-2.8860.385210.258474X-RAY DIFFRACTION100
2.886-2.9880.274190.252452X-RAY DIFFRACTION100
2.988-3.10.282270.257438X-RAY DIFFRACTION100
3.1-3.2270.387290.264414X-RAY DIFFRACTION100
3.227-3.370.298180.215406X-RAY DIFFRACTION100
3.37-3.5350.278120.223396X-RAY DIFFRACTION100
3.535-3.7250.273170.222395X-RAY DIFFRACTION100
3.725-3.9510.182180.186348X-RAY DIFFRACTION100
3.951-4.2240.235170.187324X-RAY DIFFRACTION100
4.224-4.5620.205170.171320X-RAY DIFFRACTION100
4.562-4.9960.201170.184290X-RAY DIFFRACTION100
4.996-5.5850.297190.242260X-RAY DIFFRACTION100
5.585-6.4460.26390.296242X-RAY DIFFRACTION100
6.446-7.8880.16740.293213X-RAY DIFFRACTION100
7.888-11.130.249120.216162X-RAY DIFFRACTION100
11.13-48.360.74740.331108X-RAY DIFFRACTION100

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