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- PDB-7q9q: Crystal structure of PDE6D Geranylgeranylated cystein complex -

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Basic information

Entry
Database: PDB / ID: 7q9q
TitleCrystal structure of PDE6D Geranylgeranylated cystein complex
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
O-METHYLCYSTEINE / GERAN-8-YL GERAN / 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: 1.45 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 / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)18,3266
Polymers17,7301
Non-polymers5965
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint18 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.048, 35.289, 37.645
Angle α, β, γ (deg.)77.725, 68.980, 69.228
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17730.215 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 BL21(DE3) (bacteria) / References: UniProt: O43924
#2: Chemical ChemComp-CMT / O-METHYLCYSTEINE


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 30% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→34.971 Å / Num. obs: 24436 / % possible obs: 95.9 % / Redundancy: 3.5 % / CC1/2: 1 / Net I/σ(I): 17.98
Reflection shellResolution: 1.45→1.49 Å / Num. unique obs: 1715 / CC1/2: 0.669

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Processing

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

5tb5


Resolution: 1.45→34.971 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.201 / SU B: 2.617 / SU ML: 0.096 / Average fsc free: 0.8 / Average fsc work: 0.8215 / Cross valid method: FREE R-VALUE / ESU R: 0.094 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2736 1222 5.001 %
Rwork0.2251 23214 -
all0.228 --
obs-24436 96.193 %
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: 29.697 Å2
Baniso -1Baniso -2Baniso -3
1--1.546 Å20.939 Å2-0.111 Å2
2--0.583 Å2-0.592 Å2
3---1.126 Å2
Refinement stepCycle: LAST / Resolution: 1.45→34.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 40 115 1363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d00.0131290
X-RAY DIFFRACTIONr_bond_other_d00.0171237
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.6541726
X-RAY DIFFRACTIONr_angle_other_deg1.6631.5842857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6595150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33321.18476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03315232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1931510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021424
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02294
X-RAY DIFFRACTIONr_nbd_refined0.2050.2207
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.21121
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2569
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1310.27
X-RAY DIFFRACTIONr_nbd_other0.1930.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.214
X-RAY DIFFRACTIONr_mcbond_it2.4782.891603
X-RAY DIFFRACTIONr_mcbond_other2.4742.891603
X-RAY DIFFRACTIONr_mcangle_it3.3764.309752
X-RAY DIFFRACTIONr_mcangle_other3.3764.318753
X-RAY DIFFRACTIONr_scbond_it3.2283.212687
X-RAY DIFFRACTIONr_scbond_other3.2263.218688
X-RAY DIFFRACTIONr_scangle_it4.7514.676974
X-RAY DIFFRACTIONr_scangle_other4.7494.683975
X-RAY DIFFRACTIONr_lrange_it6.1433.5211372
X-RAY DIFFRACTIONr_lrange_other6.11733.3751362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.45-1.4880.392860.36816270.3718370.4920.48893.24990.346
1.488-1.5280.369890.35416980.35418930.610.62294.40040.331
1.528-1.5730.352820.3215650.32217370.6770.71994.81860.291
1.573-1.6210.37820.29115590.29517370.7710.78294.47320.26
1.621-1.6740.346800.27515120.27916780.8170.82994.87490.245
1.674-1.7320.345780.25214780.25616300.7940.8695.46010.22
1.732-1.7980.341740.25214170.25615520.8210.86796.06960.219
1.798-1.8710.359730.25913860.26315160.810.85196.24010.225
1.871-1.9540.32690.25213090.25614290.8360.86696.43110.221
1.954-2.0490.282670.23712710.23913820.8960.90396.81620.21
2.049-2.1590.267630.22111980.22313010.8910.92396.92540.191
2.159-2.290.248610.22811600.22912540.9230.91697.36840.204
2.29-2.4470.287570.22610740.22911600.8670.997.50.202
2.447-2.6420.338540.2310220.23611000.8650.89597.81820.211
2.642-2.8930.294490.2379370.23910040.8710.89298.20720.218
2.893-3.2310.244440.2398350.2398920.9090.89798.54260.219
3.231-3.7260.246390.217480.2127940.920.93799.11840.202
3.726-4.550.179340.1766410.1776800.9540.95599.26470.168
4.55-6.3810.288260.1964990.2015300.9380.93799.05660.193
6.381-34.9710.274150.2112730.2152920.8960.998.63010.21

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