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- PDB-7qf9: Crystal structure of PDE6D bound to HRas peptide -

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Basic information

Entry
Database: PDB / ID: 7qf9
TitleCrystal structure of PDE6D bound to HRas peptide
Components
  • HRas peptide
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsTRANSPORT PROTEIN / complex / trafficking
Function / homology
Function and homology information


ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton ...ARL13B-mediated ciliary trafficking of INPP5E / GTPase inhibitor activity / response to stimulus / visual perception / cytoplasmic vesicle membrane / cilium / small GTPase binding / RAS processing / cytoplasmic vesicle / cytoskeleton / cytosol / cytoplasm
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 / 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: 1.95 Å
AuthorsYelland, T. / Ismail, I.
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
DepositionDec 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 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 2.0Dec 7, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / entity / entity_poly / entity_poly_seq / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _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
AAA: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
EEE: HRas peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,46511
Polymers35,6073
Non-polymers8588
Water2,468137
1
BBB: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8386
Polymers17,3101
Non-polymers5285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
EEE: HRas peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6285
Polymers18,2972
Non-polymers3313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.626, 82.789, 112.467
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains BBB AAA)

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Components

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Protein / Protein/peptide , 2 types, 3 molecules BBBAAAEEE

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


Mass: 17309.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D, PDED
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O43924
#2: Protein/peptide HRas peptide


Mass: 987.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 145 molecules

#3: Chemical ChemComp-FAR / FARNESYL / Farnesol


Mass: 206.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26
#4: Chemical ChemComp-CMT / O-METHYLCYSTEINE


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M Tris pH 8.5, 8% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→56.234 Å / Num. obs: 24377 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 16.9
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 1768 / CC1/2: 0.772

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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: 1.95→56.234 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.889 / SU B: 10.064 / SU ML: 0.147 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2993 1197 4.92 %
Rwork0.2295 23132 -
all0.233 --
obs-24329 99.75 %
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: 41.591 Å2
Baniso -1Baniso -2Baniso -3
1--0.543 Å20 Å20 Å2
2--2.041 Å20 Å2
3----1.499 Å2
Refinement stepCycle: LAST / Resolution: 1.95→56.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 66 137 2643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132622
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172480
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.6523525
X-RAY DIFFRACTIONr_angle_other_deg1.5381.5845737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1015313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03421.769147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52615468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.961518
X-RAY DIFFRACTIONr_chiral_restr0.040.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
X-RAY DIFFRACTIONr_nbd_refined0.1810.2380
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.22235
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21152
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.218
X-RAY DIFFRACTIONr_nbd_other0.2120.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0390.21
X-RAY DIFFRACTIONr_mcbond_it3.3593.4361244
X-RAY DIFFRACTIONr_mcbond_other3.3593.4361243
X-RAY DIFFRACTIONr_mcangle_it4.3185.1171556
X-RAY DIFFRACTIONr_mcangle_other4.3165.1171557
X-RAY DIFFRACTIONr_scbond_it3.8223.831378
X-RAY DIFFRACTIONr_scbond_other3.8213.8311379
X-RAY DIFFRACTIONr_scangle_it5.6335.5551968
X-RAY DIFFRACTIONr_scangle_other5.6315.5561969
X-RAY DIFFRACTIONr_lrange_it7.55138.7582756
X-RAY DIFFRACTIONr_lrange_other7.54738.7552756
X-RAY DIFFRACTIONr_ncsr_local_group_10.1380.054483
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
1.95-2.0010.338860.30616760.30817670.7520.7999.7170.289
2.001-2.0550.3131010.27416200.27617210.8190.8421000.254
2.055-2.1150.326810.27415850.27716660.8150.8671000.248
2.115-2.180.373960.26515650.27116610.8590.8841000.24
2.18-2.2510.288690.24314990.24515680.8910.9081000.217
2.251-2.330.276710.24814540.2515260.8910.91299.93450.217
2.33-2.4180.335640.25814070.26114710.8860.9041000.228
2.418-2.5160.293700.24713810.24914510.8930.9151000.22
2.516-2.6280.272760.23712870.23913630.8880.9221000.211
2.628-2.7560.348550.24612660.25113210.8710.9051000.22
2.756-2.9050.345630.23412020.23912650.8490.9111000.214
2.905-3.080.248570.23911340.23911920.9090.90999.91610.218
3.08-3.2920.305550.22410560.22711110.9040.9241000.207
3.292-3.5550.239490.2410210.2410700.9130.9291000.227
3.555-3.8930.262580.2129280.2159860.9410.9471000.202
3.893-4.350.296460.198480.1948940.9160.9561000.177
4.35-5.0180.236370.1697460.1727830.9470.9631000.155
5.018-6.1330.311310.2196460.2236770.9150.9531000.199
6.133-8.6230.33210.2415390.2455600.8550.9251000.228
8.623-56.2340.974110.3372720.3533360.3710.83884.22620.353
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)
10.58820.41160.49650.29590.30960.86480.04350.0726-0.02040.0480.0231-0.0027-0.00540.0465-0.06660.04930.01560.00310.0767-0.03580.073-3.139915.7239-14.5056
20.3136-0.47750.26530.7403-0.42351.2306-0.0487-0.05260.01580.03610.0705-0.0459-0.0676-0.0488-0.02180.0528-0.00060.00070.0587-0.00850.08388.022613.2101-42.7431
31.82013.054-1.45666.3088-0.23635.28390.02590.04190.25840.25010.26740.41870.1560.4436-0.29330.0342-0.00730.00150.12270.00240.073720.317310.2896-40.329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLBBB2 - 150
2X-RAY DIFFRACTION2ALLAAA4 - 150
3X-RAY DIFFRACTION3ALLEEE14 - 19

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