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- PDB-5f2u: Structure of Fully modified farnesylated INPP5E Peptide in comple... -

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Basic information

Entry
Database: PDB / ID: 5f2u
TitleStructure of Fully modified farnesylated INPP5E Peptide in complex with PDE6D
Components
  • Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, s-farnesyl-l-cysteine methyl ester
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
KeywordsLIPID BINDING PROTEIN / immunoglobulin-like / signaling protein
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
GMP phosphodiesterase, delta subunit / Retinal rod rhodopsin-sensitive cGMP 3', 5'-cyclic phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit / GMP phosphodiesterase, delta subunit superfamily / GMP-PDE, delta subunit / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta
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: 1.85 Å
AuthorsFansa, E.K. / Isamil, S. / Wittinghofer, A.
CitationJournal: Nat Commun / Year: 2016
Title: PDE6delta-mediated sorting of INPP5E into the cilium is determined by cargo-carrier affinity.
Authors: Fansa, E.K. / Koesling, S.K. / Zent, E. / Wittinghofer, A. / Ismail, S.
History
DepositionDec 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 2.0Jun 30, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code ..._entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _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_asym_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.entity_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 3.0Jul 7, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq / struct_site_gen
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.group_PDB / _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.type_symbol / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 3.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
C: Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, s-farnesyl-l-cysteine methyl ester
D: Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, s-farnesyl-l-cysteine methyl ester
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0806
Polymers35,6674
Non-polymers4132
Water1,60389
1
A: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
C: Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, s-farnesyl-l-cysteine methyl ester
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0403
Polymers17,8332
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-2 kcal/mol
Surface area7870 Å2
MethodPISA
2
B: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
D: Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, s-farnesyl-l-cysteine methyl ester
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0403
Polymers17,8332
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-2 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.470, 81.200, 117.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#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 (E. coli) / References: UniProt: O43924
#2: Protein/peptide Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, s-farnesyl-l-cysteine methyl ester


Mass: 523.602 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-FAR / FARNESYL / Farnesol


Mass: 206.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H26
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.58 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.007 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.85→19.53 Å / Num. obs: 30251 / % possible obs: 99.8 % / Redundancy: 6.39 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.42
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 6.58 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 3.09 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALE5.7.0032data scaling
MOLREP3.15phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5G

3t5g


Resolution: 1.85→19.53 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.71 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1593 5 %RANDOM
Rwork0.1719 ---
obs0.1736 30251 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.03 Å2 / Biso mean: 35.377 Å2 / Biso min: 18.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0 Å2-0 Å2
2--1.37 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 1.85→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 0 89 2617
Biso mean---40.01 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022576
X-RAY DIFFRACTIONr_bond_other_d0.0010.022500
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9613462
X-RAY DIFFRACTIONr_angle_other_deg0.8543.0075752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.56424.098122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63215471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6621518
X-RAY DIFFRACTIONr_chiral_restr0.1140.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02599
X-RAY DIFFRACTIONr_mcbond_it2.983.0411222
X-RAY DIFFRACTIONr_mcbond_other2.9693.0391220
X-RAY DIFFRACTIONr_mcangle_it3.7284.5371517
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 115 -
Rwork0.24 2170 -
all-2285 -
obs--100 %

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