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- PDB-4pxf: Crystal structure of the active G-protein-coupled receptor opsin ... -

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Basic information

Entry
Database: PDB / ID: 4pxf
TitleCrystal structure of the active G-protein-coupled receptor opsin in complex with the finger-loop peptide derived from the full-length arrestin-1
Components
  • Rhodopsin
  • S-arrestin
KeywordsSIGNALING PROTEIN / RETINAL PROTEIN / PHOTORECEPTOR / G-PROTEIN COUPLED RECEPTOR / PHOSPHOPROTEIN / PHOTORECEPTOR PROTEIN / SENSORY TRANSDUCTION / TRANSDUCER / TRANSMEMBRANE / VISION / VISUAL ARRESTIN / DESENSITISATION OF THE VISUAL TRANSDUCTION CASCADE / BINDING TO ACTICATED AND PHOSPHORYLATED RHODOPSIN / RHODOPSIN / OPSIN
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / : ...Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / sperm head plasma membrane / podosome assembly / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / : / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / phototransduction, visible light / thermotaxis / Activation of the phototransduction cascade / detection of temperature stimulus involved in thermoception / outer membrane / arrestin family protein binding / photoreceptor cell maintenance / G protein-coupled receptor internalization / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / sperm midpiece / visual perception / photoreceptor inner segment / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / phosphoprotein binding / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / signal transduction / zinc ion binding / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin E-set / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
trehalose / ACETATE ION / PALMITIC ACID / Rhodopsin / S-arrestin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSzczepek, M. / Scheerer, P.
CitationJournal: Nat Commun / Year: 2014
Title: Crystal structure of a common GPCR-binding interface for G protein and arrestin.
Authors: Szczepek, M. / Beyriere, F. / Hofmann, K.P. / Elgeti, M. / Kazmin, R. / Rose, A. / Bartl, F.J. / von Stetten, D. / Heck, M. / Sommer, M.E. / Hildebrand, P.W. / Scheerer, P.
History
DepositionMar 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / 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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin
B: S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,65010
Polymers40,2712
Non-polymers2,3808
Water19811
1
A: Rhodopsin
B: S-arrestin
hetero molecules

A: Rhodopsin
B: S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,30120
Polymers80,5424
Non-polymers4,75916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area11090 Å2
ΔGint-23 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.622, 242.622, 110.216
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Rhodopsin /


Mass: 39031.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: bovine eye / Source: (natural) Bos taurus (cattle) / References: UniProt: P02699
#2: Protein/peptide S-arrestin


Mass: 1239.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P08168

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Sugars , 3 types, 5 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 14 molecules

#6: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 3.2 M (NH4)2SO4 in 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2012 / Details: mirrors
RadiationMonochromator: Si(311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.75→40.04 Å / Num. all: 32166 / Num. obs: 32166 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 70.4 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 23.1
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 2 / Num. unique all: 4645 / Rsym value: 0 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DQB

3dqb


Resolution: 2.75→40.04 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25075 1637 5.1 %RANDOM
Rwork0.21476 ---
all0.21659 30511 --
obs0.21659 30511 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.895 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-1.17 Å2-0 Å2
2---1.17 Å20 Å2
3---3.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0 Å0 Å
Luzzati d res low-0 Å
Luzzati sigma a0 Å0 Å
Refinement stepCycle: LAST / Resolution: 2.75→40.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 159 11 2805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022872
X-RAY DIFFRACTIONr_bond_other_d0.0010.022702
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9913911
X-RAY DIFFRACTIONr_angle_other_deg0.7983.0016211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1045332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43823.421114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71315419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.246157
X-RAY DIFFRACTIONr_chiral_restr0.1540.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213080
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02681
X-RAY DIFFRACTIONr_mcbond_it13.8463.4931329
X-RAY DIFFRACTIONr_mcbond_other13.8343.491327
X-RAY DIFFRACTIONr_mcangle_it16.2865.2581657
X-RAY DIFFRACTIONr_mcangle_other16.2845.2581658
X-RAY DIFFRACTIONr_scbond_it16.4214.2371542
X-RAY DIFFRACTIONr_scbond_other16.4124.2371542
X-RAY DIFFRACTIONr_scangle_other19.4216.1472254
X-RAY DIFFRACTIONr_long_range_B_refined19.06231.1423394
X-RAY DIFFRACTIONr_long_range_B_other19.03831.1023393
X-RAY DIFFRACTIONr_rigid_bond_restr6.20835571
X-RAY DIFFRACTIONr_sphericity_free40.11752
X-RAY DIFFRACTIONr_sphericity_bonded42.81655497
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 114 -
Rwork0.339 2238 -
obs-2238 99.2 %
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)
10.29220.1504-0.14931.04990.05030.3591-0.00850.02470.0738-0.0665-0.0080.02760.0420.05690.01650.59660.003-0.03640.60750.03710.3793133.5021248.18838.3901
20.3056-1.00040.52684.5566-2.2241.13-0.138-0.1658-0.0316-0.38160.3045-0.00740.0938-0.2005-0.16640.7873-0.11840.12360.7445-0.05170.8968122.6938226.429539.1501
31.01820.30580.13070.14770.19580.637-0.15350.08350.4692-0.04820.01180.21680.2025-0.16840.14170.56610.0325-0.1350.5190.04550.5318146.9902256.145841.5382
42.43922.10430.68013.58921.84371.18310.08990.3198-0.13820.1979-0.0375-0.36430.0321-0.2306-0.05240.752-0.1793-0.05870.86780.18930.4436133.1363251.443240.2838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 326
2X-RAY DIFFRACTION2B71 - 77
3X-RAY DIFFRACTION3A401 - 411
4X-RAY DIFFRACTION4A501 - 511

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