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- PDB-6fk7: Crystal structure of N2C/D282C stabilized opsin bound to RS06 -

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Basic information

Entry
Database: PDB / ID: 6fk7
TitleCrystal structure of N2C/D282C stabilized opsin bound to RS06
ComponentsRhodopsin
KeywordsMEMBRANE PROTEIN / RHODOPSIN / G PROTEIN-COUPLED RECEPTORS / RETINITIS PIGMENTOSA / SIGNALING PROTEIN / SENSORY TRANSDUCTION / PHOTORECEPTOR PROTEIN / KINTEGRAL MEMBRANE PROTEIN / VISION / MEMBRANE / RECEPTOR / TRANSDUCER PHOTORECEPTOR / SMALL MOLECULE COMPLEX
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / rod photoreceptor outer segment / 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 bipolar cell differentiation / rod photoreceptor outer segment / 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 / G protein-coupled opsin 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 / outer membrane / detection of temperature stimulus involved in thermoception / arrestin family protein binding / photoreceptor cell maintenance / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction / response to light stimulus / photoreceptor outer segment / G-protein alpha-subunit binding / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DO5 / PALMITIC ACID / Rhodopsin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsMattle, D. / Standfuss, J. / Dawson, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
RocheRPF Switzerland
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Ligand channel in pharmacologically stabilized rhodopsin.
Authors: Mattle, D. / Kuhn, B. / Aebi, J. / Bedoucha, M. / Kekilli, D. / Grozinger, N. / Alker, A. / Rudolph, M.G. / Schmid, G. / Schertler, G.F.X. / Hennig, M. / Standfuss, J. / Dawson, R.J.P.
History
DepositionJan 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / 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.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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Jun 2, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _chem_comp.pdbx_synonyms / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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_residues
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0529
Polymers39,0351
Non-polymers3,0178
Water50428
1
A: Rhodopsin
hetero molecules

A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,10318
Polymers78,0692
Non-polymers6,03416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_466y-1,x+1,-z+11
Buried area10370 Å2
ΔGint49 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.391, 243.391, 111.547
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 , 1 types, 1 molecules A

#1: Protein Rhodopsin /


Mass: 39034.586 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-326 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RHO / Plasmid: PCMV-TET O / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: P02699

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Sugars , 2 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 5
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 , 3 types, 30 molecules

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


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-DO5 / (2~{R},3~{R})-2-(4-chlorophenyl)-3-oxidanyl-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one


Mass: 387.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22ClNO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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
Details: AMMONIUM SULPHATE, SODIUM ACETATE, D(+)-TREHALOSE, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→49.3 Å / Num. obs: 37925 / % possible obs: 100 % / Redundancy: 11.53 % / Rmerge(I) obs: 0.1991 / Rsym value: 0.1991 / Net I/σ(I): 9.62
Reflection shellResolution: 2.62→2.72 Å / Redundancy: 11.92 % / Rmerge(I) obs: 1.0205 / Mean I/σ(I) obs: 0.66 / Rsym value: 1.0205 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDS(VERSION Oct 15data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4Q

4j4q


Resolution: 2.62→47.647 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 1881 4.98 %
Rwork0.2361 --
obs0.2369 37795 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→47.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 205 28 2824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042888
X-RAY DIFFRACTIONf_angle_d0.6573930
X-RAY DIFFRACTIONf_dihedral_angle_d13.6371695
X-RAY DIFFRACTIONf_chiral_restr0.038458
X-RAY DIFFRACTIONf_plane_restr0.005459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.69090.44161520.3892678X-RAY DIFFRACTION98
2.6909-2.770.37161480.37182723X-RAY DIFFRACTION99
2.77-2.85940.35621480.35012737X-RAY DIFFRACTION100
2.8594-2.96160.33271530.33842732X-RAY DIFFRACTION99
2.9616-3.08020.32791260.3082777X-RAY DIFFRACTION100
3.0802-3.22030.29591320.28362755X-RAY DIFFRACTION100
3.2203-3.39010.26981320.25832786X-RAY DIFFRACTION100
3.3901-3.60240.23771410.23222758X-RAY DIFFRACTION100
3.6024-3.88040.21941520.20122770X-RAY DIFFRACTION100
3.8804-4.27070.21921570.19522759X-RAY DIFFRACTION100
4.2707-4.88820.20741430.19212776X-RAY DIFFRACTION100
4.8882-6.15650.24481550.21252793X-RAY DIFFRACTION100
6.1565-47.65450.23911420.22582870X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -230.7593 Å / Origin y: 39.8132 Å / Origin z: 39.5953 Å
111213212223313233
T0.4816 Å20.0109 Å2-0.0567 Å2-0.3886 Å20.0403 Å2--0.5344 Å2
L2.0773 °20.9987 °20.1563 °2-2.7863 °2-0.0495 °2--1.0761 °2
S-0.0737 Å °0.1264 Å °0.0561 Å °-0.2639 Å °0.0462 Å °0.0412 Å °0.0176 Å °-0.0374 Å °0.023 Å °
Refinement TLS groupSelection details: all

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