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- PDB-6fk8: Crystal structure of N2C/D282C stabilized opsin bound to RS08 -

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Basic information

Entry
Database: PDB / ID: 6fk8
TitleCrystal structure of N2C/D282C stabilized opsin bound to RS08
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 / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly ...Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / G protein-coupled photoreceptor activity / 11-cis retinal binding / rod photoreceptor outer segment / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / response to light intensity / photoreceptor cell maintenance / arrestin family protein binding / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction, visible light / response to light stimulus / photoreceptor outer segment / phototransduction / 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 / identical protein binding / membrane / 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 ...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-DNZ / PALMITIC ACID / Rhodopsin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 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 / Refinement description / 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 / refine_hist / 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 / _refine_hist.d_res_low / _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 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1736
Polymers39,0351
Non-polymers2,1395
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint27 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.183, 242.183, 110.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1-

ACE

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Components

#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 (domestic cattle) / Gene: RHO / Plasmid: PCMV-TET O / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: P02699
#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
#3: Chemical ChemComp-PLM / PALMITIC ACID


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


Mass: 386.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClN2O3
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Has protein modificationY

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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: 8.03 Å3/Da / Density % sol: 84.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: see publication

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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: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→45.77 Å / Num. obs: 28482 / % possible obs: 100 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.1926 / Rsym value: 0.1926 / Net I/σ(I): 12.28
Reflection shellResolution: 2.87→2.97 Å / Redundancy: 11.5 % / Rmerge(I) obs: 3.531 / Mean I/σ(I) obs: 0.72 / Rsym value: 3.531 / % 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: 2.87→45.77 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1483 5.22 %
Rwork0.2285 --
obs0.2294 28426 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 145 0 2736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092827
X-RAY DIFFRACTIONf_angle_d1.2533853
X-RAY DIFFRACTIONf_dihedral_angle_d13.921650
X-RAY DIFFRACTIONf_chiral_restr0.068443
X-RAY DIFFRACTIONf_plane_restr0.008459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8701-2.96270.41591410.37212396X-RAY DIFFRACTION99
2.9627-3.06860.43821370.36062431X-RAY DIFFRACTION100
3.0686-3.19140.38181270.32782422X-RAY DIFFRACTION100
3.1914-3.33660.30081330.28542435X-RAY DIFFRACTION100
3.3366-3.51250.2881320.24872454X-RAY DIFFRACTION100
3.5125-3.73250.23821300.23122436X-RAY DIFFRACTION100
3.7325-4.02050.21041310.20822449X-RAY DIFFRACTION100
4.0205-4.42480.21941300.18852472X-RAY DIFFRACTION100
4.4248-5.06450.22781420.18662443X-RAY DIFFRACTION100
5.0645-6.37830.24421490.22752470X-RAY DIFFRACTION100
6.3783-47.41450.21091310.22172535X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 27.9754 Å / Origin y: 389.1563 Å / Origin z: 39.0769 Å
111213212223313233
T0.4265 Å20.042 Å20.1173 Å2-0.5314 Å20.0726 Å2--0.7398 Å2
L1.8019 °2-1.1533 °20.1205 °2-3.8798 °2-0.0648 °2--1.429 °2
S0.087 Å °0.2095 Å °0.1114 Å °-0.2679 Å °-0.1133 Å °-0.3453 Å °-0.0598 Å °0.0638 Å °0.0055 Å °
Refinement TLS groupSelection details: all

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