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- PDB-6fkb: Crystal structure of N2C/D282C stabilized opsin bound to RS13 -

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Basic information

Entry
Database: PDB / ID: 6fkb
TitleCrystal structure of N2C/D282C stabilized opsin bound to RS13
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
beta-D-mannopyranose / Chem-DLH / alpha-D-mannopyranose / PALMITIC ACID / Rhodopsin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,10313
Polymers37,0581
Non-polymers3,04512
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint35 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.852, 242.852, 111.469
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: 37057.574 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 , 4 types, 10 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: 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, 4 molecules

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


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#7: Chemical ChemComp-DLH / 2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethanone


Mass: 343.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18ClNO3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 8.11 Å3/Da
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: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.03→47.55 Å / Num. obs: 24484 / % possible obs: 99.9 % / Redundancy: 11.28 % / Rmerge(I) obs: 0.2624 / Rsym value: 0.2624 / Net I/σ(I): 6.89
Reflection shellResolution: 3.03→3.13 Å / Redundancy: 11.81 % / Rmerge(I) obs: 1.0302 / Mean I/σ(I) obs: 0.65 / Rsym value: 1.0302 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDS(VERSION Oct 15data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4Q

4j4q


Resolution: 3.03→45.895 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 1140 4.95 %
Rwork0.2577 --
obs0.2584 23041 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.03→45.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 201 2 2808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042891
X-RAY DIFFRACTIONf_angle_d0.6183922
X-RAY DIFFRACTIONf_dihedral_angle_d13.3571703
X-RAY DIFFRACTIONf_chiral_restr0.039452
X-RAY DIFFRACTIONf_plane_restr0.004459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0302-3.16810.46371330.45232447X-RAY DIFFRACTION85
3.1681-3.33510.43871160.42549X-RAY DIFFRACTION88
3.3351-3.5440.3391530.35832658X-RAY DIFFRACTION92
3.544-3.81750.31491360.29842750X-RAY DIFFRACTION95
3.8175-4.20140.27521450.24952789X-RAY DIFFRACTION97
4.2014-4.80880.221370.1962869X-RAY DIFFRACTION98
4.8088-6.05640.22921640.22122874X-RAY DIFFRACTION99
6.0564-45.90.23991560.2312965X-RAY DIFFRACTION99
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)
12.32561.32510.12083.3209-0.04791.3795-0.10180.19260.0571-0.37680.180.0253-0.0209-0.02830.00420.49530.0204-0.06830.3950.05880.5339-228.973740.095936.8233
23.96931.3608-0.20962.79890.81992.6178-0.27160.17520.4493-0.16810.02460.5724-0.3676-0.2258-0.05480.6988-0.0688-0.15190.5043-0.00580.9162-236.521834.488846.0263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 328 )

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