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- PDB-5te5: Crystal structure of Bos taurus opsin regenerated with 6-carbon r... -

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Basic information

Entry
Database: PDB / ID: 5te5
TitleCrystal structure of Bos taurus opsin regenerated with 6-carbon ring retinal chromophore
ComponentsRhodopsin
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) / : / photoreceptor inner segment membrane ...Opsins / VxPx cargo-targeting to cilium / opsin binding / rod bipolar cell differentiation / rod photoreceptor outer segment / sperm head plasma membrane / absorption of visible light / The canonical retinoid cycle in rods (twilight vision) / : / photoreceptor inner segment membrane / podosome assembly / G protein-coupled opsin signaling pathway / 11-cis retinal binding / G protein-coupled photoreceptor activity / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / phototransduction, visible light / outer membrane / detection of temperature stimulus involved in thermoception / photoreceptor cell maintenance / arrestin family protein binding / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / response to light stimulus / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / photoreceptor disc membrane / microtubule cytoskeleton organization / 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. / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...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. / 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)
Similarity search - Domain/homology
Chem-7AB / Rhodopsin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.01 Å
AuthorsGulati, S. / Banerjee, S. / Katayama, K. / Kiser, P.D. / Palczewski, K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism.
Authors: Gulati, S. / Jastrzebska, B. / Banerjee, S. / Placeres, A.L. / Miszta, P. / Gao, S. / Gunderson, K. / Tochtrop, G.P. / Filipek, S. / Katayama, K. / Kiser, P.D. / Mogi, M. / Stewart, P.L. / Palczewski, K.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)39,3542
Polymers39,0571
Non-polymers2961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-0 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.725, 81.725, 200.012
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Rhodopsin


Mass: 39057.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02699
#2: Chemical ChemComp-7AB / (2E)-{(4E)-4-[(3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-ylidene]cyclohex-2-en-1-ylidene}acetaldehyde


Mass: 296.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28O

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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: 4.94 Å3/Da / Density % sol: 75.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2.8-3.4 M ammonium sulfate in 0.05-0.1 M MES, pH 6.1-6.6, or 0.05-0.1 M NaAcO buffer, pH 5.2-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.01→50 Å / Num. obs: 6944 / % possible obs: 99.8 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.243 / Net I/σ(I): 6.33
Reflection shellRmerge(I) obs: 5.625 / CC1/2: 0.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G87

2g87


Resolution: 4.01→48.53 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.886 / SU B: 132.794 / SU ML: 1.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.944 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35719 348 5 %RANDOM
Rwork0.31419 ---
obs0.31633 6594 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 310.92 Å2
Baniso -1Baniso -2Baniso -3
1-5.03 Å22.51 Å20 Å2
2--5.03 Å2-0 Å2
3----16.3 Å2
Refinement stepCycle: 1 / Resolution: 4.01→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 21 0 2770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022857
X-RAY DIFFRACTIONr_bond_other_d0.0020.022680
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9543898
X-RAY DIFFRACTIONr_angle_other_deg0.95236150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72623.462117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71215434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.463157
X-RAY DIFFRACTIONr_chiral_restr0.0650.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02699
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it30.02331.2951393
X-RAY DIFFRACTIONr_mcbond_other30.00831.2831392
X-RAY DIFFRACTIONr_mcangle_it46.38746.8691739
X-RAY DIFFRACTIONr_mcangle_other46.37346.8851740
X-RAY DIFFRACTIONr_scbond_it25.68131.3621464
X-RAY DIFFRACTIONr_scbond_other25.67331.3571465
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other41.48646.8012160
X-RAY DIFFRACTIONr_long_range_B_refined62.71111543
X-RAY DIFFRACTIONr_long_range_B_other62.70811544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.007→4.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 25 -
Rwork0.57 465 -
obs--98.99 %

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