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- PDB-5te3: Crystal structure of Bos taurus opsin at 2.7 Angstrom -

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Basic information

Entry
Database: PDB / ID: 5te3
TitleCrystal structure of Bos taurus opsin at 2.7 Angstrom
ComponentsRhodopsin
KeywordsSIGNALING PROTEIN
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
PALMITIC ACID / Rhodopsin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsGulati, S. / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _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 2.1Oct 4, 2023Group: 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

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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)41,3629
Polymers39,0311
Non-polymers2,3318
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint18 kcal/mol
Surface area17500 Å2
2
A: Rhodopsin
hetero molecules

A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,72418
Polymers78,0632
Non-polymers4,66216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9770 Å2
ΔGint18 kcal/mol
Surface area31260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.660, 242.660, 111.770
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-524-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Rhodopsin /


Mass: 39031.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P02699

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Sugars , 2 types, 4 molecules

#2: 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
#3: 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 , 3 types, 36 molecules

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


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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 % sol: 84.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: contained 2.8-3.4 M ammonium sulfate in 0.05-0.1 M NaAcO buffer, pH 5.2-5.6
PH range: 5.2-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 34545 / % possible obs: 100 % / Redundancy: 22.8 % / Net I/σ(I): 20.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4J4Q

4j4q


Resolution: 2.7→49.34 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.971 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25378 1725 5 %RANDOM
Rwork0.24496 ---
obs0.24541 32815 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.944 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å2-1.91 Å20 Å2
2---3.82 Å20 Å2
3---12.38 Å2
Refinement stepCycle: 1 / Resolution: 2.7→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 154 32 2778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192848
X-RAY DIFFRACTIONr_bond_other_d0.0010.022700
X-RAY DIFFRACTIONr_angle_refined_deg0.8661.9693867
X-RAY DIFFRACTIONr_angle_other_deg0.6973.0016206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4925327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2523.304112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66515412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.276157
X-RAY DIFFRACTIONr_chiral_restr0.0470.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02677
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_it2.1949.3231308
X-RAY DIFFRACTIONr_mcbond_other2.199.321307
X-RAY DIFFRACTIONr_mcangle_it3.69213.9841635
X-RAY DIFFRACTIONr_mcangle_other3.69113.9881636
X-RAY DIFFRACTIONr_scbond_it2.3429.8731540
X-RAY DIFFRACTIONr_scbond_other2.3429.8761541
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.97614.6412233
X-RAY DIFFRACTIONr_long_range_B_refined7.18177.2243241
X-RAY DIFFRACTIONr_long_range_B_other7.1877.2453242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.654 123 -
Rwork0.742 2398 -
obs--99.88 %

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