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- PDB-6nwe: Crystal structure of bovine opsin with beta octyl glucoside bound -

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Basic information

Entry
Database: PDB / ID: 6nwe
TitleCrystal structure of bovine opsin with beta octyl glucoside bound
Components
  • ILENLKDVGLF peptide CT2
  • Rhodopsin
KeywordsSIGNALING PROTEIN / Olfactory Receptor / Odorant
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / rod bipolar cell differentiation / 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 photoreceptor outer segment / rod bipolar cell differentiation / 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 / rhodopsin mediated 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 / detection of temperature stimulus involved in thermoception / outer membrane / arrestin family protein binding / photoreceptor cell maintenance / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / 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 / MOLECULAR REPLACEMENT / Resolution: 2.705 Å
AuthorsEger, B.T. / Morizumi, T. / Ernst, O.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)Canada Research Excellence Chair Canada
CitationJournal: To Be Published
Title: Odorant-binding site in visual opsin
Authors: Morizumi, T. / Kuroi, K. / Eger, B.T. / Ou, W.L. / Van Eps, N. / Tsukamoto, H. / Furutani, Y. / Ernst, O.P.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / 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_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 11, 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 / software / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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
B: ILENLKDVGLF peptide CT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,04812
Polymers40,2932
Non-polymers2,75510
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-31 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.169, 242.169, 110.716
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 / Protein/peptide , 2 types, 2 molecules AB

#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
#2: Protein/peptide ILENLKDVGLF peptide CT2


Mass: 1261.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle)

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Sugars , 2 types, 6 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-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
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/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)][b-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 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 13 molecules

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


Mass: 256.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H32O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 7.75 Å3/Da / Density % sol: 84.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3.1-3.3M ammonium sulfate, 0.1M sodium acetate buffer, pH 5.5

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→40.1 Å / Num. obs: 33699 / % possible obs: 99.34 % / Redundancy: 5.7 % / Net I/σ(I): 16.6
Reflection shellResolution: 2.705→2.714 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) all: 2.2 / Num. unique all: 355 / Num. unique obs: 2077 / CC1/2: 0.811 / Rpim(I) all: 0.308 / Rrim(I) all: 0.756 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4Q

4j4q


Resolution: 2.705→40.1 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.78
RfactorNum. reflection% reflection
Rfree0.2233 1670 4.96 %
Rwork0.1963 --
obs0.1976 33684 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.705→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 182 9 2872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052965
X-RAY DIFFRACTIONf_angle_d0.8424028
X-RAY DIFFRACTIONf_dihedral_angle_d15.1661779
X-RAY DIFFRACTIONf_chiral_restr0.046465
X-RAY DIFFRACTIONf_plane_restr0.005474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7051-2.78470.35151410.26322674X-RAY DIFFRACTION100
2.7847-2.87460.30361330.22942662X-RAY DIFFRACTION100
2.8746-2.97730.27611300.20482663X-RAY DIFFRACTION100
2.9773-3.09650.23151470.19932678X-RAY DIFFRACTION100
3.0965-3.23730.23381390.19862647X-RAY DIFFRACTION100
3.2373-3.40790.24791190.19962684X-RAY DIFFRACTION100
3.4079-3.62130.21091440.18882673X-RAY DIFFRACTION100
3.6213-3.90070.20181520.18962640X-RAY DIFFRACTION99
3.9007-4.29280.21081620.17952630X-RAY DIFFRACTION99
4.2928-4.91310.18911400.17622648X-RAY DIFFRACTION99
4.9131-6.18630.22861330.20292689X-RAY DIFFRACTION99
6.1863-40.10470.23031300.20662726X-RAY DIFFRACTION98
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)
11.2550.0412-0.29850.6211-0.48410.9188-0.05520.25820.1567-0.38960.0839-0.3075-0.16020.06290.00110.4125-0.0019-0.06130.34260.08070.506420.064441.609440.4035
22.18310.185-0.6290.41880.01590.1966-0.3460.6338-0.4905-0.71060.1460.16340.4193-0.2127-0.15810.799-0.1584-0.1220.40080.0010.45097.260425.761825.283
30.5901-0.5085-0.27890.7170.82041.3625-0.18050.04640.4267-0.19940.221-0.3101-0.77050.28730.38780.5414-0.0711-0.17430.35760.18110.427210.623849.225930.7158
41.3017-0.73180.00620.46920.25431.0843-0.13660.18620.3033-0.22970.15240.5856-0.082-0.30090.00010.4959-0.0407-0.11630.4915-0.02670.6059-2.001935.103742.0831
50.4060.05880.44010.05160.03240.4734-0.17310.05510.0729-0.42440.27690.2277-0.1816-0.250400.5215-0.005-0.08670.41950.04110.544713.177927.528847.1422
60.0198-0.0098-0.00030.0217-0.00660.0255-0.19670.1731-0.2839-0.4233-0.0918-0.14170.11340.13950.00010.9496-0.0913-0.09220.830.10681.3127-2.863813.749637.9456
70.0128-0.00990.01220.0311-0.02050.01590.07330.1354-0.3344-0.06290.22370.13820.35410.0387-0.00010.7512-0.1502-0.07830.75590.05351.02521.876216.757440.7868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:139)
2X-RAY DIFFRACTION2(chain A and resid 140:168)
3X-RAY DIFFRACTION3(chain A and resid 169:222)
4X-RAY DIFFRACTION4(chain A and resid 223:287)
5X-RAY DIFFRACTION5(chain A and resid 288:326)
6X-RAY DIFFRACTION6(chain B and resid 340:344)
7X-RAY DIFFRACTION7(chain B and resid 345:350)

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