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- PDB-4x1h: Opsin/G(alpha) peptide complex stabilized by nonyl-glucoside -

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Basic information

Entry
Database: PDB / ID: 4x1h
TitleOpsin/G(alpha) peptide complex stabilized by nonyl-glucoside
Components
  • C-terminal derived peptide of guanine nucleotide-binding protein G(t) subunit alpha-1
  • Rhodopsin
KeywordsSIGNALING PROTEIN / rhodopsin / GPCR / membrane protein
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: 2.29 Å
AuthorsBlankenship, E. / Lodowski, D.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY019718 United States
CitationJournal: Structure / Year: 2015
Title: The High-Resolution Structure of Activated Opsin Reveals a Conserved Solvent Network in the Transmembrane Region Essential for Activation.
Authors: Blankenship, E. / Vahedi-Faridi, A. / Lodowski, D.T.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_unobs_or_zero_occ_atoms / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.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 2.1Sep 27, 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
C: C-terminal derived peptide of guanine nucleotide-binding protein G(t) subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5558
Polymers40,2562
Non-polymers2,2996
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint27 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.136, 242.136, 109.721
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 AC

#1: Protein Rhodopsin /


Mass: 39031.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: retina / References: UniProt: P02699
#2: Protein/peptide C-terminal derived peptide of guanine nucleotide-binding protein G(t) subunit alpha-1


Mass: 1224.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle)

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Sugars , 3 types, 4 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-D-mannopyranose-(1-2)-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
DManpb1-2DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c2-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 67 molecules

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


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe C-terminal derived peptide of guanine nucleotide-binding protein G(t) is derived from 340-350 ...The C-terminal derived peptide of guanine nucleotide-binding protein G(t) is derived from 340-350 positions in the transducin alpha subunit utilizing a phage display library derived from the C terminal region of transducin (Aris, L, et al 2001) with sequence "IKENLKDCGLF". The construct in this structure has the following sequence: "VLEDLKSCGLF." Hence there are the following mutations I340V, K341L, N342D, and D346S.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 3.1M ammonium sulfate, 100mM citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2014
RadiationMonochromator: CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.23→39.91 Å / Num. all: 193355 / Num. obs: 57205 / % possible obs: 96 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 56.7
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.2 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CAP

3cap


Resolution: 2.29→39.907 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 2554 5.04 %Derived from 3CAP, extended to higher resolution
Rwork0.2171 ---
obs0.2177 50642 91.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→39.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 144 65 2886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042972
X-RAY DIFFRACTIONf_angle_d0.8784046
X-RAY DIFFRACTIONf_dihedral_angle_d13.421082
X-RAY DIFFRACTIONf_chiral_restr0.036465
X-RAY DIFFRACTIONf_plane_restr0.004488
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.33410.34051170.36722346X-RAY DIFFRACTION81
2.3341-2.38170.34251310.33862577X-RAY DIFFRACTION89
2.3817-2.43350.37431460.33692587X-RAY DIFFRACTION90
2.4335-2.49010.34741370.31642603X-RAY DIFFRACTION90
2.4901-2.55240.27261550.28152574X-RAY DIFFRACTION90
2.5524-2.62140.29081210.2782607X-RAY DIFFRACTION90
2.6214-2.69850.31641140.28522613X-RAY DIFFRACTION89
2.6985-2.78560.34271350.26292496X-RAY DIFFRACTION86
2.7856-2.88510.27291250.2372515X-RAY DIFFRACTION85
2.8851-3.00060.27131390.22622703X-RAY DIFFRACTION94
3.0006-3.13710.24931580.22132745X-RAY DIFFRACTION95
3.1371-3.30240.24321420.21572775X-RAY DIFFRACTION96
3.3024-3.50920.22881790.21672766X-RAY DIFFRACTION96
3.5092-3.77990.21121530.19412697X-RAY DIFFRACTION93
3.7799-4.160.19441550.19082857X-RAY DIFFRACTION98
4.16-4.76110.1871580.18782884X-RAY DIFFRACTION99
4.7611-5.99520.20391430.18772882X-RAY DIFFRACTION98
5.9952-39.91350.17991460.19452861X-RAY DIFFRACTION95
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)
14.3454-3.7707-1.16879.41115.41673.6838-0.08990.1805-0.1110.44860.11611.10120.6999-0.2875-0.01740.5952-0.0511-0.00940.30350.18780.913719.7998-65.4033-38.4804
21.3209-0.8568-0.02392.37690.14241.224-0.0543-0.0749-0.03580.27660.0101-0.38660.0365-0.01350.02540.34870.00850.05160.24480.07140.61219.7868-38.1699-40.1027
35.83540.46220.60782.77070.1154.3955-0.3995-0.66580.41050.72930.14180.6164-0.5508-0.22010.21630.60980.09610.11780.35570.02220.40047.5914-25.9207-24.6398
42.9529-1.8031-2.24043.27212.81122.6611-0.6457-0.1799-0.59550.6260.29940.22850.3123-0.20010.23380.63070.11550.12580.35540.16740.774918.7642-51.7568-31.3877
53.8289-0.9699-1.21470.40760.87762.8306-0.2181-0.3094-0.92320.34260.10430.07960.8015-0.1626-0.04130.71970.01880.20010.4380.19650.870610.2418-52.5469-29.1612
63.9705-4.38283.32237.7854-5.86346.3582-0.3453-0.32350.42240.40630.35850.7425-0.3517-0.7067-0.06940.38190.060.15380.4732-0.00060.7845-8.581-25.413-36.9252
75.7948-5.02131.2676.4099-1.13362.9001-0.1855-0.13890.07040.04770.124-0.23630.1319-0.3690.08380.3277-0.00220.11610.3766-0.03940.6612-0.204-35.4983-42.5854
80.7960.31291.27970.29440.20592.5966-0.0355-0.1077-1.15660.84170.01540.37361.0210.0694-0.15850.7080.03910.19330.35190.04521.102410.729-46.3657-43.7458
95.76086.3862-4.49938.9413-2.40539.02820.15320.07680.1745-0.03880.12510.0566-0.35620.0972-0.39730.52370.09140.0550.34210.07460.812514.6797-16.953-48.2677
109.9619-2.95194.9014.1923-0.09292.9687-0.26390.30750.82620.92780.24870.9118-1.4576-0.77780.17420.61740.19550.14190.50030.13750.8582-0.6051-14.9053-38.9274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 168 )
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 212 )
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 240 )
7X-RAY DIFFRACTION7chain 'A' and (resid 241 through 277 )
8X-RAY DIFFRACTION8chain 'A' and (resid 278 through 306 )
9X-RAY DIFFRACTION9chain 'A' and (resid 307 through 326 )
10X-RAY DIFFRACTION10chain 'C' and (resid 340 through 350 )

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