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- PDB-5en0: Crystal Structure of T94I rhodopsin mutant -

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Basic information

Entry
Database: PDB / ID: 5en0
TitleCrystal Structure of T94I rhodopsin mutant
Components
  • Guanine nucleotide-binding protein G(t) subunit alpha-3
  • Rhodopsin
KeywordsSIGNALING PROTEIN / Rhodopsin / G protein-coupled receptors / Congenital stationary night blindness / constitutive activity
Function / homology
Function and homology information


Adenylate cyclase inhibitory pathway / Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / sensory perception of umami taste / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway ...Adenylate cyclase inhibitory pathway / Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / sensory perception of umami taste / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / podosome assembly / G protein-coupled photoreceptor activity / 11-cis retinal binding / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / sensory perception of sweet taste / rod photoreceptor outer segment / cellular response to light stimulus / detection of chemical stimulus involved in sensory perception of bitter taste / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / response to light intensity / photoreceptor cell maintenance / arrestin family protein binding / ADP signalling through P2Y purinoceptor 12 / Extra-nuclear estrogen signaling / photoreceptor outer segment membrane / G alpha (i) signalling events / phototransduction, visible light / response to light stimulus / photoreceptor outer segment / phototransduction / G-protein alpha-subunit binding / photoreceptor inner segment / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / heterotrimeric G-protein complex / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / GTP binding / zinc ion binding / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
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 / G-protein alpha subunit, group I ...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 / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PALMITIC ACID / RETINAL / Rhodopsin / Guanine nucleotide-binding protein G(t) subunit alpha-3
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsSinghal, A. / Guo, Y. / Matkovic, M. / Schertler, G. / Deupi, X. / Yan, E. / Standfuss, J.
CitationJournal: Embo Rep. / Year: 2016
Title: Structural role of the T94I rhodopsin mutation in congenital stationary night blindness.
Authors: Singhal, A. / Guo, Y. / Matkovic, M. / Schertler, G. / Deupi, X. / Yan, E.C. / Standfuss, J.
History
DepositionNov 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Jan 10, 2024Group: 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhodopsin
B: Guanine nucleotide-binding protein G(t) subunit alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,65311
Polymers40,3082
Non-polymers2,3459
Water45025
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-4 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.269, 242.269, 111.147
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: 39046.641 Da / Num. of mol.: 1 / Mutation: N2C, T94I, D282C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RHO / Plasmid: pCMV-tet O / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: P02699
#2: Protein/peptide Guanine nucleotide-binding protein G(t) subunit alpha-3 / Gustducin alpha-3 chain


Mass: 1261.487 Da / Num. of mol.: 1 / Fragment: UNP residues 344-354 / Source method: obtained synthetically
Details: GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-3 peptide
Source: (synth.) Bos taurus (domestic cattle) / References: UniProt: P0C7Q4*PLUS

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Sugars , 2 types, 3 molecules

#3: 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
#6: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
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 , 5 types, 31 molecules

#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Mutation: N2C, T94I, D282C
Source method: isolated from a genetically manipulated source
Formula: C20H28O / Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RHO / Plasmid: pCMV-tet O / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human)
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PLM / PALMITIC ACID


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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, hanging drop / Details: Ammonium sulfate, Sodium acetate / PH range: 4-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 30386 / % possible obs: 99.5 % / Redundancy: 5.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.722 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A4M

4a4m


Resolution: 2.81→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.623 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25314 1569 5.2 %RANDOM
Rwork0.20705 ---
obs0.20937 28815 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.989 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å2-1.25 Å2-0 Å2
2---2.5 Å2-0 Å2
3---8.12 Å2
Refinement stepCycle: 1 / Resolution: 2.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2701 0 137 25 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022924
X-RAY DIFFRACTIONr_bond_other_d0.0020.022792
X-RAY DIFFRACTIONr_angle_refined_deg2.1182.0023971
X-RAY DIFFRACTIONr_angle_other_deg1.11436429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09623.202114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96515430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.826157
X-RAY DIFFRACTIONr_chiral_restr0.10.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213146
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02687
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_it4.2655.5651350
X-RAY DIFFRACTIONr_mcbond_other4.2525.5581347
X-RAY DIFFRACTIONr_mcangle_it6.1848.3431681
X-RAY DIFFRACTIONr_mcangle_other6.1848.3451682
X-RAY DIFFRACTIONr_scbond_it5.5946.2041574
X-RAY DIFFRACTIONr_scbond_other5.5416.1921570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.359.0752285
X-RAY DIFFRACTIONr_long_range_B_refined9.746.7143340
X-RAY DIFFRACTIONr_long_range_B_other9.68146.7263336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.805→2.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 117 -
Rwork0.362 2075 -
obs--96.61 %

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