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- PDB-2x72: CRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,D2C,D282C RH... -

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Entry
Database: PDB / ID: 2x72
TitleCRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,D2C,D282C RHODOPSIN MUTANT WITH BOUND GALPHACT PEPTIDE.
Components
  • GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1
  • RHODOPSIN
KeywordsSIGNALING PROTEIN / CHROMOPHORE / LIPOPROTEIN / GLYCOPROTEIN / TRANSMEMBRANE / RETINAL PROTEIN / G-PROTEIN COUPLED RECEPTOR / SENSORY TRANSDUCTION / PHOTORECEPTOR 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 / negative regulation of cyclic-nucleotide phosphodiesterase activity / 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 / negative regulation of cyclic-nucleotide phosphodiesterase activity / 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 / acyl binding / 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 / photoreceptor inner segment / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / microtubule cytoskeleton organization / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / GTP binding / protein kinase binding / zinc ion binding / membrane / identical protein binding / metal ion 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 / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx ...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 / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / 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 / Chem-LPP / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / PALMITIC ACID / RETINAL / Rhodopsin / Guanine nucleotide-binding protein G(t) subunit alpha-1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStandfuss, J. / Edwards, P.C. / Dantona, A. / Fransen, M. / Xie, G. / Oprian, D.D. / Schertler, G.F.X.
Citation
Journal: Nature / Year: 2011
Title: The Structural Basis of Agonist Induced Activation in Constitutively Active Rhodopsin
Authors: Standfuss, J. / Edwards, P.C. / Dantona, A. / Fransen, M. / Xie, G. / Oprian, D.D. / Schertler, G.F.X.
#1: Journal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of a Thermally Stable Rhodopsin Mutant.
Authors: Standfuss, J. / Xie, G. / Edwards, P.C. / Burghammer, M. / Oprian, D.D. / Schertler, G.F.X.
History
DepositionFeb 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.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 / _pdbx_database_status.status_code_sf / _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 2.1Dec 20, 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
B: GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,69910
Polymers40,2992
Non-polymers3,4008
Water32418
1
A: RHODOPSIN
B: GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1
hetero molecules

A: RHODOPSIN
B: GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,39920
Polymers80,5984
Non-polymers6,80116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area15700 Å2
ΔGint-36.8 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.986, 243.986, 109.156
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: 39033.602 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: RETINA / Cell: ROD PHOTORECEPTOR / Organ: EYE / Cell line (production host): HEK293S GNTI- CELLS / Production host: HOMO SAPIENS (human) / References: UniProt: P02699
#2: Protein/peptide GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1 / GACT PEPTIDE / TRANSDUCIN ALPHA-1 CHAIN


Mass: 1265.499 Da / Num. of mol.: 1 / Fragment: RESIDUES 340-350 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) BOS TAURUS (cattle) / References: UniProt: P04695

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Sugars , 2 types, 2 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 1
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 , 6 types, 24 molecules

#4: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL / Phosphatidylethanolamine


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#7: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#8: Chemical ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H69O8P / Comment: phospholipid*YM
#9: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 2 TO CYS ENGINEERED RESIDUE IN CHAIN A, GLU 113 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ASN 2 TO CYS ENGINEERED RESIDUE IN CHAIN A, GLU 113 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASP 282 TO CYS ENGINEERED RESIDUE IN CHAIN B, LYS 341 TO LEU
Nonpolymer details2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE (LPP): PARTIALLY DISORDERED N- ...2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE (LPP): PARTIALLY DISORDERED N-ACETYL-D-GLUCOSAMINE (NAG): PART OF THE N-GLYCAN DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE (PEF): PART OF THE N-GLYCAN PALMITIC ACID (PLM): PALMITOYLATION OF CYSTEINS ALPHA-D-MANNOSE (MAN): PART OF N-GLYCAN BETA-D-MANNOSE (BMA): PART OF N-GLYCAN ACETYL GROUP (ACE): ACETYLATION OF N-TERMINUS

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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: 7.62 Å3/Da / Density % sol: 81.7 % / Description: NONE
Crystal growpH: 4.5
Details: 3.0-3.4 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 25221 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 69.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.1 / % possible all: 65.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DQB AND 1GZM

3dqb

1gzm


Resolution: 3→39.94 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1158 5.1 %
Rwork0.21 --
obs0.212 22912 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.21 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 80.4 Å2
Baniso -1Baniso -2Baniso -3
1--20.3635 Å20 Å20 Å2
2---20.3635 Å20 Å2
3---40.7269 Å2
Refinement stepCycle: LAST / Resolution: 3→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 224 18 2921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013003
X-RAY DIFFRACTIONf_angle_d1.524058
X-RAY DIFFRACTIONf_dihedral_angle_d21.7151135
X-RAY DIFFRACTIONf_chiral_restr0.082453
X-RAY DIFFRACTIONf_plane_restr0.005480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.13650.3336960.31461903X-RAY DIFFRACTION65
3.1365-3.30180.29281290.27452224X-RAY DIFFRACTION75
3.3018-3.50850.28921420.24722865X-RAY DIFFRACTION98
3.5085-3.77920.22391540.21252931X-RAY DIFFRACTION99
3.7792-4.15920.20911670.17542929X-RAY DIFFRACTION99
4.1592-4.76020.19431450.16682957X-RAY DIFFRACTION100
4.7602-5.99410.23841880.18772928X-RAY DIFFRACTION100
5.9941-39.94340.25281370.22123017X-RAY DIFFRACTION98

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