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- PDB-7zbc: Dark state crystal structure of bovine rhodopsin in Lipidic Cubic... -

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Basic information

Entry
Database: PDB / ID: 7zbc
TitleDark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA)
ComponentsRhodopsin
KeywordsMEMBRANE PROTEIN / GPCR / Opsin
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly ...Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / 11-cis retinal binding / G protein-coupled photoreceptor activity / rod photoreceptor outer segment / cellular response to light stimulus / 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 / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction, visible light / G-protein alpha-subunit binding / phototransduction / photoreceptor outer segment / 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 / identical protein binding / membrane / 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. / : / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...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. / : / 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)
Similarity search - Domain/homology
ACETYL GROUP / LAURIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITIC ACID / RETINAL / Rhodopsin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P. / Cirelli, C. ...Gruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / Dworkowski, F. / Baath, P. / Kekilli, D. / Oserov, D. / Tanaka, R. / Glover, H. / Bacellar, C. / Bruenle, S. / Casadei, C. / Diethelm, A. / Gashi, D. / Gotthard, G. / Guixa-Gonzalez, R. / Joti, Y. / Kabanova, V. / Knopp, G. / Lesca, E. / Ma, P. / Martiel, I. / Muehle, J. / Owada, S. / Pamula, F. / Sarabi, S. / Tejero, O. / Tsai, C.J. / Varma, N. / Wach, A. / Boutet, S. / Tono, K. / Nogly, P. / Deupi, X. / Iwata, S. / Neutze, R. / Standfuss, J. / Schertler, G.F.X. / Panneels, V.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation153145 Switzerland
Swiss National Science Foundation192760 Switzerland
Citation
Journal: Nature / Year: 2023
Title: Ultrafast structural changes direct the first molecular events of vision.
Authors: Gruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / ...Authors: Gruhl, T. / Weinert, T. / Rodrigues, M.J. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / Dworkowski, F. / Bath, P. / Kekilli, D. / Ozerov, D. / Tanaka, R. / Glover, H. / Bacellar, C. / Brunle, S. / Casadei, C.M. / Diethelm, A.D. / Gashi, D. / Gotthard, G. / Guixa-Gonzalez, R. / Joti, Y. / Kabanova, V. / Knopp, G. / Lesca, E. / Ma, P. / Martiel, I. / Muhle, J. / Owada, S. / Pamula, F. / Sarabi, D. / Tejero, O. / Tsai, C.J. / Varma, N. / Wach, A. / Boutet, S. / Tono, K. / Nogly, P. / Deupi, X. / Iwata, S. / Neutze, R. / Standfuss, J. / Schertler, G. / Panneels, V.
#1: Journal: Biorxiv / Year: 2022
Title: ULTRAFAST STRUCTURAL CHANGES DIRECT THE FIRST MOLECULAR EVENTS OF VISION
Authors: Gruhl, T. / Weinert, T. / Rodrigues, M. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / ...Authors: Gruhl, T. / Weinert, T. / Rodrigues, M. / Milne, C.J. / Ortolani, G. / Nass, K. / Nango, E. / Sen, S. / Johnson, P.J.M. / Cirelli, C. / Furrer, A. / Mous, S. / Skopintsev, P. / James, D. / Dworkowski, F. / Bath, P. / Kekilli, D. / Ozerov, D. / Tanaka, R. / Glover, H. / Bacellar, C. / Brunle, S. / Casadei, C.M. / Diethelm, A.D. / Gashi, D. / Gotthard, G. / Guixa-Gonzalez, R. / Joti, Y. / Kabanova, V. / Knopp, G. / Lesca, E. / Ma, P. / Martiel, I. / Muhle, J. / Owada, S. / Pamula, F. / Sarabi, D. / Tejero, O. / Tsai, C.J. / Varma, N. / Wach, A. / Boutet, S. / Tono, K. / Nogly, P. / Deupi, X. / Iwata, S. / Neutze, R. / Standfuss, J. / Schertler, G.F. / Panneels, V.
History
DepositionMar 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.source_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin
B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,35926
Polymers78,0632
Non-polymers7,29624
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint1 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.290, 90.810, 150.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Rhodopsin


Mass: 39031.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02699

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 188 molecules

#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#7: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C21H40O4
#8: Chemical ChemComp-PLM / PALMITIC ACID


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase / pH: 9 / Details: 36 % PEG 600, 100 mM Bicine pH 9.0

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Data collection

DiffractionMean temperature: 294 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.8→10.47 Å / Num. obs: 78209 / % possible obs: 100 % / Redundancy: 1342.8 % / Biso Wilson estimate: 27.71 Å2 / CC1/2: 0.9977 / CC star: 0.9994 / R split: 0.0675 / Net I/σ(I): 8.87
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 963.9 % / Num. unique obs: 7715 / CC1/2: 0.7391 / CC star: 0.9219 / R split: 0.777 / % possible all: 100
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U19

1u19


Resolution: 1.8→10.47 Å / SU ML: 0.1969 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2232 1127 1.45 %
Rwork0.1979 76791 -
obs0.1983 77918 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4805 0 371 168 5344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095501
X-RAY DIFFRACTIONf_angle_d0.95797457
X-RAY DIFFRACTIONf_chiral_restr0.0611828
X-RAY DIFFRACTIONf_plane_restr0.0078912
X-RAY DIFFRACTIONf_dihedral_angle_d12.90172005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.3331380.30679494X-RAY DIFFRACTION99.88
1.88-1.980.3071400.25529551X-RAY DIFFRACTION99.98
1.98-2.10.26941400.21359510X-RAY DIFFRACTION99.98
2.1-2.260.2271410.18489548X-RAY DIFFRACTION99.99
2.26-2.490.20861390.17719589X-RAY DIFFRACTION99.95
2.49-2.840.20091410.1699613X-RAY DIFFRACTION99.97
2.84-3.560.20491420.18039704X-RAY DIFFRACTION99.99
3.56-10.470.21481460.20479782X-RAY DIFFRACTION97.96
Refinement TLS params.Method: refined / Origin x: -5.38409103868 Å / Origin y: 28.2563757254 Å / Origin z: 37.4549285311 Å
111213212223313233
T0.216890330049 Å2-0.0194679243814 Å2-0.0123579982097 Å2-0.193585385315 Å2-0.00896818888222 Å2--0.216185034324 Å2
L0.671529409509 °2-0.210429217084 °2-0.318269690981 °2-0.422394705104 °20.0650177452374 °2--0.368164389989 °2
S-0.00849542910314 Å °0.0243818383139 Å °0.00580895595372 Å °0.00167872780138 Å °-0.00702567872836 Å °-0.00845391329705 Å °0.0132279074875 Å °-0.0225400839254 Å °0.000373116207558 Å °
Refinement TLS groupSelection details: all

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