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- PDB-6i9k: Crystal structure of Jumping Spider Rhodopsin-1 bound to 9-cis retinal -

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Basic information

Entry
Database: PDB / ID: 6i9k
TitleCrystal structure of Jumping Spider Rhodopsin-1 bound to 9-cis retinal
ComponentsKumopsin1
KeywordsMEMBRANE PROTEIN / Rhodopsin / GPCR / Light-sensitive / Retinal
Function / homology
Function and homology information


photoreceptor activity / phototransduction / visual perception / G protein-coupled receptor activity / membrane
Similarity search - Function
Opsin lateral eye type / 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 coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...Opsin lateral eye type / 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 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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Kumopsin1
Similarity search - Component
Biological speciesHasarius adansoni (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.145 Å
AuthorsVarma, N. / Mutt, E. / Muehle, J. / Panneels, V. / Terakita, A. / Deupi, X. / Nogly, P. / Schertler, F.X.G. / Lesca, E.
Funding support France, Switzerland, 4items
OrganizationGrant numberCountry
European UnionITN 637295
Human Frontier Science ProgramRGP0034/2014 France
Swiss National Science Foundation173335 Switzerland
European Communitys Seventh Framework ProgrammeFP7/2007-2013
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Crystal structure of jumping spider rhodopsin-1 as a light sensitive GPCR.
Authors: Varma, N. / Mutt, E. / Muhle, J. / Panneels, V. / Terakita, A. / Deupi, X. / Nogly, P. / Schertler, G.F.X. / Lesca, E.
History
DepositionNov 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kumopsin1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,80313
Polymers42,5961
Non-polymers4,20612
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-1 kcal/mol
Surface area14720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.955, 130.638, 77.309
Angle α, β, γ (deg.)90.000, 100.550, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Kumopsin1 / Rhodopsin-1 (JSR1)


Mass: 42596.293 Da / Num. of mol.: 1 / Mutation: C-tail 1D4 epitope (ETSQVAPA)
Source method: isolated from a genetically manipulated source
Details: Residues 1-19, 257-262 and 336-380 are not modelled due to lack of electron density
Source: (gene. exp.) Hasarius adansoni (spider) / Gene: HaRh1 / Plasmid: pcDNA 3.0(+) / Details (production host): stable cell line / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: B1B1U5
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.52 Å3/Da / Density % sol: 65.04 % / Description: Rectangular plate like crystals
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5 / Details: PEG 400, Bis-Tris pH6.5 / Temp details: Crystallization set up at 4 then moved to 20

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→46.773 Å / Num. obs: 18992 / % possible obs: 90.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 38.56 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.092 / Rrim(I) all: 0.17 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.39 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.748 / Num. unique obs: 938 / CC1/2: 0.537 / % possible all: 51.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
STARANISOdata scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z73

2z73


Resolution: 2.145→46.773 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 1167 6.15 %Random Selection
Rwork0.2146 ---
obs0.2172 18977 69.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.69 Å2 / Biso mean: 39.1137 Å2 / Biso min: 20.86 Å2
Refinement stepCycle: final / Resolution: 2.145→46.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 153 54 2605
Biso mean--49.72 39.76 -
Num. residues----310
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.145-2.24230.27849188
2.2423-2.36050.292945490
2.3605-2.50840.320885151647
2.5084-2.70210.3204201293093
2.7021-2.9740.26782030.21823189100
2.974-3.40420.25042080.2143317199
3.4042-4.28850.22022040.1923313698

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