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- PDB-6fuf: Crystal structure of the rhodopsin-mini-Go complex -

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Basic information

Entry
Database: PDB / ID: 6fuf
TitleCrystal structure of the rhodopsin-mini-Go complex
Components
  • Guanine nucleotide-binding protein G(o) subunit alpha
  • Rhodopsin
KeywordsSIGNALING PROTEIN / GPCR Complex Rhodopsin
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 / mu-type opioid receptor binding / phototransduction, visible light / corticotropin-releasing hormone receptor 1 binding / 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 / dopamine receptor signaling pathway / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor outer segment / G-protein alpha-subunit binding / G protein-coupled serotonin receptor binding / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / muscle contraction / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / microtubule cytoskeleton organization / photoreceptor disc membrane / heterotrimeric G-protein complex / cell-cell junction / Ca2+ pathway / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / GTPase activity / GTP 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) / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RETINAL / Rhodopsin / Guanine nucleotide-binding protein G(o) subunit alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.117 Å
AuthorsTsai, C.-J. / Weinert, T. / Muehle, J. / Pamula, F. / Nehme, R. / Flock, T. / Nogly, P. / Edwards, P.C. / Carpenter, B. / Gruhl, T. ...Tsai, C.-J. / Weinert, T. / Muehle, J. / Pamula, F. / Nehme, R. / Flock, T. / Nogly, P. / Edwards, P.C. / Carpenter, B. / Gruhl, T. / Ma, P. / Deupi, X. / Standfuss, J. / Tate, C.G. / Schertler, G.F.X.
Funding support Switzerland, United Kingdom, 5items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_153145 Switzerland
Swiss National Science Foundation310030B_173335 Switzerland
Swiss National Science Foundation310030B_173335 Switzerland
Swiss National Science Foundation31003A_159558 Switzerland
European Research CouncilEMPSI, 339995 United Kingdom
CitationJournal: Sci Adv / Year: 2018
Title: Crystal structure of rhodopsin in complex with a mini-Gosheds light on the principles of G protein selectivity.
Authors: Tsai, C.J. / Pamula, F. / Nehme, R. / Muhle, J. / Weinert, T. / Flock, T. / Nogly, P. / Edwards, P.C. / Carpenter, B. / Gruhl, T. / Ma, P. / Deupi, X. / Standfuss, J. / Tate, C.G. / Schertler, G.F.X.
History
DepositionFeb 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_radiation_wavelength.wavelength / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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(o) subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6244
Polymers60,1192
Non-polymers5062
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel-filtrated sample shows the components for complex assembly in SDS-PAGE. It is a heterodimer of chains A and B in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-10 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.359, 151.359, 96.652
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Rhodopsin /


Mass: 35800.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RHO / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P02699
#2: Protein Guanine nucleotide-binding protein G(o) subunit alpha


Mass: 24317.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAO1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09471
#3: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 5.65 Å3/Da / Density % sol: 78.23 % / Description: Rod/needle up to 1 cm long 5-30 micron thick
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M MES pH 5.5 10-20% PEG4000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
51001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06SA21
SYNCHROTRONSLS X06SA31
SYNCHROTRONSLS X06SA41
SYNCHROTRONSLS X06SA51
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELMay 14, 2017
DECTRIS EIGER X 16M2PIXELMay 14, 2017
DECTRIS EIGER X 16M3PIXELMay 14, 2017
DECTRIS EIGER X 16M4PIXELMay 16, 2017
DECTRIS EIGER X 16M5PIXELMay 16, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
5SINGLE WAVELENGTHMx-ray5
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
31
41
51
ReflectionResolution: 3.02→49.544 Å / Num. obs: 14856 / % possible obs: 57.99 % / Redundancy: 37.3 % / Biso Wilson estimate: 91.8 Å2 / CC1/2: 0.9997 / Rpim(I) all: 0.06 / Rrim(I) all: 0.368 / Net I/σ(I): 9.416
Reflection shellResolution: 3.02→3.508 Å / Redundancy: 30.7 % / Rmerge(I) obs: 5.087 / Mean I/σ(I) obs: 1.937 / Num. unique obs: 719 / CC1/2: 0.8612 / Rpim(I) all: 0.93 / Rrim(I) all: 5.172 / % possible all: 8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A4M, 5G53

4a4m

5g53


Resolution: 3.117→49.544 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.26
RfactorNum. reflection% reflection
Rfree0.2801 1479 9.96 %
Rwork0.2568 --
obs0.2592 14851 65.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 208.72 Å2 / Biso mean: 93.4663 Å2 / Biso min: 22.91 Å2
Refinement stepCycle: final / Resolution: 3.117→49.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 35 0 4008
Biso mean--124.13 --
Num. residues----497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1169-3.21750.3516140.341185995
3.2175-3.33250.3053220.353320522711
3.3325-3.46590.3438370.30234638319
3.4659-3.62360.3731540.304153358729
3.6236-3.81460.3311200.28471108122859
3.8146-4.05340.34931930.26871770196397
4.0534-4.36620.29592080.23618672075100
4.3662-4.80530.26622050.213718292034100
4.8053-5.49990.25862060.230418652071100
5.4999-6.92620.30642170.298918642081100
6.9262-49.55010.2462030.262319002103100

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