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- PDB-3aym: Crystal structure of the batho intermediate of squid rhodopsin -

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Basic information

Entry
Database: PDB / ID: 3aym
TitleCrystal structure of the batho intermediate of squid rhodopsin
ComponentsRhodopsin
KeywordsSIGNALING PROTEIN / transmembrane protein / Photoreceptor / Chromophore / Glycoprotein / Lipoprotein / Gq-type G-protein / Phosphorylation / membrane
Function / homology
Function and homology information


G protein-coupled photoreceptor activity / cellular response to light stimulus / retinal binding / phototransduction / visual perception / cell projection / membrane / plasma membrane
Similarity search - Function
XYPPX repeat / XYPPX repeat (two copies) / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...XYPPX repeat / XYPPX repeat (two copies) / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITIC ACID / RETINAL / Rhodopsin
Similarity search - Component
Biological speciesTodarodes pacificus (Japanese flying squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMurakami, M. / Kouyama, T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystallographic Analysis of the Primary Photochemical Reaction of Squid Rhodopsin
Authors: Murakami, M. / Kouyama, T.
History
DepositionMay 9, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: 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

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Assembly

Deposited unit
A: Rhodopsin
B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0429
Polymers99,7452
Non-polymers2,2967
Water1,06359
1
A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7064
Polymers49,8731
Non-polymers8333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3365
Polymers49,8731
Non-polymers1,4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.360, 122.360, 158.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Rhodopsin


Mass: 49872.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Todarodes pacificus (Japanese flying squid)
References: UniProt: P31356
#3: 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, 64 molecules

#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.43 Å3/Da / Density % sol: 64.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 3.2M ammonium sulfate, 20mM MES, 75mM EDTA, 10mM beta-mercaptoethanol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW14A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 22, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→88 Å / Num. obs: 31468 / % possible obs: 95.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2 / Num. unique all: 4562 / % possible all: 95

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Processing

Software
NameClassification
MAR345data collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z73

2z73


Resolution: 2.8→15 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2354525.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.3448 1080 3.3 %RANDOM
Rwork0.2953 21149 --
all-33086 --
obs-22229 67.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.1863 Å2
Displacement parametersBiso max: 135.11 Å2 / Biso mean: 58.7828 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--10.272 Å2-14.469 Å20 Å2
2---10.272 Å20 Å2
3---20.545 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.61 Å
Luzzati d res low-5 Å
Luzzati sigma a1.06 Å1.02 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 141 59 5742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.8211.5
X-RAY DIFFRACTIONc_scbond_it2.6392
X-RAY DIFFRACTIONc_mcangle_it3.0482
X-RAY DIFFRACTIONc_scangle_it4.12.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.547 178 5 %
Rwork0.534 3377 -
obs--64.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ret-trans.param
X-RAY DIFFRACTION5bog.param

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