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- PDB-3ug9: Crystal Structure of the Closed State of Channelrhodopsin -

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Basic information

Entry
Database: PDB / ID: 3ug9
TitleCrystal Structure of the Closed State of Channelrhodopsin
ComponentsArchaeal-type opsin 1, Archaeal-type opsin 2
KeywordsMEMBRANE PROTEIN / microbialrhodopsin / seven-transmembrane / light-gated cation channel
Function / homology
Function and homology information


membrane / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2400 / Rhinovirus 14, subunit 4 - #80 / Rhinovirus 14, subunit 4 / Other non-globular / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2400 / Rhinovirus 14, subunit 4 - #80 / Rhinovirus 14, subunit 4 / Other non-globular / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
OLEIC ACID / RETINAL / Archaeal-type opsin 2 / Archaeal-type opsin 1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKato, H.E. / Ishitani, R. / Nureki, O.
CitationJournal: Nature / Year: 2012
Title: Crystal structure of the channelrhodopsin light-gated cation channel
Authors: Kato, H.E. / Zhang, F. / Yizhar, O. / Ramakrishnan, C. / Nishizawa, T. / Hirata, K. / Ito, J. / Aita, Y. / Tsukazaki, T. / Hayashi, S. / Hegemann, P. / Maturana, A.D. / Ishitani, R. / Deisseroth, K. / Nureki, O.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Jun 27, 2012Group: Structure summary
Revision 1.4Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Archaeal-type opsin 1, Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4218
Polymers37,4421
Non-polymers1,9797
Water77543
1
A: Archaeal-type opsin 1, Archaeal-type opsin 2
hetero molecules

A: Archaeal-type opsin 1, Archaeal-type opsin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,84216
Polymers74,8842
Non-polymers3,95814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11310 Å2
ΔGint0 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.471, 139.114, 90.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Archaeal-type opsin 1, Archaeal-type opsin 2 / Channelopsin-1 / Chlamyopsin 4 light-gated ion channel / Retinal binding protein / Sensory opsin B


Mass: 37441.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera protein of Archaeal-type opsin 1 (UNP residues 24-245) and Archaeal-type opsin 2 (UNP residues 207-309) from Chlamydomonas reinhardtii
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: acop1, acop2, CHLREDRAFT_182032, cop4, CSOB / Plasmid: pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q93WP2, UniProt: Q8RUT8
#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 30% PEG 500 DME, 100mM Na Citrate (pH6.0), 100mM MgCl2, 100mM NaCl, 100mM (NH4)2SO4, lipid cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→37.8 Å / Num. obs: 18985 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.440.8280.9361.9416827269925811.01795.6
2.44-2.610.4880.5683.4116904253624750.61597.6
2.61-2.810.2760.3375.6816066238523470.36498.4
2.81-3.080.1620.1959.1214184219121630.21298.7
3.08-3.440.0950.11915.0613547199319670.12998.7
3.44-3.970.0470.05728.1611400177017420.06298.4
3.97-4.860.0240.03542.489928151514980.03898.9
4.86-6.830.0270.03939.87441119511790.04398.7
6.830.0160.02455.2741977267090.02697.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→36.569 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8366 / SU ML: 0.78 / σ(F): 1.34 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 1672 10.01 %
Rwork0.204 --
obs0.2088 16709 98.4 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.334 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 165.72 Å2 / Biso mean: 51.5985 Å2 / Biso min: 21.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.9262 Å2-0 Å20 Å2
2---15.2461 Å20 Å2
3---12.3199 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 85 43 2307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082329
X-RAY DIFFRACTIONf_angle_d1.3063151
X-RAY DIFFRACTIONf_chiral_restr0.086356
X-RAY DIFFRACTIONf_plane_restr0.006382
X-RAY DIFFRACTIONf_dihedral_angle_d19.077799
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.36770.32261360.28321222135898
2.3677-2.44410.33841390.27781245138499
2.4441-2.53140.33491340.24381207134198
2.5314-2.63280.24221370.20321238137598
2.6328-2.75260.23421370.17571224136198
2.7526-2.89760.27311380.18011250138898
2.8976-3.07910.29121380.19221247138599
3.0791-3.31670.25781390.19641249138898
3.3167-3.65020.22751390.18351258139799
3.6502-4.17770.24181430.19171278142199
4.1777-5.2610.24411410.19421269141099
5.261-36.57330.22581510.22761350150198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3306-0.0954-0.30520.2033-0.17550.3972-0.0752-0.0048-0.29260.0521-0.0444-0.78040.01520.0249-0.00020.289-0.009-0.03680.31280.02150.555611.906721.127817.7379
20.3886-0.13-0.21060.1729-0.04150.1863-0.02620.12640.0351-0.24270.08470.078-0.04220.005300.3153-0.0281-0.03830.30250.00730.2196-0.244841.380313.7198
31.15480.13670.44710.3542-0.07590.1438-0.15690.16710.1571-0.28380.18590.0727-0.0590.081200.3281-0.06120.05090.2847-0.01230.255310.065646.94627.767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 49:156)A49 - 156
2X-RAY DIFFRACTION2chain 'A' and (resseq 157:241)A157 - 241
3X-RAY DIFFRACTION3chain 'A' and (resseq 242:342) or chain 'A' and (resseq 401)A242 - 401

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