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- PDB-6csn: Crystal structure of the designed light-gated anion channel iC++ ... -

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Basic information

Entry
Database: PDB / ID: 6csn
TitleCrystal structure of the designed light-gated anion channel iC++ at pH8.5
ComponentsiC++
KeywordsMEMBRANE PROTEIN / rhodopsin / channelrhodopsin / anion channel / optogenetics
Function / homologyOLEIC ACID / RETINAL
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKato, H.E. / Kim, Y. / Yamashita, K. / Kobilka, B.K. / Deisseroth, K.
Funding support Japan, United States, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR1782 Japan
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH075957 United States
CitationJournal: Nature / Year: 2018
Title: Structural mechanisms of selectivity and gating in anion channelrhodopsins.
Authors: Kato, H.E. / Kim, Y.S. / Paggi, J.M. / Evans, K.E. / Allen, W.E. / Richardson, C. / Inoue, K. / Ito, S. / Ramakrishnan, C. / Fenno, L.E. / Yamashita, K. / Hilger, D. / Lee, S.Y. / Berndt, A. ...Authors: Kato, H.E. / Kim, Y.S. / Paggi, J.M. / Evans, K.E. / Allen, W.E. / Richardson, C. / Inoue, K. / Ito, S. / Ramakrishnan, C. / Fenno, L.E. / Yamashita, K. / Hilger, D. / Lee, S.Y. / Berndt, A. / Shen, K. / Kandori, H. / Dror, R.O. / Kobilka, B.K. / Deisseroth, K.
History
DepositionMar 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: iC++
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6464
Polymers33,0431
Non-polymers6023
Water362
1
A: iC++
hetero molecules

A: iC++
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2918
Polymers66,0872
Non-polymers1,2056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7500 Å2
ΔGint-66 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.520, 142.520, 91.250
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 iC++


Mass: 33043.379 Da / Num. of mol.: 1 / Mutation: N61Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Spodoptera frugiperda (fall armyworm)
#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-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.5
Details: 28% PEG 350MME, 100 mM Tris pH 8.5, 100 mM ammonium phosphate dibasic, 7-8% formamide

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.0332
SYNCHROTRONAPS 23-ID-D21.0332
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→47.546 Å / Num. obs: 9042 / % possible obs: 99.3 % / Redundancy: 5.878 % / Biso Wilson estimate: 62.38 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.338 / Rrim(I) all: 0.372 / Χ2: 1.296 / Net I/σ(I): 7.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.9-3.085.8924.7810.8614680.2915.2699.4
3.08-3.296.0142.1031.4313280.5192.30799.6
3.29-3.555.861.0332.512480.6971.13799.5
3.55-3.895.9410.4824.9811780.9210.52999.6
3.89-4.355.9540.2479.1210680.9630.27299.7
4.35-5.025.8670.15912.159350.9910.17599.5
5.02-6.145.870.16412.088030.980.18199
6.14-8.675.6740.08917.456420.9960.09899.1
8.67-47.5465.3680.04925.93720.9990.05495.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UG9

3ug9


Resolution: 2.9→47.546 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.2602 458 5.1 %
Rwork0.2316 --
obs0.2331 8985 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.23 Å2 / Biso mean: 64.3686 Å2 / Biso min: 21.15 Å2
Refinement stepCycle: final / Resolution: 2.9→47.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 34 2 2231
Biso mean--73.85 38.97 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022296
X-RAY DIFFRACTIONf_angle_d0.9713122
X-RAY DIFFRACTIONf_chiral_restr0.11352
X-RAY DIFFRACTIONf_plane_restr0.003379
X-RAY DIFFRACTIONf_dihedral_angle_d14.7611297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9001-3.31970.30011560.2942773292998
3.3197-4.1820.26221460.230528252971100
4.182-47.55250.24591560.21252929308599
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)
10.0971-0.0562-0.14110.03890.03960.9518-0.1428-0.02170.0609-0.03780.02930.34810.17450.5258-0.13830.4236-0.134-0.13810.32410.09051.4067-3.02891.659618.2507
20.05020.15810.0430.18610.0080.02160.4707-0.0398-0.043-0.1740.099-0.11240.7775-0.45950.00040.57420.0066-0.05660.53560.07420.6376-5.7004-7.814519.2675
30.30731.0871-0.0658.04-0.76560.011-0.5450.2173-0.14622.27130.47010.6846-0.519-0.3334-0.02440.5895-0.0764-0.12920.83160.03331.1263-22.3109-32.753113.1022
40.75110.3863-0.25340.22050.07480.0622-0.09750.11610.20360.38830.0730.94840.1998-0.389800.4692-0.0030.06990.4836-0.0150.6344-16.7434-37.017421.4876
50.5336-0.12790.1740.59040.0810.62340.01580.10610.0506-0.3553-0.02530.4589-0.2779-0.0768-0.00380.37180.00630.01620.348-0.00060.2694-5.7618-30.474818.315
63.91980.24031.9341-0.01580.11911.0502-0.4649-1.2573-0.4723-0.46310.1069-1.68470.7652-0.2458-0.01180.6780.0353-0.01930.5492-0.10280.8369-3.6423-57.538517.7738
71.4471-0.1844-0.2950.27390.350.7824-0.09560.2092-0.3506-0.34930.1514-0.41750.12550.10720.00040.3948-0.08440.06120.4098-0.01610.22423.7727-40.14611.6045
80.3773-0.1736-0.28390.5497-0.23740.4489-0.05490.13050.208-0.81490.27240.11130.06120.06640.00010.7636-0.1399-0.11170.52520.06170.5003-8.5311-37.42865.6273
9-0.03360.046-0.00440.1279-0.1290.0333-0.44240.1404-0.2131-0.27330.38550.58570.1086-0.21070.00080.5883-0.1227-0.1060.40230.02990.7504-17.6058-56.894512.0581
100.2712-0.01480.05260.0434-0.04220.017-0.3008-0.2124-0.0923-0.22120.8248-0.38440.04930.2818-0.00030.9271-0.05820.11540.4863-0.13341.0819-6.174-69.37278.6505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 66 )A51 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 84 )A67 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 110 )A85 - 110
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 139 )A111 - 139
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 176 )A140 - 176
6X-RAY DIFFRACTION6chain 'A' and (resid 177 through 187 )A177 - 187
7X-RAY DIFFRACTION7chain 'A' and (resid 188 through 241 )A188 - 241
8X-RAY DIFFRACTION8chain 'A' and (resid 242 through 296 )A242 - 296
9X-RAY DIFFRACTION9chain 'A' and (resid 297 through 317 )A297 - 317
10X-RAY DIFFRACTION10chain 'A' and (resid 318 through 342 )A318 - 342

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