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

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Basic information

Entry
Database: PDB / ID: 6cso
TitleCrystal structure of the designed light-gated anion channel iC++ at pH6.5
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: 3.2 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

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Assembly

Deposited unit
A: iC++
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1313
Polymers34,5641
Non-polymers5672
Water00
1
A: iC++
hetero molecules

A: iC++
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2626
Polymers69,1282
Non-polymers1,1344
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7270 Å2
ΔGint-42 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.960, 141.100, 90.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein iC++


Mass: 34564.047 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2

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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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30% PEG 350MME, 100 mM sodium phosphate pH 6.5, 200 mM sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→47.053 Å / Num. obs: 6602 / % possible obs: 99.9 % / Redundancy: 8.884 % / Biso Wilson estimate: 63.96 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.518 / Rrim(I) all: 0.551 / Χ2: 1.33 / Net I/σ(I): 6.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.2-3.398.6983.3131.1910200.4123.527100
3.39-3.639.3381.7122.210120.7581.813100
3.63-3.929.2060.9923.589120.8231.053100
3.92-4.298.9840.5226.078510.9360.55499.9
4.29-4.89.0430.378.087720.9380.393100
4.8-5.548.4610.3437.546900.9630.366100
5.54-6.787.9610.3077.825870.9450.3399.8
6.78-9.569.2220.14315.214740.9930.151100
9.56-47.0538.5350.10222.032840.9970.10998.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UG9

3ug9


Resolution: 3.2→47.053 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 325 4.94 %
Rwork0.2208 --
obs0.2234 6577 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→47.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 33 0 2227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032285
X-RAY DIFFRACTIONf_angle_d1.0413106
X-RAY DIFFRACTIONf_dihedral_angle_d16.6171288
X-RAY DIFFRACTIONf_chiral_restr0.11351
X-RAY DIFFRACTIONf_plane_restr0.003377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2003-4.03160.30761570.23623077X-RAY DIFFRACTION100
4.0316-47.05830.25141680.21233175X-RAY DIFFRACTION100
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)
10.14090.1919-0.40490.5067-0.38131.5433-0.10650.03610.6151-0.071-0.05030.20190.17770.4332-0.00580.08920.0567-0.09450.36780.0490.8374-4.6859-3.551218.6992
20.0884-0.3226-0.08823.9728-1.33072.3041-0.524-0.03270.21390.693-0.03870.1934-0.69760.0252-0.34820.2763-0.0105-0.11640.58030.06660.8109-22.1419-32.022412.8472
30.3574-0.03670.15040.0031-0.00740.0559-0.3615-0.18750.54630.06630.39660.05880.2782-0.0645-0.00330.46160.01430.06850.370.03790.5447-16.4734-36.596121.3535
41.84190.39720.3750.71641.05542.0828-0.04790.259-0.40520.06610.186-0.0565-0.0111-0.09860.01510.2006-0.0760.03320.2095-0.04920.145-0.6247-38.131114.5998
51.1591-0.6681-0.29961.60660.47910.86730.0957-0.06010.133-0.59410.4431-0.20220.46560.10960.47830.3174-0.2090.03840.283-0.06460.2034-7.035-39.98884.225
60.85260.0161-0.01560.4597-0.42550.5394-0.66140.1258-0.49420.12610.7112-0.3619-0.03060.12520.09530.5076-0.1676-0.0090.2576-0.01040.4885-12.6823-52.52579.8123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 109 )
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 241 )
5X-RAY DIFFRACTION5chain 'A' and (resid 242 through 280 )
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 342 )

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