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- PDB-6csm: Crystal structure of the natural light-gated anion channel GtACR1 -

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Basic information

Entry
Database: PDB / ID: 6csm
TitleCrystal structure of the natural light-gated anion channel GtACR1
ComponentsGtACR1
KeywordsMEMBRANE PROTEIN / rhodopsin / channelrhodopsin / anion channel / optogenetics
Function / homology
Function and homology information


light-activated monoatomic ion channel activity / photoreceptor activity / phototransduction / identical protein binding / plasma membrane
Similarity search - Function
Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
OLEIC ACID / RETINAL / Uncharacterized protein
Similarity search - Component
Biological speciesGuillardia theta CCMP2712 (eukaryote)
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 / diffrn_radiation_wavelength
Item: _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_radiation_wavelength.wavelength
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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GtACR1
B: GtACR1
C: GtACR1
D: GtACR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,79013
Polymers125,2404
Non-polymers2,5509
Water724
1
A: GtACR1
B: GtACR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0367
Polymers62,6202
Non-polymers1,4165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-31 kcal/mol
Surface area23760 Å2
MethodPISA
2
C: GtACR1
D: GtACR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7546
Polymers62,6202
Non-polymers1,1344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-31 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.780, 150.030, 90.690
Angle α, β, γ (deg.)90.000, 97.430, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 4 through 273)
21(chain B and (resid 4 through 262 or (resid 263...
31(chain C and (resid 4 through 262 or (resid 263...
41(chain D and (resid 4 through 262 or (resid 263...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEPROPRO(chain A and resid 4 through 273)AA4 - 2731 - 270
21ILEILEVALVAL(chain B and (resid 4 through 262 or (resid 263...BB4 - 2621 - 259
22LYSLYSLYSLYS(chain B and (resid 4 through 262 or (resid 263...BB263260
23ILEILERETRET(chain B and (resid 4 through 262 or (resid 263...BB - H4 - 4011
24ILEILERETRET(chain B and (resid 4 through 262 or (resid 263...BB - H4 - 4011
25ILEILERETRET(chain B and (resid 4 through 262 or (resid 263...BB - H4 - 4011
26ILEILERETRET(chain B and (resid 4 through 262 or (resid 263...BB - H4 - 4011
31ILEILEVALVAL(chain C and (resid 4 through 262 or (resid 263...CC4 - 2621 - 259
32LYSLYSLYSLYS(chain C and (resid 4 through 262 or (resid 263...CC263260
33ILEILERETRET(chain C and (resid 4 through 262 or (resid 263...CC - J4 - 4011
34ILEILERETRET(chain C and (resid 4 through 262 or (resid 263...CC - J4 - 4011
35ILEILERETRET(chain C and (resid 4 through 262 or (resid 263...CC - J4 - 4011
36ILEILERETRET(chain C and (resid 4 through 262 or (resid 263...CC - J4 - 4011
41ILEILEVALVAL(chain D and (resid 4 through 262 or (resid 263...DD4 - 2621 - 259
42LYSLYSLYSLYS(chain D and (resid 4 through 262 or (resid 263...DD263260
43ILEILERETRET(chain D and (resid 4 through 262 or (resid 263...DD - L4 - 4011
44ILEILERETRET(chain D and (resid 4 through 262 or (resid 263...DD - L4 - 4011
45ILEILERETRET(chain D and (resid 4 through 262 or (resid 263...DD - L4 - 4011
46ILEILERETRET(chain D and (resid 4 through 262 or (resid 263...DD - L4 - 4011

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Components

#1: Protein
GtACR1


Mass: 31309.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Guillardia theta CCMP2712 (eukaryote) / Gene: GUITHDRAFT_111593 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: L1J207
#2: Chemical
ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 10-12% (w/v) Polypropylene glycol P 400 (PPG P400), 100 mM MES pH 6.0, 100 mM potassium formate, 1-3% 1-butanol.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.0332
SYNCHROTRONAPS 23-ID-D21.0332
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELJun 21, 2017
DECTRIS PILATUS 6M2PIXELNov 22, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
21
ReflectionResolution: 2.9→45.166 Å / Num. obs: 33398 / % possible obs: 99.9 % / Redundancy: 14.52 % / Biso Wilson estimate: 59.86 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.736 / Rrim(I) all: 0.76 / Χ2: 1.278 / Net I/σ(I): 3.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.9-3.0813.7895.4960.5753580.335.695100
3.08-3.2914.7113.0160.9650410.5143.118100
3.29-3.5514.7022.0011.4747380.7152.06899.9
3.55-3.8914.3971.2172.4342960.8311.257100
3.89-4.3414.9170.6124.7239500.9190.632100
4.34-5.0114.6040.4536.6134570.9360.46999.9
5.01-6.1214.7490.4315.8629330.9610.445100
6.12-8.5914.6720.2728.8723030.9910.27999.9
8.59-45.16614.3280.1914.1213220.9860.19699.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UG9

3ug9


Resolution: 2.9→45.166 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.1
RfactorNum. reflection% reflection
Rfree0.2862 1650 4.99 %
Rwork0.2528 --
obs0.2545 33037 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.52 Å2 / Biso mean: 58.8251 Å2 / Biso min: 23.44 Å2
Refinement stepCycle: final / Resolution: 2.9→45.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8619 0 164 4 8787
Biso mean--52.28 54.24 -
Num. residues----1092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029030
X-RAY DIFFRACTIONf_angle_d0.55712292
X-RAY DIFFRACTIONf_chiral_restr0.041401
X-RAY DIFFRACTIONf_plane_restr0.0031464
X-RAY DIFFRACTIONf_dihedral_angle_d10.6855275
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5046X-RAY DIFFRACTION12.123TORSIONAL
12B5046X-RAY DIFFRACTION12.123TORSIONAL
13C5046X-RAY DIFFRACTION12.123TORSIONAL
14D5046X-RAY DIFFRACTION12.123TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.98530.35211290.36312514264394
2.9853-3.08170.34041310.35542517264897
3.0817-3.19180.37781370.33042625276299
3.1918-3.31960.35411400.317526212761100
3.3196-3.47060.34241360.311426262762100
3.4706-3.65350.34821400.294726342774100
3.6535-3.88230.30671380.25226272765100
3.8823-4.18180.26521400.238926512791100
4.1818-4.60230.22671380.209826242762100
4.6023-5.26740.27311390.217826502789100
5.2674-6.6330.24681400.237126432783100
6.633-45.17190.24381420.19722655279798

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