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- PDB-7l1e: The Crystal Structure of Bromide-Bound GtACR1 -

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Basic information

Entry
Database: PDB / ID: 7l1e
TitleThe Crystal Structure of Bromide-Bound GtACR1
ComponentsAnion channelrhodopsin-1
KeywordsTRANSPORT PROTEIN / Bromide-Bound / Anion Tunnel / anion channel / rhodopsin
Function / homologyArchaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / monoatomic ion channel activity / membrane => GO:0016020 / BROMIDE ION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Uncharacterized protein
Function and homology information
Biological speciesGuillardia theta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLi, H. / Huang, C.Y. / Wang, M. / Spudich, J.L. / Zheng, L.
Funding support United States, Switzerland, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM027750-39 United States
Robert A. Welch FoundationAU-0009 United States
H2020 Marie Curie Actions of the European Commission701647 Switzerland
CitationJournal: Elife / Year: 2021
Title: The crystal structure of bromide-bound Gt ACR1 reveals a pre-activated state in the transmembrane anion tunnel.
Authors: Li, H. / Huang, C.Y. / Govorunova, E.G. / Sineshchekov, O.A. / Yi, A. / Rothschild, K.J. / Wang, M. / Zheng, L. / Spudich, J.L.
History
DepositionDec 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 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: Anion channelrhodopsin-1
B: Anion channelrhodopsin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,63012
Polymers61,1472
Non-polymers2,48310
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, it is homologous to 6EDQ, which exists as a dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-35 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.660, 77.640, 73.630
Angle α, β, γ (deg.)90.00, 95.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Anion channelrhodopsin-1 / ACR1


Mass: 30573.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Guillardia theta (eukaryote) / Gene: GTHE00462_37052 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A6U6DEE4
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 15% 2-methyl-2,4-pentanediol (MPD), 0.1 M NaBr with buffer 0.1 MES, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→44.94 Å / Num. obs: 11033 / % possible obs: 95.6 % / Redundancy: 20 % / CC1/2: 0.975 / Net I/σ(I): 2.84
Reflection shellResolution: 3.2→3.28 Å / Num. unique obs: 11033 / CC1/2: 0.975
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: COC film / Sample holding: IMISX h1 holder / Support base: IMISX h1 holder

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660)refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EDQ

6edq


Resolution: 3.2→44.94 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 547 5.05 %
Rwork0.2412 --
obs0.2435 10833 93.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4257 0 164 17 4438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034531
X-RAY DIFFRACTIONf_angle_d0.7196128
X-RAY DIFFRACTIONf_dihedral_angle_d20.0921638
X-RAY DIFFRACTIONf_chiral_restr0.041691
X-RAY DIFFRACTIONf_plane_restr0.005720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.520.35681320.31222427X-RAY DIFFRACTION89
3.52-4.030.32021390.25812623X-RAY DIFFRACTION97
4.03-5.080.25161390.21792635X-RAY DIFFRACTION96
5.08-44.940.26111370.21892601X-RAY DIFFRACTION93

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