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- PDB-6vw9: C-terminal regulatory domain of the chloride transporter KCC-1 fr... -

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Basic information

Entry
Database: PDB / ID: 6vw9
TitleC-terminal regulatory domain of the chloride transporter KCC-1 from C. elegans, proteolyzed during crystallization
Components(K+/Cl-Cotransporter) x 2
KeywordsTRANSPORT PROTEIN / Cation-chloride-cotransporter / Slc transporter / cytosolic domain
Function / homologychloride:monoatomic cation symporter activity / SLC12A transporter, C-terminal / Solute carrier family 12 / SLC12A transporter family / Amino acid permease/ SLC12A domain / Amino acid permease / membrane / Solute carrier family 12 member 6
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsZimanyi, C.M. / Cheung, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Simons Foundation Autism Research Initiative534503 United States
CitationJournal: Structure / Year: 2020
Title: Structure of the Regulatory Cytosolic Domain of a Eukaryotic Potassium-Chloride Cotransporter.
Authors: Zimanyi, C.M. / Guo, M. / Mahmood, A. / Hendrickson, W.A. / Hirsh, D. / Cheung, J.
History
DepositionFeb 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: K+/Cl-Cotransporter
B: K+/Cl-Cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1536
Polymers34,5502
Non-polymers6034
Water1,20767
1
A: K+/Cl-Cotransporter
B: K+/Cl-Cotransporter
hetero molecules

A: K+/Cl-Cotransporter
B: K+/Cl-Cotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,30612
Polymers69,1004
Non-polymers1,2058
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area13720 Å2
ΔGint-75 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.320, 65.546, 56.523
Angle α, β, γ (deg.)90.000, 97.174, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein K+/Cl-Cotransporter


Mass: 26443.824 Da / Num. of mol.: 1 / Fragment: C-terminal regulatory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: kcc-1, CELE_R13A1.2, R13A1.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S6FCX2
#2: Protein K+/Cl-Cotransporter


Mass: 8106.339 Da / Num. of mol.: 1 / Fragment: C-terminal regulatory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: kcc-1, CELE_R13A1.2, R13A1.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S6FCX2
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe protein was internally proteolyzed during crystallization, as demonstrated by gel ...The protein was internally proteolyzed during crystallization, as demonstrated by gel electrophoresis. It is uncertain how much was cleaved. It is assumed that the residues missing from the electron density represent the residues that were removed proteolytically

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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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M TRIS pH 8.5, 5% w/v PEG 8000, 20% w/v PEG 300, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.796→40.79 Å / Num. obs: 34639 / % possible obs: 97.87 % / Redundancy: 9.4 % / Biso Wilson estimate: 43.2 Å2 / CC1/2: 0.999 / CC star: 1 / Rsym value: 0.072 / Net I/σ(I): 13.83
Reflection shellResolution: 1.796→1.86 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 29973 / CC1/2: 0.454 / CC star: 0.79 / % possible all: 91.01

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
Cootmodel building
ARP/wARPmodel building
BUCCANEERmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→40.79 Å / SU ML: 0.2208 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.5095 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2145 1717 4.96 %
Rwork0.1826 32895 -
obs0.1843 34612 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 40 67 2488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012505
X-RAY DIFFRACTIONf_angle_d1.1143376
X-RAY DIFFRACTIONf_dihedral_angle_d13.829953
X-RAY DIFFRACTIONf_chiral_restr0.267387
X-RAY DIFFRACTIONf_plane_restr0.006422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.36431240.34682435X-RAY DIFFRACTION88.45
1.85-1.910.32191430.32722776X-RAY DIFFRACTION99.08
1.91-1.980.31091550.27662751X-RAY DIFFRACTION98.88
1.98-2.060.2991420.25172745X-RAY DIFFRACTION98.5
2.06-2.150.28591290.23652743X-RAY DIFFRACTION97.92
2.15-2.260.25251690.21132785X-RAY DIFFRACTION99.33
2.26-2.40.22951290.1972762X-RAY DIFFRACTION99.21
2.4-2.590.21981310.19752783X-RAY DIFFRACTION99.01
2.59-2.850.24241390.21542728X-RAY DIFFRACTION97.25
2.85-3.260.24371480.20212812X-RAY DIFFRACTION99.43
3.26-4.110.20071470.17272761X-RAY DIFFRACTION97.95
4.11-40.790.17921610.14652814X-RAY DIFFRACTION98.51
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)
14.7265491545-0.7530371752421.493504072410.958473683958-1.382897997215.39133753288-0.0972398206328-0.1410399837150.03131044459960.0628996454621-0.0746348884006-0.09536880819980.05358731084030.1514833114850.1616049205510.34016549685-0.010983693507-0.003647077372950.321396025501-0.04673251485490.2724398841944.843070420339.601640358514.5856200265
28.86599009396-0.646404184531-0.8833575662344.67480798541.01338770335.35128267882-0.155918653317-0.2005297986290.05191441875240.2802660880340.05091910687690.983397919449-0.122545433939-1.18867756770.01100846411450.5258329823510.2203677589020.003133989217540.6872057846550.02698964512870.57822965112519.436922736548.77745595368.79751952536
35.030727901751.250168690830.379940889777.015608813870.7949524477764.645069094560.0855037974531-0.105836898296-0.102354595840.281900677048-0.035156796240.4218355085520.264360316063-0.62826760116-0.1185028593230.2725674555660.0186234214061-0.01450734279010.5631196988-0.06484261970880.36849293005523.187828610335.36789664199.82830111348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 660 through 819 )
2X-RAY DIFFRACTION2chain 'A' and (resid 820 through 879 )
3X-RAY DIFFRACTION3chain 'A' and (resid 880 through 892) or chain 'B' and (resid 996 through 1063)

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