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- PDB-6o7c: Crystal structure of the LjCASTOR gating ring in the Ca2+ and K+ state -

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Basic information

Entry
Database: PDB / ID: 6o7c
TitleCrystal structure of the LjCASTOR gating ring in the Ca2+ and K+ state
ComponentsIon channel CASTOR
KeywordsTRANSPORT PROTEIN / calcium channel / RCK domain / gating ring / CASTOR / membrane protein
Function / homologyCASTOR/POLLUX/SYM8 ion channel, conserved domain / Ion channel CASTOR/POLLUX/SYM8-like / Castor and Pollux, part of voltage-gated ion channel / monoatomic ion transmembrane transport / nuclear membrane / : / Ion channel CASTOR
Function and homology information
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsJiang, Y. / Kim, S.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Y.J. United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Welch FoundationI-1578 United States
CitationJournal: Nat Commun / Year: 2019
Title: Ca2+-regulated Ca2+channels with an RCK gating ring control plant symbiotic associations.
Authors: Kim, S. / Zeng, W. / Bernard, S. / Liao, J. / Venkateshwaran, M. / Ane, J.M. / Jiang, Y.
History
DepositionMar 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion channel CASTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7447
Polymers60,5371
Non-polymers2076
Water5,278293
1
A: Ion channel CASTOR
hetero molecules

A: Ion channel CASTOR
hetero molecules

A: Ion channel CASTOR
hetero molecules

A: Ion channel CASTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,97628
Polymers242,1494
Non-polymers82724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area9560 Å2
ΔGint-272 kcal/mol
Surface area81710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.569, 125.569, 82.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ion channel CASTOR


Mass: 60537.285 Da / Num. of mol.: 1 / Fragment: gating ring (UNP residues 312-853)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Gene: CASTOR / Variant: Gifu / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q5H8A6

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Non-polymers , 5 types, 299 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.7 Å3/Da / Density % sol: 54.37 % / Description: Thin rectangular prism with smooth edge
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 21% w/v PEG550 MME, 50 mM magnesium acetate, 100 mM Tris, pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99996 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 55045 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 39.01 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.025 / Rrim(I) all: 0.068 / Rsym value: 0.063 / Net I/av σ(I): 42.512 / Net I/σ(I): 23.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.67 / Mean I/σ(I) obs: 1 / Num. unique obs: 2759 / CC1/2: 0.69 / Rpim(I) all: 0.668 / Rrim(I) all: 1.799 / Rsym value: 1.67 / Χ2: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000HKL2000_v712-Linuxdata collection
HKL-2000HKL2000_v712-Linuxdata reduction
HKL-2000HKL2000_v712-Linuxdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→39.71 Å / SU ML: 0.1896 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3623
RfactorNum. reflection% reflection
Rfree0.2096 1998 3.63 %
Rwork0.1734 --
obs0.1747 55036 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.12 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 6 293 4269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01954026
X-RAY DIFFRACTIONf_angle_d1.72765441
X-RAY DIFFRACTIONf_chiral_restr0.1101631
X-RAY DIFFRACTIONf_plane_restr0.0128707
X-RAY DIFFRACTIONf_dihedral_angle_d11.80252492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.25881370.25363633X-RAY DIFFRACTION96.67
1.89-1.940.29851390.23813753X-RAY DIFFRACTION99.97
1.94-20.2371430.21323849X-RAY DIFFRACTION100
2-2.070.23121450.19843761X-RAY DIFFRACTION99.97
2.07-2.140.24511420.19473772X-RAY DIFFRACTION99.97
2.14-2.220.23711410.19663812X-RAY DIFFRACTION100
2.22-2.330.21281440.19453776X-RAY DIFFRACTION100
2.33-2.450.23911470.19383802X-RAY DIFFRACTION100
2.45-2.60.24151410.1953787X-RAY DIFFRACTION99.97
2.6-2.80.22361400.19373790X-RAY DIFFRACTION99.97
2.8-3.080.25571430.20223809X-RAY DIFFRACTION100
3.08-3.530.21661450.18123801X-RAY DIFFRACTION99.97
3.53-4.450.19741430.15023849X-RAY DIFFRACTION100
4.45-39.720.16651480.14513844X-RAY DIFFRACTION98.96
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)
11.01473546155-0.0865359421041-0.2187581920521.119197551080.3225731966041.71809914199-0.0315673717682-0.0120828671684-0.004027570224440.107870946709-0.06097685464780.1023339069750.132500149533-0.147424826741.0837049214E-50.32686241003-0.0103673584595-0.01325510577170.304052748965-0.04080206197370.361926076813-33.624350525614.115562247-28.0022122764
21.910719822610.954803534897-1.223953008961.35993446503-1.689560875162.222951596-0.0506358518236-0.0156287377862-0.004717388838650.0789120351328-0.161835002385-0.148621251778-0.08261670814190.362953101373-5.15747914886E-60.4004825947980.025350813783-0.0920697897430.410056984010.02096915501040.429565897432-16.75533098320.7930129647-45.5111194285
31.90258245757-0.515849644759-0.1671597411180.876583115438-0.05679462539412.452765747210.07548771362290.2301809733610.310329264341-0.325902038732-0.2243581304870.131087508628-0.532262720568-0.3390933083671.08203507349E-50.5133390983790.118925621133-0.07440264999110.429399051846-0.04095238385450.452169008898-42.708511863132.1986726828-36.0080002493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 320 through 606 )
2X-RAY DIFFRACTION2chain 'A' and (resid 607 through 766 )
3X-RAY DIFFRACTION3chain 'A' and (resid 767 through 852 )

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