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- PDB-6o7a: Crystal structure of the LjCASTOR gating ring in the Ca2+-free state -

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Basic information

Entry
Database: PDB / ID: 6o7a
TitleCrystal structure of the LjCASTOR gating ring in the Ca2+-free 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: 3.3 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion channel CASTOR
C: Ion channel CASTOR
B: Ion channel CASTOR
D: Ion channel CASTOR


Theoretical massNumber of molelcules
Total (without water)247,8274
Polymers247,8274
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-33 kcal/mol
Surface area85750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.433, 116.015, 113.027
Angle α, β, γ (deg.)90.000, 113.920, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

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
11GLNGLNCYSCYS(chain 'B' and (resid 320 through 380 or resid 382...BC320 - 38011 - 71
12SERSERLEULEU(chain 'B' and (resid 320 through 380 or resid 382...BC382 - 39173 - 82
13LYSLYSLEULEU(chain 'B' and (resid 320 through 380 or resid 382...BC393 - 40584 - 96
14GLYGLYASPASP(chain 'B' and (resid 320 through 380 or resid 382...BC409 - 415100 - 106
15ALAALALEULEU(chain 'B' and (resid 320 through 380 or resid 382...BC418 - 419109 - 110
16THRTHRLEULEU(chain 'B' and (resid 320 through 380 or resid 382...BC421 - 432112 - 123
17GLYGLYVALVAL(chain 'B' and (resid 320 through 380 or resid 382...BC434 - 449125 - 140
18LEULEUASPASP(chain 'B' and (resid 320 through 380 or resid 382...BC451 - 455142 - 146
19VALVALVALVAL(chain 'B' and (resid 320 through 380 or resid 382...BC457 - 461148 - 152
110HISHISCYSCYS(chain 'B' and (resid 320 through 380 or resid 382...BC463 - 473154 - 164
111GLNGLNGLUGLU(chain 'B' and (resid 320 through 380 or resid 382...BC476 - 490167 - 181
112CYSCYSLYSLYS(chain 'B' and (resid 320 through 380 or resid 382...BC492 - 497183 - 188
113TRPTRPGLYGLY(chain 'B' and (resid 320 through 380 or resid 382...BC499 - 528190 - 219
114ILEILEASPASP(chain 'B' and (resid 320 through 380 or resid 382...BC531 - 553222 - 244
115ASPASPPROPRO(chain 'B' and (resid 320 through 380 or resid 382...BC555 - 563246 - 254
116VALVALSERSER(chain 'B' and (resid 320 through 380 or resid 382...BC565 - 569256 - 260
117PROPROPROPRO(chain 'B' and (resid 320 through 380 or resid 382...BC571262
118ASPASPASPASP(chain 'B' and (resid 320 through 380 or resid 382...BC573264
119SERSERARGARG(chain 'B' and (resid 320 through 380 or resid 382...BC579 - 589270 - 280
120ASPASPPROPRO(chain 'B' and (resid 320 through 380 or resid 382...BC591 - 616282 - 307
121LYSLYSLEULEU(chain 'B' and (resid 320 through 380 or resid 382...BC618 - 629309 - 320
122ILEILESERSER(chain 'B' and (resid 320 through 380 or resid 382...BC631 - 632322 - 323
123LEULEUASNASN(chain 'B' and (resid 320 through 380 or resid 382...BC634 - 636325 - 327
124SERSERARGARG(chain 'B' and (resid 320 through 380 or resid 382...BC638 - 649329 - 340
125HISHISILEILE(chain 'B' and (resid 320 through 380 or resid 382...BC651 - 689342 - 380
126ASPASPARGARG(chain 'B' and (resid 320 through 380 or resid 382...BC691 - 695382 - 386
127THRTHRLEULEU(chain 'B' and (resid 320 through 380 or resid 382...BC727 - 734418 - 425
128VALVALARGARG(chain 'B' and (resid 320 through 380 or resid 382...BC751 - 768442 - 459
129ILEILELEULEU(chain 'B' and (resid 320 through 380 or resid 382...BC770 - 774461 - 465
130GLUGLUARGARG(chain 'B' and (resid 320 through 380 or resid 382...BC776 - 788467 - 479
131ALAALALEULEU(chain 'B' and (resid 320 through 380 or resid 382...BC790 - 807481 - 498
132ALAALAGLNGLN(chain 'B' and (resid 320 through 380 or resid 382...BC809 - 811500 - 502
133GLUGLUGLUGLU(chain 'B' and (resid 320 through 380 or resid 382...BC814 - 825505 - 516
134ALAALATHRTHR(chain 'B' and (resid 320 through 380 or resid 382...BC827 - 835518 - 526
135ARGARGARGARG(chain 'B' and (resid 320 through 380 or resid 382...BC838529
136TRPTRPGLUGLU(chain 'B' and (resid 320 through 380 or resid 382...BC840 - 851531 - 542
237GLNGLNCYSCYS(chain 'C' and (resid 320 through 380 or resid 382...CB320 - 38011 - 71
238SERSERLEULEU(chain 'C' and (resid 320 through 380 or resid 382...CB382 - 39173 - 82
239LYSLYSLEULEU(chain 'C' and (resid 320 through 380 or resid 382...CB393 - 40584 - 96
240GLYGLYASPASP(chain 'C' and (resid 320 through 380 or resid 382...CB409 - 415100 - 106
241ALAALALEULEU(chain 'C' and (resid 320 through 380 or resid 382...CB418 - 419109 - 110
242THRTHRLEULEU(chain 'C' and (resid 320 through 380 or resid 382...CB421 - 432112 - 123
243GLYGLYVALVAL(chain 'C' and (resid 320 through 380 or resid 382...CB434 - 449125 - 140
244LEULEUASPASP(chain 'C' and (resid 320 through 380 or resid 382...CB451 - 455142 - 146
245VALVALVALVAL(chain 'C' and (resid 320 through 380 or resid 382...CB457 - 461148 - 152
246HISHISCYSCYS(chain 'C' and (resid 320 through 380 or resid 382...CB463 - 473154 - 164
247GLNGLNGLUGLU(chain 'C' and (resid 320 through 380 or resid 382...CB476 - 490167 - 181
248CYSCYSLYSLYS(chain 'C' and (resid 320 through 380 or resid 382...CB492 - 497183 - 188
249TRPTRPGLYGLY(chain 'C' and (resid 320 through 380 or resid 382...CB499 - 528190 - 219
250ILEILEASPASP(chain 'C' and (resid 320 through 380 or resid 382...CB531 - 553222 - 244
251ASPASPPROPRO(chain 'C' and (resid 320 through 380 or resid 382...CB555 - 563246 - 254
252VALVALSERSER(chain 'C' and (resid 320 through 380 or resid 382...CB565 - 569256 - 260
253PROPROPROPRO(chain 'C' and (resid 320 through 380 or resid 382...CB571262
254ASPASPASPASP(chain 'C' and (resid 320 through 380 or resid 382...CB573264
255SERSERARGARG(chain 'C' and (resid 320 through 380 or resid 382...CB579 - 589270 - 280
256ASPASPPROPRO(chain 'C' and (resid 320 through 380 or resid 382...CB591 - 616282 - 307
257LYSLYSLEULEU(chain 'C' and (resid 320 through 380 or resid 382...CB618 - 629309 - 320
258ILEILESERSER(chain 'C' and (resid 320 through 380 or resid 382...CB631 - 632322 - 323
259LEULEUASNASN(chain 'C' and (resid 320 through 380 or resid 382...CB634 - 636325 - 327
260SERSERARGARG(chain 'C' and (resid 320 through 380 or resid 382...CB638 - 649329 - 340
261HISHISILEILE(chain 'C' and (resid 320 through 380 or resid 382...CB651 - 689342 - 380
262ASPASPARGARG(chain 'C' and (resid 320 through 380 or resid 382...CB691 - 695382 - 386
263THRTHRLEULEU(chain 'C' and (resid 320 through 380 or resid 382...CB727 - 734418 - 425
264VALVALARGARG(chain 'C' and (resid 320 through 380 or resid 382...CB751 - 768442 - 459
265ILEILELEULEU(chain 'C' and (resid 320 through 380 or resid 382...CB770 - 774461 - 465
266GLUGLUARGARG(chain 'C' and (resid 320 through 380 or resid 382...CB776 - 788467 - 479
267ALAALALEULEU(chain 'C' and (resid 320 through 380 or resid 382...CB790 - 807481 - 498
268ALAALAGLNGLN(chain 'C' and (resid 320 through 380 or resid 382...CB809 - 811500 - 502
269GLUGLUGLUGLU(chain 'C' and (resid 320 through 380 or resid 382...CB814 - 825505 - 516
270ALAALATHRTHR(chain 'C' and (resid 320 through 380 or resid 382...CB827 - 835518 - 526
271ARGARGARGARG(chain 'C' and (resid 320 through 380 or resid 382...CB838529
272TRPTRPGLUGLU(chain 'C' and (resid 320 through 380 or resid 382...CB840 - 851531 - 542
373GLNGLNCYSCYS(chain 'D' and (resid 320 through 380 or resid 382...DD320 - 38011 - 71
374SERSERLEULEU(chain 'D' and (resid 320 through 380 or resid 382...DD382 - 39173 - 82
375LYSLYSLEULEU(chain 'D' and (resid 320 through 380 or resid 382...DD393 - 40584 - 96
376GLYGLYASPASP(chain 'D' and (resid 320 through 380 or resid 382...DD409 - 415100 - 106
377ALAALALEULEU(chain 'D' and (resid 320 through 380 or resid 382...DD418 - 419109 - 110
378THRTHRLEULEU(chain 'D' and (resid 320 through 380 or resid 382...DD421 - 432112 - 123
379GLYGLYVALVAL(chain 'D' and (resid 320 through 380 or resid 382...DD434 - 449125 - 140
380LEULEUASPASP(chain 'D' and (resid 320 through 380 or resid 382...DD451 - 455142 - 146
381VALVALVALVAL(chain 'D' and (resid 320 through 380 or resid 382...DD457 - 461148 - 152
382HISHISCYSCYS(chain 'D' and (resid 320 through 380 or resid 382...DD463 - 473154 - 164
383GLNGLNGLUGLU(chain 'D' and (resid 320 through 380 or resid 382...DD476 - 490167 - 181
384CYSCYSLYSLYS(chain 'D' and (resid 320 through 380 or resid 382...DD492 - 497183 - 188
385TRPTRPGLYGLY(chain 'D' and (resid 320 through 380 or resid 382...DD499 - 528190 - 219
386ILEILEASPASP(chain 'D' and (resid 320 through 380 or resid 382...DD531 - 553222 - 244
387ASPASPPROPRO(chain 'D' and (resid 320 through 380 or resid 382...DD555 - 563246 - 254
388VALVALSERSER(chain 'D' and (resid 320 through 380 or resid 382...DD565 - 569256 - 260
389PROPROPROPRO(chain 'D' and (resid 320 through 380 or resid 382...DD571262
390ASPASPASPASP(chain 'D' and (resid 320 through 380 or resid 382...DD573264
391SERSERARGARG(chain 'D' and (resid 320 through 380 or resid 382...DD579 - 589270 - 280
392ASPASPPROPRO(chain 'D' and (resid 320 through 380 or resid 382...DD591 - 616282 - 307
393LYSLYSLEULEU(chain 'D' and (resid 320 through 380 or resid 382...DD618 - 629309 - 320
394ILEILESERSER(chain 'D' and (resid 320 through 380 or resid 382...DD631 - 632322 - 323
395LEULEUASNASN(chain 'D' and (resid 320 through 380 or resid 382...DD634 - 636325 - 327
396SERSERARGARG(chain 'D' and (resid 320 through 380 or resid 382...DD638 - 649329 - 340
397HISHISILEILE(chain 'D' and (resid 320 through 380 or resid 382...DD651 - 689342 - 380
398ASPASPARGARG(chain 'D' and (resid 320 through 380 or resid 382...DD691 - 695382 - 386
399THRTHRLEULEU(chain 'D' and (resid 320 through 380 or resid 382...DD727 - 734418 - 425
3100VALVALARGARG(chain 'D' and (resid 320 through 380 or resid 382...DD751 - 768442 - 459
3101ILEILELEULEU(chain 'D' and (resid 320 through 380 or resid 382...DD770 - 774461 - 465
3102GLUGLUARGARG(chain 'D' and (resid 320 through 380 or resid 382...DD776 - 788467 - 479
3103ALAALALEULEU(chain 'D' and (resid 320 through 380 or resid 382...DD790 - 807481 - 498
3104ALAALAGLNGLN(chain 'D' and (resid 320 through 380 or resid 382...DD809 - 811500 - 502
3105GLUGLUGLUGLU(chain 'D' and (resid 320 through 380 or resid 382...DD814 - 825505 - 516
3106ALAALATHRTHR(chain 'D' and (resid 320 through 380 or resid 382...DD827 - 835518 - 526
3107ARGARGARGARG(chain 'D' and (resid 320 through 380 or resid 382...DD838529
3108TRPTRPGLUGLU(chain 'D' and (resid 320 through 380 or resid 382...DD840 - 851531 - 542

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Components

#1: Protein
Ion channel CASTOR


Mass: 61956.867 Da / Num. of mol.: 4 / 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG3350, 100 mM lithium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 35911 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.049 / Rrim(I) all: 0.096 / Rsym value: 0.083 / Net I/av σ(I): 22.26 / Net I/σ(I): 18.9
Reflection shellResolution: 3.3→3.36 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 1776 / Rpim(I) all: 0.324 / Rrim(I) all: 0.637 / Rsym value: 0.548 / Χ2: 1.221

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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: 3.3→41.47 Å / SU ML: 0.5164 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.7708
RfactorNum. reflection% reflection
Rfree0.2841 1996 5.57 %
Rwork0.2291 --
obs0.2321 35804 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 93.85 Å2
Refinement stepCycle: LAST / Resolution: 3.3→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15882 0 0 0 15882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004916105
X-RAY DIFFRACTIONf_angle_d0.775721760
X-RAY DIFFRACTIONf_chiral_restr0.04742524
X-RAY DIFFRACTIONf_plane_restr0.00512824
X-RAY DIFFRACTIONf_dihedral_angle_d13.35779972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.380.37761330.3142355X-RAY DIFFRACTION97.91
3.38-3.470.35821470.2922399X-RAY DIFFRACTION99.92
3.47-3.570.32531460.28032412X-RAY DIFFRACTION99.96
3.57-3.690.32551340.28232390X-RAY DIFFRACTION99.88
3.69-3.820.36111500.27392415X-RAY DIFFRACTION99.96
3.82-3.970.33831370.26162407X-RAY DIFFRACTION99.88
3.97-4.150.35281450.25782439X-RAY DIFFRACTION100
4.15-4.370.32961500.23862401X-RAY DIFFRACTION100
4.37-4.650.2651390.21552417X-RAY DIFFRACTION100
4.65-50.25781400.21112409X-RAY DIFFRACTION99.92
5-5.510.30471420.23172426X-RAY DIFFRACTION99.92
5.51-6.30.34141450.25572415X-RAY DIFFRACTION99.92
6.3-7.930.26231430.23062441X-RAY DIFFRACTION99.85
7.93-41.470.18361450.15972482X-RAY DIFFRACTION99.55

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