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- PDB-5egi: Structure of a Trimeric Intracellular Cation channel from C. eleg... -

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Basic information

Entry
Database: PDB / ID: 5egi
TitleStructure of a Trimeric Intracellular Cation channel from C. elegans with bound Ca2+
ComponentsUncharacterized protein Y57A10A.10
KeywordsMEMBRANE PROTEIN / ion channel
Function / homologyTRIC channel / TRIC channel / potassium channel activity / endoplasmic reticulum membrane / identical protein binding / Chem-PT5 / Trimeric intracellular cation channel type 1B.1
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsYang, H.T. / Hu, M.H. / Liu, Z.F.
Funding support China, 2items
OrganizationGrant numberCountry
National 973 project2014CB910301 China
Chinese Academy of SciencesXDB08020302 China
CitationJournal: Nature / Year: 2016
Title: Pore architecture of TRIC channels and insights into their gating mechanism.
Authors: Yang, H.T. / Hu, M.H. / Guo, J.L. / Ou, X.M. / Cai, T.X. / Liu, Z.F.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Mar 20, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Y57A10A.10
B: Uncharacterized protein Y57A10A.10
C: Uncharacterized protein Y57A10A.10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1788
Polymers86,5143
Non-polymers3,6645
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-68 kcal/mol
Surface area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.050, 102.050, 279.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-302-

CA

21B-401-

HOH

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Components

#1: Protein Uncharacterized protein Y57A10A.10


Mass: 28837.941 Da / Num. of mol.: 3 / Fragment: UNP residues 1-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_Y57A10A.10, Y57A10A.10 / Plasmid: pPICZA / Production host: Komagataella pastoris GS115 (fungus) / Strain (production host): GS115 / References: UniProt: Q9NA75
#2: Chemical ChemComp-PT5 / [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate / Phosphatidylinositol 4,5-bisphosphate / PtdIns(4,5)P2


Mass: 1047.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C47H85O19P3 / Comment: phospholipid*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.57 Å3/Da / Density % sol: 72.84 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20-24% PEG400, 10% glycerol, 50 mM ADA buffer (pH6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 23166 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 91.8 Å2 / Rsym value: 0.115 / Net I/σ(I): 11.1
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→50 Å / Cross valid method: FREE R-VALUE / σ(F): 42
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 989 4.3 %random selection
Rwork0.2631 22049 --
obs-23038 99.6 %-
Solvent computationBsol: 75.8288 Å2
Displacement parametersBiso max: 221.57 Å2 / Biso mean: 116.8833 Å2 / Biso min: 46.21 Å2
Baniso -1Baniso -2Baniso -3
1-7.476 Å20 Å20 Å2
2--7.476 Å20 Å2
3----14.953 Å2
Refinement stepCycle: final / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5480 0 217 7 5704
Biso mean--125.53 69.16 -
Num. residues----697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.43
X-RAY DIFFRACTIONc_mcbond_it1.7051.5
X-RAY DIFFRACTIONc_scbond_it1.8352
X-RAY DIFFRACTIONc_mcangle_it3.1152
X-RAY DIFFRACTIONc_scangle_it3.1172.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.420.33151080.313521432251100
3.42-3.550.312990.27192146224599.8
3.55-3.720.32571090.282167227699.9
3.72-3.910.33681050.29172162226799.8
3.91-4.160.25811120.25922153226599.8
4.16-4.480.24721130.21942177229099.8
4.48-4.930.2395800.20342210229099.5
4.93-5.640.2694950.21542232232799.7
5.64-7.10.3179840.30442266235099.4
7.1-500.2364840.28762393247798.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param
X-RAY DIFFRACTION6lipid_detergent.param

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