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

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Basic information

Entry
Database: PDB / ID: 5eik
TitleStructure of a Trimeric Intracellular Cation channel from C. elegans in the absence of Ca2+
ComponentsUncharacterized protein Y57A10A.28
KeywordsMEMBRANE PROTEIN / cation channel
Function / homologyTRIC channel / TRIC channel / potassium channel activity / membrane => GO:0016020 / endoplasmic reticulum membrane / ACETATE ION / Chem-CPL / Chem-PT5 / Trimeric intracellular cation channel type 1B.2
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHu, M.H. / Yang, H.T. / 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 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Y57A10A.28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,20613
Polymers29,1511
Non-polymers4,05512
Water1,58588
1
A: Uncharacterized protein Y57A10A.28
hetero molecules

A: Uncharacterized protein Y57A10A.28
hetero molecules

A: Uncharacterized protein Y57A10A.28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,61839
Polymers87,4533
Non-polymers12,16536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19920 Å2
ΔGint-142 kcal/mol
Surface area36130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.340, 126.340, 135.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein Uncharacterized protein Y57A10A.28


Mass: 29151.152 Da / Num. of mol.: 1 / Fragment: UNP residues 1-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_Y57A10A.28, Y57A10A.28 / Plasmid: pPICZC / Production host: Komagataella pastoris GS115 (fungus) / Strain (production host): GS115 / References: UniProt: Q9NA73
#6: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 5 types, 96 molecules

#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 / Phosphatidylinositol 4,5-bisphosphate


Mass: 1047.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H85O19P3 / Comment: phospholipid*YM
#3: Chemical ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 758.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.57 Å3/Da / Density % sol: 65.56 % / Description: rhombohedral
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 20% PEG400, 50 mM NaAc buffer (pH 4.4), 50 mM MgAc2, 10 mM betaine hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.53062 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.53062 Å / Relative weight: 1
ReflectionResolution: 2.3→85 Å / Num. obs: 18464 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 52.41 Å2 / Rsym value: 0.116 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EGI

5egi


Resolution: 2.3→50 Å / Cross valid method: FREE R-VALUE / σ(F): 12
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 901 4.8 %Random selection
Rwork0.2139 17563 --
obs-18464 98.9 %-
Solvent computationBsol: 87.5353 Å2
Displacement parametersBiso max: 172.65 Å2 / Biso mean: 63.0185 Å2 / Biso min: 2.98 Å2
Baniso -1Baniso -2Baniso -3
1--13.685 Å20 Å20 Å2
2---13.685 Å20 Å2
3---27.371 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 346 5 2202
Biso mean--93.29 67.84 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.634
X-RAY DIFFRACTIONc_mcbond_it4.471.5
X-RAY DIFFRACTIONc_scbond_it6.0642
X-RAY DIFFRACTIONc_mcangle_it6.2872
X-RAY DIFFRACTIONc_scangle_it8.1972.5
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 (%)
2.3-2.380.3776930.35281741183499.1
2.38-2.480.3719920.30431730182299.4
2.48-2.590.314830.26521752183599.5
2.59-2.730.2524930.23141756184999.5
2.73-2.90.3032870.21281753184099.5
2.9-3.120.2103980.18351742184099.7
3.12-3.440.2244980.17391777187599.6
3.44-3.930.2769910.20591768185999.8
3.93-4.950.1767930.18171788188199.8
4.95-500.2759730.22921756182993.5
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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