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- PDB-5iwp: Structure of Transient Receptor Potential (TRP) channel TRPV6 in ... -

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Basic information

Entry
Database: PDB / ID: 5iwp
TitleStructure of Transient Receptor Potential (TRP) channel TRPV6 in the presence of calcium
ComponentsTransient receptor potential cation channel subfamily V member 6
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / response to calcium ion / calcium ion transmembrane transport / calcium channel activity ...parathyroid hormone secretion / TRP channels / calcium-activated cation channel activity / calcium ion import / calcium ion import across plasma membrane / calcium ion homeostasis / calcium channel complex / response to calcium ion / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / protein homotetramerization / calmodulin binding / apical plasma membrane / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily V member 6 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeats (many copies) / Transient receptor potential cation channel subfamily V / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential cation channel subfamily V member 6 / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeats (many copies) / Transient receptor potential cation channel subfamily V / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Chem-DTB / Transient receptor potential cation channel subfamily V member 6
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsSaotome, K. / Singh, A.K. / Yelshanskaya, M.V. / Sobolevsky, A.I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS083660 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008281 United States
CitationJournal: Nature / Year: 2016
Title: Crystal structure of the epithelial calcium channel TRPV6.
Authors: Saotome, K. / Singh, A.K. / Yelshanskaya, M.V. / Sobolevsky, A.I.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Data collection
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily V member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4835
Polymers77,1481
Non-polymers3344
Water00
1
A: Transient receptor potential cation channel subfamily V member 6
hetero molecules

A: Transient receptor potential cation channel subfamily V member 6
hetero molecules

A: Transient receptor potential cation channel subfamily V member 6
hetero molecules

A: Transient receptor potential cation channel subfamily V member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,93220
Polymers308,5944
Non-polymers1,33816
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
Buried area18920 Å2
ΔGint-153 kcal/mol
Surface area109600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.350, 144.350, 113.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-701-

CA

21A-702-

CA

31A-703-

CA

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Components

#1: Protein Transient receptor potential cation channel subfamily V member 6 / TrpV6 / Calcium transport protein 1 / CaT1 / Epithelial calcium channel 2 / ECaC2


Mass: 77148.469 Da / Num. of mol.: 1 / Mutation: I102Y, L132N, L535Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Trpv6 / Production host: Homo sapiens (human) / References: UniProt: Q9R186
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DTB / 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID / D-DESTHIOBIOTIN


Mass: 214.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N2O3

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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: 3.85 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20-24% PEG 350 MME, 50 mM NaCl, and 50 mM Tris-HCl pH 8.0-8.5
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.75 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 3.65→49.56 Å / Num. obs: 25439 / % possible obs: 99.9 % / Redundancy: 26.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.01 / Net I/σ(I): 25
Reflection shellResolution: 3.65→3.78 Å / Redundancy: 17.2 % / Rmerge(I) obs: 1.431 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFA

2rfa


Resolution: 3.65→49.556 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2832 1265 4.98 %Random Selection
Rwork0.2726 ---
obs0.2731 25414 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.65→49.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4717 0 18 0 4735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044839
X-RAY DIFFRACTIONf_angle_d1.0356572
X-RAY DIFFRACTIONf_dihedral_angle_d14.7181762
X-RAY DIFFRACTIONf_chiral_restr0.038749
X-RAY DIFFRACTIONf_plane_restr0.005832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.65-3.79610.41091350.37652675X-RAY DIFFRACTION99
3.7961-3.96880.31431440.33182671X-RAY DIFFRACTION100
3.9688-4.17790.31681420.31042704X-RAY DIFFRACTION100
4.1779-4.43960.27251350.27862665X-RAY DIFFRACTION100
4.4396-4.78210.251430.25382676X-RAY DIFFRACTION100
4.7821-5.26280.2631420.25442713X-RAY DIFFRACTION100
5.2628-6.02320.341420.28552664X-RAY DIFFRACTION100
6.0232-7.58430.32271460.26382706X-RAY DIFFRACTION100
7.5843-49.56050.24011360.25422675X-RAY DIFFRACTION100

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