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- PDB-5iwk: Structure of Transient Receptor Potential (TRP) channel TRPV6 -

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Basic information

Entry
Database: PDB / ID: 5iwk
TitleStructure of Transient Receptor Potential (TRP) channel TRPV6
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 / calcium ion transmembrane transport / calcium channel activity / response to calcium ion ...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 / calcium ion transmembrane transport / calcium channel activity / response to calcium ion / calcium ion transport / protein homotetramerization / calmodulin binding / apical plasma membrane / identical protein binding / metal ion 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: 3.247 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)T32GM008281 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: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type
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:
MolmilJmol/JSmol

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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)77,4033
Polymers77,1481
Non-polymers2542
Water0
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)309,61112
Polymers308,5944
Non-polymers1,0178
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area19820 Å2
ΔGint-293 kcal/mol
Surface area108630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.818, 143.818, 113.224
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

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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, M136Q, 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.: 1 / 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: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20-24% PEG 350MME, 50 mM NaCl, 50 mM Tris-HCl pH 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.247→49.464 Å / Num. obs: 18531 / % possible obs: 96 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/av σ(I): 16.89 / Net I/σ(I): 16.9
Reflection shellResolution: 3.247→3.36 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.326 / Mean I/σ(I) obs: 1.3 / % possible all: 94.7

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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: 3.247→49.464 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2883 927 5 %Random Selection
Rwork0.2612 ---
obs0.2625 18529 95.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.247→49.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 16 0 4743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074849
X-RAY DIFFRACTIONf_angle_d1.2086587
X-RAY DIFFRACTIONf_dihedral_angle_d15.4361761
X-RAY DIFFRACTIONf_chiral_restr0.056751
X-RAY DIFFRACTIONf_plane_restr0.01835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2474-3.41860.3781270.40732397X-RAY DIFFRACTION94
3.4186-3.63270.42251330.34862525X-RAY DIFFRACTION98
3.6327-3.91310.32741320.30132523X-RAY DIFFRACTION98
3.9131-4.30670.28091330.26662506X-RAY DIFFRACTION97
4.3067-4.92940.25391320.22282523X-RAY DIFFRACTION97
4.9294-6.20860.31071330.25662526X-RAY DIFFRACTION96
6.2086-49.46980.25881370.24582602X-RAY DIFFRACTION93

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