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- PDB-3te3: Coiled-coil oligomerization domain of the polycystin transient re... -

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Basic information

Entry
Database: PDB / ID: 3te3
TitleCoiled-coil oligomerization domain of the polycystin transient receptor potential channel PKD2L1
ComponentsPolycystic kidney disease 2-like 1 protein
KeywordsMETAL TRANSPORT / trimeric coiled-coil / oligomerization domain / C-terminal cytoplasmic regulatory domain
Function / homology
Function and homology information


sour taste receptor activity / detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / response to water / calcium-activated potassium channel activity / detection of mechanical stimulus / muscle alpha-actinin binding / cellular response to acidic pH / calcium-activated cation channel activity ...sour taste receptor activity / detection of chemical stimulus involved in sensory perception of sour taste / detection of chemical stimulus involved in sensory perception of taste / sensory perception of sour taste / response to water / calcium-activated potassium channel activity / detection of mechanical stimulus / muscle alpha-actinin binding / cellular response to acidic pH / calcium-activated cation channel activity / sodium channel activity / non-motile cilium / inorganic cation transmembrane transport / ciliary membrane / smoothened signaling pathway / monoatomic cation transport / alpha-actinin binding / sodium ion transmembrane transport / monoatomic cation channel activity / potassium ion transmembrane transport / calcium channel complex / cytoskeletal protein binding / calcium channel activity / actin cytoskeleton / cytoplasmic vesicle / protein homotetramerization / transmembrane transporter binding / receptor complex / intracellular membrane-bounded organelle / calcium ion binding / cell surface / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Ferredoxin I 4Fe-4S cluster domain / Polycystin domain / Polycystin domain / Polycystic kidney disease type 2 protein / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily
Similarity search - Domain/homology
Polycystin-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.694 Å
AuthorsYernool, D.A. / Molland, K.M.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Crystal structure and characterization of coiled-coil domain of the transient receptor potential channel PKD2L1.
Authors: Molland, K.L. / Paul, L.N. / Yernool, D.A.
History
DepositionAug 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Polycystic kidney disease 2-like 1 protein
B: Polycystic kidney disease 2-like 1 protein
C: Polycystic kidney disease 2-like 1 protein
D: Polycystic kidney disease 2-like 1 protein
E: Polycystic kidney disease 2-like 1 protein
F: Polycystic kidney disease 2-like 1 protein


Theoretical massNumber of molelcules
Total (without water)25,9866
Polymers25,9866
Non-polymers00
Water1448
1
A: Polycystic kidney disease 2-like 1 protein
B: Polycystic kidney disease 2-like 1 protein
C: Polycystic kidney disease 2-like 1 protein


Theoretical massNumber of molelcules
Total (without water)12,9933
Polymers12,9933
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-42 kcal/mol
Surface area6650 Å2
MethodPISA
2
D: Polycystic kidney disease 2-like 1 protein
E: Polycystic kidney disease 2-like 1 protein
F: Polycystic kidney disease 2-like 1 protein


Theoretical massNumber of molelcules
Total (without water)12,9933
Polymers12,9933
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-42 kcal/mol
Surface area6510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.634, 74.634, 185.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein/peptide
Polycystic kidney disease 2-like 1 protein / Polycystin-2 homolog / Polycystin-2L1 / Polycystin-L / Polycystin-L1


Mass: 4331.021 Da / Num. of mol.: 6 / Fragment: UNP residues 699-737
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2L1, PKD2L, PKDL / Plasmid: pEV-L8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysS / References: UniProt: Q9P0L9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT THE REGION CRYSTALLIZED IS ONLY PART OF ORIGINAL PROTEIN TARGET DUE TO IN-DROP ...AUTHOR STATES THAT THE REGION CRYSTALLIZED IS ONLY PART OF ORIGINAL PROTEIN TARGET DUE TO IN-DROP PROTEOLYSIS. THEY HAVE ATTEMPTED TO CRYSTALLIZE THE ENTIRE 137 AA PROTEIN, HOWEVER, MASS SPECTROSCOPIC ANALYSIS OF THE CRYSTALS REVEALED THAT THERE HAD BEEN SOME PROTEOLYSIS DURING THE CRYSTALLIZATION PROCESS, AND THE CRYSTAL ONLY HAD A MASS OF 4338 DA. THIS MASS CORRESPONDS TO THE COILED-COIL DOMAIN OF THE FULL LENGTH PROTEIN. SERRES RECORD IN THE PDB FILE REPRESETS UNP RESIDUES 699-737.

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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: 2.87 Å3/Da / Density % sol: 57.2 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.69→30 Å / Num. all: 8840 / Num. obs: 8840 / Redundancy: 11.3 % / Biso Wilson estimate: 57.17 Å2
Reflection shellHighest resolution: 2.694 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345mosic 300data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.694→29.091 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2898 417 4.72 %
Rwork0.2534 --
obs0.255 8840 97.42 %
all-8840 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.886 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 57.17 Å2
Baniso -1Baniso -2Baniso -3
1-5.8546 Å20 Å2-0 Å2
2--5.8546 Å2-0 Å2
3----11.7092 Å2
Refinement stepCycle: LAST / Resolution: 2.694→29.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 0 8 1565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221711
X-RAY DIFFRACTIONf_angle_d1.1212115
X-RAY DIFFRACTIONf_dihedral_angle_d18.113539
X-RAY DIFFRACTIONf_chiral_restr0.067261
X-RAY DIFFRACTIONf_plane_restr0.004268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.694-3.08330.30461520.26262605X-RAY DIFFRACTION94
3.0833-3.88310.30571220.22252799X-RAY DIFFRACTION98
3.8831-29.09280.27811430.26553019X-RAY DIFFRACTION100

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