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- PDB-4gif: C-terminal coiled-coil domain of transient receptor potential cha... -

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Basic information

Entry
Database: PDB / ID: 4gif
TitleC-terminal coiled-coil domain of transient receptor potential channel TRPP3 (PKD2L1, Polycystin-L)
ComponentsPolycystic kidney disease 2-like 1 protein
KeywordsTRANSPORT PROTEIN / coiled-coil / trimer / TRP channel / transient receptor potential channel / polycystic kidney disease (PKD) / membrane
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: 2.8 Å
AuthorsYu, Y. / Ulbrich, M.H. / Li, M.-H. / Dobbins, S. / Zhang, W.K. / Tong, L. / Isacoff, E.Y. / Yang, J.
CitationJournal: Nat Commun / Year: 2012
Title: Molecular mechanism of the assembly of an acid-sensing receptor ion channel complex.
Authors: Yu, Y. / Ulbrich, M.H. / Li, M.H. / Dobbins, S. / Zhang, W.K. / Tong, L. / Isacoff, E.Y. / Yang, J.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Feb 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


Theoretical massNumber of molelcules
Total (without water)5,1031
Polymers5,1031
Non-polymers00
Water79344
1
A: Polycystic kidney disease 2-like 1 protein

A: Polycystic kidney disease 2-like 1 protein

A: Polycystic kidney disease 2-like 1 protein


Theoretical massNumber of molelcules
Total (without water)15,3093
Polymers15,3093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area3830 Å2
ΔGint-36 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.527, 44.527, 62.306
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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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: 5102.927 Da / Num. of mol.: 1 / Fragment: UNP residues 699-743
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2L1, PKD2L, PKDL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P0L9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE IS: ...THE CRYSTALLIZED SEQUENCE IS: MGSSHHHHHHSQDPKEELAGQKDELQLSDLLKQGYNKTLLRLRLRKERVSDVQKVLQGGEQEIQFEDFTNTLRELGHAEHEITELTATFTKFDRDGNRILDEKEQEKMRQDLEEERVALNTEIEKLGRSIVSSPQGKSGPEAARA(GGWVSGEEFYMLTRRVLQLETVLEGVVSQIDAVGSKLKMLERKGW)LAPSPGVKEQAIWKHPQPAPAVTPDPWGVQGGQESEVPYKREEEALEERRLSRGEIPTLQRS OF WHICH THE SEGMENT LISTED IN SEQRES RECORD WAS OBSERVED IN THE ELECTRON DENSITY. THE AUTHORS BELIEVE THAT THE PROTEIN WAS DEGRADED DURING THE PROCESS OF CRYSTALLIZATION AND ONLY THE COILED COIL DOMAIN WAS CRYSTALLIZATION. TO TEST THIS POSSIBILITY, THE AUTHORS COLLECTED SOME CRYSTALS AND RAN IT ON SDS-PAGE. ONLY A DEGRADED BAND WITH A MOLECULAR WEIGHT MATCH THE COILED COIL DOMAIN WAS SHOWN ON THE GEL. HOWEVER THE AUTHORS DO NOT KNOW HOW MANY AMINO ACIDS ARE MISSING FROM THE N- AND C-TERMINUS DUE TO DISORDER.

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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: 3.49 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 18-20% PEG 8000, 100 mM HEPES, pH 7.5, 3.9 mM HEGA-9, EVAPORATION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 5, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 1938 / Num. obs: 1928 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 36.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 25.2 / Num. unique all: 184 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 177 -RANDOM
Rwork0.235 ---
obs0.24 1896 97.4 %-
all-1928 --
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms357 0 0 44 401
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.8→2.9 Å /
RfactorNum. reflection
Rfree0.307 14
Rwork0.267 -
obs-177

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