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- PDB-3hrn: crystal structure of a C-terminal coiled coil domain of Transient... -

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Basic information

Entry
Database: PDB / ID: 3hrn
Titlecrystal structure of a C-terminal coiled coil domain of Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2, polycystic kidney disease 2)
ComponentsTransient receptor potential (TRP) channel subfamily P member 2 (TRPP2)
KeywordsTRANSPORT PROTEIN / coiled coil / helix bundle / trimer / Calcium / Disease mutation / Glycoprotein / Ion transport / Ionic channel / Membrane / Phosphoprotein / Polymorphism / Transmembrane / Transport
Function / homology
Function and homology information


detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / determination of liver left/right asymmetry ...detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / determination of liver left/right asymmetry / renal tubule morphogenesis / metanephric ascending thin limb development / HLH domain binding / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / basal cortex / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / detection of mechanical stimulus / calcium-induced calcium release activity / voltage-gated monoatomic ion channel activity / muscle alpha-actinin binding / cation channel complex / regulation of calcium ion import / placenta blood vessel development / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / cellular response to fluid shear stress / non-motile cilium / cellular response to osmotic stress / actinin binding / voltage-gated monoatomic cation channel activity / motile cilium / transcription regulator inhibitor activity / aorta development / determination of left/right symmetry / inorganic cation transmembrane transport / voltage-gated sodium channel activity / neural tube development / ciliary membrane / protein heterotetramerization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / negative regulation of ryanodine-sensitive calcium-release channel activity / cytoplasmic side of endoplasmic reticulum membrane / centrosome duplication / cell surface receptor signaling pathway via JAK-STAT / voltage-gated potassium channel activity / potassium channel activity / embryonic placenta development / voltage-gated calcium channel activity / sodium ion transmembrane transport / monoatomic cation channel activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / cytoskeletal protein binding / potassium ion transmembrane transport / cellular response to calcium ion / liver development / basal plasma membrane / ciliary basal body / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / phosphoprotein binding / protein tetramerization / calcium ion transmembrane transport / cytoplasmic vesicle membrane / cilium / mitotic spindle / Wnt signaling pathway / intracellular calcium ion homeostasis / cellular response to reactive oxygen species / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cell-cell junction / lamellipodium / heart development / regulation of cell population proliferation / ATPase binding / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein homotetramerization / transmembrane transporter binding / cell surface receptor signaling pathway / regulation of cell cycle / negative regulation of cell population proliferation / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / Polycystin domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsYu, Y. / Ulbrich, M.H. / Li, M.-H. / Buraei, Z. / Chen, X.-Z. / Ong, A.C.M. / Tong, L. / Isacoff, E.Y. / Yang, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural and molecular basis of the assembly of the TRPP2/PKD1 complex.
Authors: Yu, Y. / Ulbrich, M.H. / Li, M.H. / Buraei, Z. / Chen, X.Z. / Ong, A.C. / Tong, L. / Isacoff, E.Y. / Yang, J.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2)


Theoretical massNumber of molelcules
Total (without water)7,3531
Polymers7,3531
Non-polymers00
Water1,982110
1
A: Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2)

A: Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2)

A: Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2)


Theoretical massNumber of molelcules
Total (without water)22,0583
Polymers22,0583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area4780 Å2
ΔGint-46 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.642, 43.642, 200.351
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2) / Polycystin-2 / Polycystic kidney disease 2 protein / Autosomal dominant polycystic kidney disease ...Polycystin-2 / Polycystic kidney disease 2 protein / Autosomal dominant polycystic kidney disease type II protein / Polycystwin / R48321


Mass: 7352.629 Da / Num. of mol.: 1
Fragment: C-terminal of Coiled Coil Domain, UNP residues 833-895
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q13563
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Dioxane, NaAc, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 6163 / Num. obs: 6163 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.068 / Χ2: 1.329 / Net I/σ(I): 36.178
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 9.93 / Num. unique all: 585 / Χ2: 1.173 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZIJ

1zij


Resolution: 1.9→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.839 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 624 10.1 %RANDOM
Rwork0.199 ---
all0.222 6101 --
obs0.205 5883 95.6 %-
Solvent computationBsol: 54.761 Å2
Displacement parametersBiso max: 79.05 Å2 / Biso mean: 28.006 Å2 / Biso min: 5.61 Å2
Baniso -1Baniso -2Baniso -3
1-5.421 Å20 Å20 Å2
2--5.421 Å20 Å2
3----10.842 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms553 0 0 110 663
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_d1.299
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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