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- PDB-3hro: Crystal structure of a C-terminal coiled coil domain of Transient... -

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Basic information

Entry
Database: PDB / ID: 3hro
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), also called Polycystin-2 or polycystic kidney disease 2(PKD2)
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 / renal tubule morphogenesis ...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 / renal tubule morphogenesis / determination of liver left/right asymmetry / metanephric ascending thin limb development / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / basal cortex / placenta blood vessel development / renal artery morphogenesis / HLH domain binding / VxPx cargo-targeting to cilium / cilium organization / migrasome / neural tube development / cellular response to fluid shear stress / muscle alpha-actinin binding / regulation of calcium ion import / calcium-induced calcium release activity / detection of mechanical stimulus / determination of left/right symmetry / voltage-gated monoatomic ion channel activity / embryonic placenta development / cellular response to hydrostatic pressure / aorta development / cation channel complex / branching involved in ureteric bud morphogenesis / non-motile cilium / outward rectifier potassium channel activity / motile cilium / actinin binding / cellular response to osmotic stress / negative regulation of G1/S transition of mitotic cell cycle / voltage-gated sodium channel activity / heart looping / spinal cord development / ciliary membrane / voltage-gated monoatomic cation channel activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / protein heterotetramerization / cytoplasmic side of endoplasmic reticulum membrane / potassium channel activity / voltage-gated potassium channel activity / centrosome duplication / transcription regulator inhibitor activity / cell surface receptor signaling pathway via JAK-STAT / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / monoatomic cation channel activity / cytoskeletal protein binding / cellular response to calcium ion / cellular response to cAMP / liver development / potassium ion transmembrane transport / cytoplasmic vesicle membrane / basal plasma membrane / sodium ion transmembrane transport / lumenal side of endoplasmic reticulum membrane / cellular response to reactive oxygen species / protein tetramerization / phosphoprotein binding / Wnt signaling pathway / mitotic spindle / positive regulation of nitric oxide biosynthetic process / calcium ion transmembrane transport / heart development / calcium ion transport / transmembrane transport / cell-cell junction / cilium / regulation of cell population proliferation / lamellipodium / ATPase binding / ciliary basal body / protein homotetramerization / basolateral plasma membrane / transmembrane transporter binding / regulation of cell cycle / cell surface receptor signaling pathway / negative regulation of cell population proliferation / signaling receptor binding / positive regulation of gene expression / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
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 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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), also called Polycystin-2 or polycystic kidney disease 2(PKD2)


Theoretical massNumber of molelcules
Total (without water)5,0531
Polymers5,0531
Non-polymers00
Water57632
1
A: Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2), also called Polycystin-2 or polycystic kidney disease 2(PKD2)

A: Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2), also called Polycystin-2 or polycystic kidney disease 2(PKD2)

A: Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2), also called Polycystin-2 or polycystic kidney disease 2(PKD2)


Theoretical massNumber of molelcules
Total (without water)15,1593
Polymers15,1593
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 area4120 Å2
ΔGint-49 kcal/mol
Surface area6790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.388, 32.388, 70.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein/peptide Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2), also called Polycystin-2 or polycystic kidney disease 2(PKD2) / 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: 5052.893 Da / Num. of mol.: 1
Fragment: C-terminal of Coiled Coil Domain, UNP residues 833-872
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2 / Plasmid: pET-28a(+) / 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.: 32 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 6000, LiCl, Citric Acid, pH 4.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97927 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 3273 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.052 / Χ2: 1.124 / Net I/σ(I): 32.805
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 5.1 / Num. unique all: 290 / Χ2: 1.226 / % possible all: 92.9

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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
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZIJ

1zij


Resolution: 1.9→30 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.872 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 281 8.5 %RANDOM
Rwork0.194 ---
all0.217 3190 --
obs0.197 2991 90 %-
Solvent computationBsol: 56.794 Å2
Displacement parametersBiso max: 52.47 Å2 / Biso mean: 26.404 Å2 / Biso min: 14.36 Å2
Baniso -1Baniso -2Baniso -3
1-5.439 Å20 Å20 Å2
2--5.439 Å20 Å2
3----10.877 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms299 0 0 32 331
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d1.227
X-RAY DIFFRACTIONc_mcbond_it1.4861.5
X-RAY DIFFRACTIONc_scbond_it3.0792
X-RAY DIFFRACTIONc_mcangle_it2.1312
X-RAY DIFFRACTIONc_scangle_it4.3312.5
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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