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- PDB-4rax: A regulatory domain of an ion channel -

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Basic information

Entry
Database: PDB / ID: 4rax
TitleA regulatory domain of an ion channel
ComponentsPiezo-type mechanosensitive ion channel component 1
KeywordsSTRUCTURAL PROTEIN / sandwich fold / novel structure / extra-cellular / regulatory domain / regulatory
Function / homology
Function and homology information


mechanosensitive monoatomic cation channel activity / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / regulation of membrane potential ...mechanosensitive monoatomic cation channel activity / positive regulation of cell-cell adhesion mediated by integrin / detection of mechanical stimulus / mechanosensitive monoatomic ion channel activity / positive regulation of integrin activation / positive regulation of myotube differentiation / lamellipodium membrane / monoatomic cation transport / monoatomic cation channel activity / regulation of membrane potential / endoplasmic reticulum-Golgi intermediate compartment membrane / cellular response to mechanical stimulus / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
Piezo family / Piezo non-specific cation channel, R-Ras-binding domain / Piezo domain / Piezo non-specific cation channel, R-Ras-binding domain / Piezo
Similarity search - Domain/homology
Piezo-type mechanosensitive ion channel component 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsGe, J. / Yang, M.
CitationJournal: Nature / Year: 2015
Title: Architecture of the mammalian mechanosensitive Piezo1 channel.
Authors: Jingpeng Ge / Wanqiu Li / Qiancheng Zhao / Ningning Li / Maofei Chen / Peng Zhi / Ruochong Li / Ning Gao / Bailong Xiao / Maojun Yang /
Abstract: Piezo proteins are evolutionarily conserved and functionally diverse mechanosensitive cation channels. However, the overall structural architecture and gating mechanisms of Piezo channels have ...Piezo proteins are evolutionarily conserved and functionally diverse mechanosensitive cation channels. However, the overall structural architecture and gating mechanisms of Piezo channels have remained unknown. Here we determine the cryo-electron microscopy structure of the full-length (2,547 amino acids) mouse Piezo1 (Piezo1) at a resolution of 4.8 Å. Piezo1 forms a trimeric propeller-like structure (about 900 kilodalton), with the extracellular domains resembling three distal blades and a central cap. The transmembrane region has 14 apparently resolved segments per subunit. These segments form three peripheral wings and a central pore module that encloses a potential ion-conducting pore. The rather flexible extracellular blade domains are connected to the central intracellular domain by three long beam-like structures. This trimeric architecture suggests that Piezo1 may use its peripheral regions as force sensors to gate the central ion-conducting pore.
History
DepositionSep 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Piezo-type mechanosensitive ion channel component 1


Theoretical massNumber of molelcules
Total (without water)28,3471
Polymers28,3471
Non-polymers00
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.492, 89.492, 89.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Piezo-type mechanosensitive ion channel component 1 / Protein FAM38A


Mass: 28346.787 Da / Num. of mol.: 1 / Fragment: UNP residues 2214-2457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Piezo1, Fam38a / Production host: Escherichia coli (E. coli) / References: UniProt: E2JF22
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 41.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Magnesium chloride, 0.1M Hepes pH 7.5, 25% w/w PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 42523 / Num. obs: 42493 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.079 / Rsym value: 0.107
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.45-1.51100
1.5-1.561100
1.56-1.631100
1.63-1.721100
1.72-1.831100
1.83-1.971100
1.97-2.171100
2.17-2.481100
2.48-3.121100
3.12-50199.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→36.535 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 16.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1759 2143 5.05 %
Rwork0.1513 --
obs0.1525 42455 99.81 %
all-42523 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→36.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 0 352 2159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061854
X-RAY DIFFRACTIONf_angle_d1.0652528
X-RAY DIFFRACTIONf_dihedral_angle_d13.745699
X-RAY DIFFRACTIONf_chiral_restr0.061277
X-RAY DIFFRACTIONf_plane_restr0.005336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48380.26341180.16872690X-RAY DIFFRACTION100
1.4838-1.52090.19121210.14522665X-RAY DIFFRACTION100
1.5209-1.5620.16141570.13422659X-RAY DIFFRACTION100
1.562-1.6080.18521330.1292673X-RAY DIFFRACTION100
1.608-1.65990.17521500.1322659X-RAY DIFFRACTION100
1.6599-1.71920.15051630.13492638X-RAY DIFFRACTION100
1.7192-1.7880.2011440.13762674X-RAY DIFFRACTION100
1.788-1.86940.18881490.13792686X-RAY DIFFRACTION100
1.8694-1.96790.17571280.13652684X-RAY DIFFRACTION100
1.9679-2.09120.1621420.13872684X-RAY DIFFRACTION100
2.0912-2.25270.16151480.1422680X-RAY DIFFRACTION100
2.2527-2.47930.19511480.15442699X-RAY DIFFRACTION100
2.4793-2.8380.19421390.16662709X-RAY DIFFRACTION100
2.838-3.57510.15621510.16142732X-RAY DIFFRACTION100
3.5751-36.54650.17441520.16242780X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -1.2043 Å / Origin y: 16.0277 Å / Origin z: 34.498 Å
111213212223313233
T0.0927 Å2-0.0089 Å2-0.0003 Å2-0.0635 Å20.0012 Å2--0.0835 Å2
L0.8195 °2-0.0675 °20.084 °2-0.394 °2-0.134 °2--0.9057 °2
S-0.0246 Å °0.0839 Å °0.0384 Å °0.0104 Å °-0.0138 Å °-0.0277 Å °-0.0887 Å °0.0189 Å °-0.0081 Å °
Refinement TLS groupSelection details: all

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