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- SASDEF7: Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 6.5 ... -

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Basic information

Entry
Database: SASBDB / ID: SASDEF7
SampleHuman TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 6.5 without Calcium
  • Transient receptor potential channel mucolipin 2 (protein), TRPML2, Homo sapiens
Function / homology
Function and homology information


macrophage migration / positive regulation of macrophage inflammatory protein 1 alpha production / NAADP-sensitive calcium-release channel activity / iron ion transmembrane transporter activity / positive regulation of chemokine (C-C motif) ligand 5 production / neutrophil migration / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / TRP channels / calcium ion transmembrane transport ...macrophage migration / positive regulation of macrophage inflammatory protein 1 alpha production / NAADP-sensitive calcium-release channel activity / iron ion transmembrane transporter activity / positive regulation of chemokine (C-C motif) ligand 5 production / neutrophil migration / positive regulation of monocyte chemotactic protein-1 production / positive regulation of chemokine (C-X-C motif) ligand 2 production / TRP channels / calcium ion transmembrane transport / calcium channel activity / recycling endosome membrane / protein transport / late endosome membrane / adaptive immune response / lysosome / innate immune response / identical protein binding / membrane / plasma membrane
Similarity search - Function
Mucolipin / : / Mucolipin, extracytosolic domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
CitationJournal: Structure / Year: 2019
Title: Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain.
Authors: Kerstin K Viet / Annika Wagner / Kevin Schwickert / Nils Hellwig / Martha Brennich / Nicole Bader / Tanja Schirmeister / Nina Morgner / Hermann Schindelin / Ute A Hellmich /
Abstract: TRPML2 is the least structurally characterized mammalian transient receptor potential mucolipin ion channel. The TRPML family hallmark is a large extracytosolic/lumenal domain (ELD) between ...TRPML2 is the least structurally characterized mammalian transient receptor potential mucolipin ion channel. The TRPML family hallmark is a large extracytosolic/lumenal domain (ELD) between transmembrane helices S1 and S2. We present crystal structures of the tetrameric human TRPML2 ELD at pH 6.5 (2.0 Å) and 4.5 (2.95 Å), corresponding to the pH values in recycling endosomes and lysosomes. Isothermal titration calorimetry shows Ca binding to the highly acidic central pre-pore loop which is abrogated at low pH, in line with a pH-dependent channel regulation model. Small angle X-ray scattering confirms the ELD dimensions in solution. Changes in pH or Ca concentration do not affect the protein's secondary structure, but can influence ELD oligomer integrity according to native mass spectrometry. Our data thus complete the set of high-resolution views of human TRPML channel ELDs and reveal some structural responses to the conditions the TRPML2 ELD encounters as the channel traffics through the endolysosomal system.
Contact author
  • Martha Brennich (EMBL, European Molecular Biology Laboratory (EMBL) - Grenoble Outstation, Grenoble, France)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Models

Model #2588
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 1.05 / P-value: 0.378170
Search similar-shape structures of this assembly by Omokage search (details)
Model #2589
Type: dummy / Radius of dummy atoms: 1.80 A / Chi-square value: 1.121 / P-value: 0.354436
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 6.5 without Calcium
Specimen concentration: 0.65 mg/ml
BufferName: 10 mM HEPES pH 6.5 150 mM NaCl / pH: 6.5
Entity #1357Name: TRPML2 / Type: protein
Description: Transient receptor potential channel mucolipin 2
Formula weight: 23.354 / Num. of mol.: 4 / Source: Homo sapiens / References: UniProt: Q8IZK6
Sequence: GLSNQLVVAF KEDNTVAFKH LFLKGYSGTD EDDYSCSVYT QEDAYESIFF AINQYHQLKD ITLGTLGYGE NEDNRIGLKV CKQHYKKGTM FPSNETLNID NDVELDCVQL DLQDLSKKPP DWKNSSFFRL EFYRLLQVEI SFHLKGIDLQ TIHSRELPDC YVFQNTIIFD ...Sequence:
GLSNQLVVAF KEDNTVAFKH LFLKGYSGTD EDDYSCSVYT QEDAYESIFF AINQYHQLKD ITLGTLGYGE NEDNRIGLKV CKQHYKKGTM FPSNETLNID NDVELDCVQL DLQDLSKKPP DWKNSSFFRL EFYRLLQVEI SFHLKGIDLQ TIHSRELPDC YVFQNTIIFD NKAHSGKIKI YFDSDAKIEE CKDLNIFGST QK

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Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.849 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 6.5 without Calcium
Measurement date: Oct 18, 2018 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 1200 / Unit: 1/nm /
MinMax
Q0.0354 4.9462
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 452 /
MinMax
Q0.219169 2.3447
P(R) point1 452
R0 8.9
Result
Type of curve: sec
Comments: The experimental mass was determined via correlated volume.
ExperimentalPorod
MW95 kDa88 kDa
Volume-140 nm3

P(R)GuinierGuinier error
Forward scattering, I058.11 58.86 0.13
Radius of gyration, Rg3.361 nm3.41 nm0.03

MinMax
D-8.9
Guinier point10 73

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