SASDEG7: Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 4.5 ...

Basic information

• Entry: Database: SASBDB / ID: SASDEG7

Sample

Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 4.5 without Calcium

• Transient receptor potential channel mucolipin 2 (protein), TRPML2, Homo sapiens

Function / homology

Function:

positive regulation of macrophage inflammatory protein 1 alpha production / NAADP-sensitive calcium-release channel activity / macrophage migration / 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 / membrane / identical protein binding / plasma membrane

Domain/homology:

: / Mucolipin, extracytosolic domain / Mucolipin / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel

Component:

Mucolipin-2

• Biological species: Homo sapiens (human)
• Citation: Journal: 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 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)

Models

• Model #2593: ; Type: atomic / Radius of dummy atoms: 1.90 A / Symmetry: P2 / Chi-square value: 1.28 / P-value: 0.000892; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2594: ; Type: dummy / Radius of dummy atoms: 2.00 A / Symmetry: P42 / Chi-square value: 1.508 / P-value: 0.000197; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 4.5 without Calcium; Specimen concentration: 0.35 mg/ml
• Buffer: Name: 10 mM Hepes, pH 4.5, 150 mM NaCl / pH: 4.5

Entity #1358

Name: TRPML2 / Type: protein
Description: Transient receptor potential channel mucolipin 2
Formula weight: 23.354 / Num. of mol.: 8 / Source: Homo sapiens / References: UniProt: Q8IZK6
Sequence:

GLSNQLVVAF KEDNTVAFKH LFLKGYSGTD EDDYSCSVYT QEDAYESIFF AINQYHQLKD ITLGTLGYGE NEDNRIGLKV CKQHYKKGTM FPSNETLNID NDVELDCVQL DLQDLSKKPP DWKNSSFFRL EFYRLLQVEI SFHLKGIDLQ TIHSRELPDC YVFQNTIIFD NKAHSGKIKI YFDSDAKIEE CKDLNIFGST QK

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.849 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 4.5 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 /

	Min	Max
Q	0.0354	4.9462

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 433 /

	Min	Max
Q	0.101346	2.13733
P(R) point	1	433
R	0	10

Result

Type of curve: sec
Comments: The experimental mass was determined via correlated volume.

	Experimental	Porod
MW	180 kDa	180 kDa
Volume	-	285 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	75.06	75.5	0.1
Radius of gyration, Rg	3.666 nm	3.74 nm	0.2

	Min	Max
D	-	10
Guinier point	15	67