6HRR | pdb_00006hrr

Structure of the TRPML2 ELD at pH 6.5

PDB DOI: https://doi.org/10.2210/pdb6HRR/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-09-28 Released: 2019-06-19
Deposition Author(s): Bader, N., Viet, K.K., Wagner, A., Hellmich, U.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.217 (Depositor), 0.188 (DCC)
R-Value Work:
0.186 (Depositor), 0.185 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain.

Viet, K.K., Wagner, A., Schwickert, K., Hellwig, N., Brennich, M., Bader, N., Schirmeister, T., Morgner, N., Schindelin, H., Hellmich, U.A.

(2019) Structure 27: 1246-1257.e5

PubMed: 31178222 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2019.04.016
Primary Citation Related Structures:
6HRR, 6HRS

PubMed 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 ²⁺ 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 ²⁺ 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.

Organizational Affiliation

Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, 60438 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 46.17 kDa
Atom Count: 3,279
Modeled Residue Count: 346
Deposited Residue Count: 382
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucolipin-2	A, B	191	Homo sapiens	Mutation(s): 0 Gene Names: MCOLN2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZK6 (Homo sapiens) Explore Q8IZK6 Go to UniProtKB: Q8IZK6
PHAROS: Q8IZK6 GTEx: ENSG00000153898
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IZK6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	K [auth A], S [auth B], T [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	D [auth A], E [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.217 (Depositor), 0.188 (DCC)
R-Value Work: 0.186 (Depositor), 0.185 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.471	α = 90
b = 109.471	β = 90
c = 149.744	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 1.1: 2019-08-14
Changes: Data collection, Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary