[English] 日本語
Yorodumi
- PDB-6hrs: Structure of the TRPML2 ELD at pH 4.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hrs
TitleStructure of the TRPML2 ELD at pH 4.5
ComponentsMucolipin-2
KeywordsMEMBRANE PROTEIN / TRPML Channel Mucolipin Cation Channel Endolysosomal System
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsBader, N. / Viet, K.K. / Wagner, A. / Hellmich, U.A. / Schindelin, H.
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.
History
DepositionSep 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mucolipin-2
B: Mucolipin-2
C: Mucolipin-2
D: Mucolipin-2
E: Mucolipin-2
F: Mucolipin-2
G: Mucolipin-2
H: Mucolipin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,84710
Polymers184,6628
Non-polymers1842
Water32418
1
A: Mucolipin-2
B: Mucolipin-2
C: Mucolipin-2
D: Mucolipin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5156
Polymers92,3314
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-46 kcal/mol
Surface area36820 Å2
MethodPISA
2
E: Mucolipin-2
F: Mucolipin-2
G: Mucolipin-2
H: Mucolipin-2


Theoretical massNumber of molelcules
Total (without water)92,3314
Polymers92,3314
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-48 kcal/mol
Surface area35880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.523, 142.473, 85.195
Angle α, β, γ (deg.)90.000, 104.490, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Mucolipin-2 / Transient receptor potential channel mucolipin 2 / TRPML2


Mass: 23082.801 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCOLN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IZK6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 25% PEG 550 MME 0.1 M Na-Acetate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.95→48.61 Å / Num. obs: 35855 / % possible obs: 98.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 102.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.058 / Net I/σ(I): 9.8
Reflection shellResolution: 2.95→3.09 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.937 / Mean I/σ(I) obs: 1 / Num. unique obs: 4798 / CC1/2: 0.411 / Rpim(I) all: 0.749 / % possible all: 99.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HRR

6hrr


Resolution: 2.95→28.13 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.357
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1868 5.22 %RANDOM
Rwork0.182 ---
obs0.184 35800 98.8 %-
Displacement parametersBiso max: 291.63 Å2 / Biso mean: 117.1 Å2 / Biso min: 47.32 Å2
Baniso -1Baniso -2Baniso -3
1--14.2361 Å20 Å211.6703 Å2
2--8.3436 Å20 Å2
3---5.8925 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.95→28.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12215 0 12 18 12245
Biso mean--138.1 77.11 -
Num. residues----1491
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6821SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3927HARMONIC5
X-RAY DIFFRACTIONt_it24229HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1586SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact24972SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d24229HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg43607HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion3.38
LS refinement shellResolution: 2.95→3.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2502 158 5.36 %
Rwork0.2271 2789 -
all0.2283 2947 -
obs--99.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44590.11460.39223.55880.10116.0888-0.11180.03430.61710.32620.1151-0.3188-0.70440.2966-0.0033-0.0605-0.0308-0.1155-0.3366-0.0053-0.040517.722529.153217.5975
22.6737-0.35550.44152.1910.80285.45210.0622-0.2973-0.49630.14590.04570.70690.5613-0.5966-0.1079-0.2787-0.09570.0963-0.22920.00890.0612-11.723-13.916315.7506
33.21151.287-0.73133.9163-0.50992.11950.0105-0.74550.02360.8408-0.16420.1212-0.3413-0.38250.15370.20390.12970.15820.0423-0.0838-0.36290.74358.439742.5819
44.38641.8780.18045.3441-0.00021.8501-0.15280.68220.1633-0.98980.12130.2392-0.2406-0.07090.0315-0.0252-0.0109-0.0311-0.07350.0024-0.37854.75046.7573-9.3218
51.7451-0.566-1.13533.57361.75486.10680.1132-0.2647-0.7586-0.0510.1060.09540.88350.0046-0.2193-0.0229-0.0947-0.0729-0.36880.13230.1188-12.547942.0275-12.0048
63.7248-0.5218-0.49231.78290.43024.97690.04740.07410.3655-0.50510.11310.7286-0.433-0.6235-0.1605-0.23870.0496-0.2336-0.15120.08150.1093-39.570884.0707-26.9677
73.4688-1.06540.73355.3043-1.8583.6198-0.0023-0.6332-0.26540.68250.06840.7189-0.0166-0.6706-0.0661-0.3566-0.05160.23370.12490.1167-0.2212-32.105167.63865.8301
83.2287-0.87162.01434.8598-1.40383.7890.18140.7499-0.3985-0.8382-0.07490.23890.42370.0893-0.10650.112-0.0934-0.0797-0.1909-0.202-0.4134-20.8458.7493-43.8779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A86 - 281
2X-RAY DIFFRACTION2{ B|* }B86 - 284
3X-RAY DIFFRACTION3{ C|* }C89 - 283
4X-RAY DIFFRACTION4{ D|* }D89 - 283
5X-RAY DIFFRACTION5{ E|* }E88 - 283
6X-RAY DIFFRACTION6{ F|* }F86 - 282
7X-RAY DIFFRACTION7{ G|* }G89 - 283
8X-RAY DIFFRACTION8{ H|* }H89 - 282

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more