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- PDB-6hrs: Structure of the TRPML2 ELD at pH 4.5 -

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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


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 ...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
Similarity search - Function
Mucolipin / 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: Viet, K.K. / Wagner, A. / Schwickert, K. / Hellwig, N. / Brennich, M. / Bader, N. / Schirmeister, T. / Morgner, N. / Schindelin, H. / Hellmich, U.A.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.37 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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