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- PDB-6hrr: Structure of the TRPML2 ELD at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 6hrr
TitleStructure of the TRPML2 ELD at pH 6.5
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 Å
AuthorsBader, N. / Viet, K.K. / Wagner, A. / Hellmich, U.A.
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,17020
Polymers44,4262
Non-polymers1,74418
Water3,711206
1
A: Mucolipin-2
hetero molecules

A: Mucolipin-2
hetero molecules

A: Mucolipin-2
hetero molecules

A: Mucolipin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,91440
Polymers88,8514
Non-polymers3,06336
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area11910 Å2
ΔGint-126 kcal/mol
Surface area34160 Å2
MethodPISA
2
B: Mucolipin-2
hetero molecules

B: Mucolipin-2
hetero molecules

B: Mucolipin-2
hetero molecules

B: Mucolipin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,76540
Polymers88,8514
Non-polymers3,91436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area13500 Å2
ΔGint-68 kcal/mol
Surface area34420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.471, 109.471, 149.744
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-301-

K

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 22212.836 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 224 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.52 Å3/Da / Density % sol: 51.28 % / Description: Cube
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% Jeffamine M-600 0.1 M MES pH 6.5 50 mM CsCl

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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→46.53 Å / Num. obs: 31030 / % possible obs: 99.9 % / Redundancy: 27.2 % / Biso Wilson estimate: 47.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.002 / Net I/σ(I): 21.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 28.8 % / Rmerge(I) obs: 3.556 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2240 / CC1/2: 0.645 / Rpim(I) all: 0.673 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSJan 26, 2018data reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TJA

5tja


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.166 / SU Rfree Blow DPI: 0.143 / SU Rfree Cruickshank DPI: 0.141
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1560 5.03 %RANDOM
Rwork0.186 ---
obs0.188 30988 99.9 %-
Displacement parametersBiso max: 202.68 Å2 / Biso mean: 61.21 Å2 / Biso min: 23.95 Å2
Baniso -1Baniso -2Baniso -3
1-5.5228 Å20 Å20 Å2
2--5.5228 Å20 Å2
3----11.0455 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 106 212 3159
Biso mean--84.06 60.66 -
Num. residues----346
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1715SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes989HARMONIC5
X-RAY DIFFRACTIONt_it5971HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion386SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6327SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5971HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10713HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion3.07
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2486 152 5.39 %
Rwork0.2214 2669 -
all0.2229 2821 -
obs--100 %
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)
12.6966-0.5502-0.50681.66210.19751.9923-0.0141-0.11820.2281-0.00190.0450.0751-0.0594-0.0601-0.031-0.16930.0347-0.0032-0.1590.0027-0.1744-15.66920.7254-14.1139
23.0913-0.1158-0.23962.2564-0.29691.2179-0.0772-0.096-0.42760.03230.0143-0.18330.14990.0560.0629-0.19060.03270.001-0.21730.0433-0.0957-39.878433.8884-27.2479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A92 - 282
2X-RAY DIFFRACTION2{ B|* }B92 - 282

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