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- PDB-5vre: Crystal structure of a lysosomal potassium-selective channel TMEM... -

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Basic information

Entry
Database: PDB / ID: 5vre
TitleCrystal structure of a lysosomal potassium-selective channel TMEM175 homolog from Chamaesiphon Minutus
ComponentsPutative integral membrane protein
KeywordsTRANSPORT PROTEIN / potassium channel
Function / homologyEndosomal/lysomomal potassium channel TMEM175 / Endosomal/lysosomal potassium channel TMEM175 / proton channel activity / potassium channel activity / potassium ion transmembrane transport / protein homotetramerization / identical protein binding / membrane / Potassium channel Cha6605_3372
Function and homology information
Biological speciesChamaesiphon minutus PCC 6605 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.299 Å
AuthorsLee, C. / Guo, J. / Jiang, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Welch FoundationI-1578 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2017
Title: The lysosomal potassium channel TMEM175 adopts a novel tetrameric architecture.
Authors: Lee, C. / Guo, J. / Zeng, W. / Kim, S. / She, J. / Cang, C. / Ren, D. / Jiang, Y.
History
DepositionMay 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / pdbx_audit_support / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization / _struct.title
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative integral membrane protein
B: Putative integral membrane protein
C: Putative integral membrane protein
D: Putative integral membrane protein


Theoretical massNumber of molelcules
Total (without water)90,7784
Polymers90,7784
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-123 kcal/mol
Surface area32160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.660, 108.880, 119.330
Angle α, β, γ (deg.)90.00, 117.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative integral membrane protein


Mass: 22694.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chamaesiphon minutus PCC 6605 (bacteria)
Gene: Cha6605_3372 / Production host: Escherichia coli (E. coli) / References: UniProt: K9UJK2

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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: 4.86 Å3/Da / Density % sol: 74.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 16-22% PEG 1000, 50 mM CaCl2, 50 mM MgCl2, 100 mM NaAc pH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.299→50 Å / Num. obs: 21668 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 30.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data scaling
autoSHARPphasing
HKL-2000data reduction
RefinementMethod to determine structure: SIRAS / Resolution: 3.299→42.465 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.44
RfactorNum. reflection% reflection
Rfree0.2818 1087 5.02 %
Rwork0.2594 --
obs0.2606 21648 82.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.299→42.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5972 0 0 0 5972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116148
X-RAY DIFFRACTIONf_angle_d1.288396
X-RAY DIFFRACTIONf_dihedral_angle_d17.63484
X-RAY DIFFRACTIONf_chiral_restr0.069996
X-RAY DIFFRACTIONf_plane_restr0.011008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2994-3.44950.4027230.3542425X-RAY DIFFRACTION14
3.4495-3.63130.3523910.31291667X-RAY DIFFRACTION54
3.6313-3.85870.33081610.30343050X-RAY DIFFRACTION99
3.8587-4.15640.27291620.26683101X-RAY DIFFRACTION100
4.1564-4.57420.25981630.23573100X-RAY DIFFRACTION100
4.5742-5.23510.26491650.23833128X-RAY DIFFRACTION100
5.2351-6.59170.27531630.30093108X-RAY DIFFRACTION100
6.5917-42.46870.28181590.23672982X-RAY DIFFRACTION93
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)
12.6658-0.5795-0.23863.3554-0.89982.02620.104-0.22110.380.04-0.4252-0.689-0.29610.71410.27530.5004-0.1833-0.06150.76630.26390.608919.53753.956521.2753
22.0372-0.11051.99161.93420.6882.1901-0.0366-0.52130.3734-0.2269-0.546-1.4609-0.50020.9873-0.00070.6854-0.4053-0.07751.48410.27051.235129.132512.444618.7575
30.51-0.571-0.12461.34320.71680.51920.29530.26560.50810.19741.0602-1.48370.24081.0103-0.39720.8579-0.3326-0.0561.8406-0.04771.325338.15629.736423.8708
40.6218-0.33980.08650.8035-0.01220.0072-0.0156-0.20980.8564-0.1358-0.0085-0.6275-0.11610.14660.0030.2245-0.2470.1082.29180.66971.454533.9265-0.076117.6338
52.54620.36710.36833.82361.56141.84-0.2595-0.3605-0.10630.3101-0.17810.1017-0.1504-0.63950.47040.5134-0.1590.0160.7681-0.15630.5085-3.56582.117628.6077
60.34030.2733-1.11571.8085-0.55953.9301-0.0023-0.774-0.17290.2922-0.1520.85290.922-1.33560.34670.6388-0.26890.22091.102-0.16640.7731-12.9763-6.270732.1225
71.49240.2117-0.0291.70810.35840.0812-0.4028-0.0691-0.49620.765-0.01021.33090.4385-0.5582-0.22340.6005-0.56370.50581.68080.22091.0535-17.0486-3.749341.6698
80.6487-0.4282-0.16871.6413-0.27570.31310.4784-0.7051-0.33060.9844-0.66631.14780.56550.3520.12250.9321-0.26480.38281.6903-0.33210.9022-17.76325.997733.8763
92.28710.1176-2.08393.52370.03522.4269-0.147-0.3128-0.3947-0.0425-0.2792-0.08350.68320.06170.35610.6676-0.07060.09670.42030.16290.43488.7775-9.180324.2849
102.3441-1.65951.5571.1655-1.21691.55460.07380.2289-1.07850.7429-0.2111-0.07411.0880.7010.2231.04990.24360.01010.88290.2420.711817.9243-18.845324.2253
111.7982-0.0582-1.58190.64520.44681.6534-0.2834-0.5999-1.2610.2121-0.7778-0.42490.45250.8796-1.17671.88650.3075-0.4130.40230.41591.106917.1985-25.872130.6114
121.3871-0.67061.05010.3084-0.74077.6497-0.0957-0.3473-0.85290.9741-0.9612-1.1291-0.03451.06230.52451.3607-0.3412-0.05740.6990.2151.06115.4072-24.042926.6186
133.1751-0.454-0.04752.67960.57861.4906-0.1055-0.39840.58120.2075-0.3578-0.1605-0.9226-0.00130.35060.9202-0.2167-0.22120.5042-0.06630.64165.40317.234425.9276
141.8367-0.0106-0.7751.5282-0.35863.71870.3082-0.40270.9091-0.6254-0.5290.5644-0.37230.1996-1.21332.03990.7694-0.27750.6705-0.74361.11113.361732.211935.1171
151.188-0.49240.37070.2797-0.6873.67830.4955-0.91370.91021.2465-0.4350.6215-0.722-0.83810.19052.0368-0.5023-0.48430.83240.02671.178210.814230.379524.7704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 114 )
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 143 )
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 181 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 203 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 114 )
6X-RAY DIFFRACTION6chain 'B' and (resid 115 through 143 )
7X-RAY DIFFRACTION7chain 'B' and (resid 144 through 181 )
8X-RAY DIFFRACTION8chain 'B' and (resid 182 through 203 )
9X-RAY DIFFRACTION9chain 'C' and (resid 7 through 116 )
10X-RAY DIFFRACTION10chain 'C' and (resid 117 through 143 )
11X-RAY DIFFRACTION11chain 'C' and (resid 144 through 181 )
12X-RAY DIFFRACTION12chain 'C' and (resid 182 through 203 )
13X-RAY DIFFRACTION13chain 'D' and (resid 7 through 143 )
14X-RAY DIFFRACTION14chain 'D' and (resid 144 through 181 )
15X-RAY DIFFRACTION15chain 'D' and (resid 182 through 203 )

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