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- PDB-8oqh: Structure of the cytosolic domain of lysosome-associated TMEM55B -

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Basic information

Entry
Database: PDB / ID: 8oqh
TitleStructure of the cytosolic domain of lysosome-associated TMEM55B
ComponentsType 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
KeywordsMEMBRANE PROTEIN / membrane trafficking / lysosomes / JIP4
Function / homology
Function and homology information


phosphatidylinositol-4,5-bisphosphate 4-phosphatase / phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity / proton-transporting V-type ATPase complex assembly / response to sterol depletion / Synthesis of PIPs in the nucleus / phosphatidylinositol dephosphorylation / lysosome localization / PI5P Regulates TP53 Acetylation / cholesterol metabolic process / phospholipid metabolic process ...phosphatidylinositol-4,5-bisphosphate 4-phosphatase / phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity / proton-transporting V-type ATPase complex assembly / response to sterol depletion / Synthesis of PIPs in the nucleus / phosphatidylinositol dephosphorylation / lysosome localization / PI5P Regulates TP53 Acetylation / cholesterol metabolic process / phospholipid metabolic process / positive regulation of TORC1 signaling / regulation of signal transduction by p53 class mediator / phagocytic vesicle membrane / late endosome membrane / lysosomal membrane / nucleoplasm / plasma membrane
Similarity search - Function
Phosphatidylinositol 4,5-bisphosphate 4-phosphatase / Transmembrane protein 55A
Similarity search - Domain/homology
Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsWaschbusch, D. / Khan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland20/FFP-A/8446 Ireland
CitationJournal: To be published
Title: Structure of the cytosolic domain of lysosome-associated TMEM55B
Authors: Washcbusch, D. / Khan, A.R.
History
DepositionApr 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
B: Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8836
Polymers19,6212
Non-polymers2624
Water1,31573
1
A: Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9413
Polymers9,8111
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9413
Polymers9,8111
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.412, 84.445, 32.177
Angle α, β, γ (deg.)90.000, 98.320, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase / Type 1 PtdIns-4 / 5-P2 4-Ptase / PtdIns-4 / 5-P2 4-Ptase I / Transmembrane protein 55B


Mass: 9810.661 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4P1, C14orf9, TMEM55B / Production host: Escherichia coli (E. coli)
References: UniProt: Q86T03, phosphatidylinositol-4,5-bisphosphate 4-phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH8.5, 0.2M Sodium acetate trihydrate, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→42.22 Å / Num. obs: 15173 / % possible obs: 98.06 % / Redundancy: 3.8 % / Biso Wilson estimate: 28.17 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1141 / Rpim(I) all: 0.06663 / Rrim(I) all: 0.1327 / Net I/σ(I): 6.67
Reflection shellResolution: 1.76→1.823 Å / Rmerge(I) obs: 1.378 / Num. unique obs: 1517 / CC1/2: 0.493 / Rpim(I) all: 0.8001

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDS20220110data reduction
Aimless0.7.8data scaling
PHASER1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→42.22 Å / SU ML: 0.1357 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 24.2171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224 760 5.02 %
Rwork0.1942 14369 -
obs0.1957 15129 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.94 Å2
Refinement stepCycle: LAST / Resolution: 1.76→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 4 73 1281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01451228
X-RAY DIFFRACTIONf_angle_d1.36051664
X-RAY DIFFRACTIONf_chiral_restr0.0804194
X-RAY DIFFRACTIONf_plane_restr0.0142214
X-RAY DIFFRACTIONf_dihedral_angle_d6.4618172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.90.28761720.27152844X-RAY DIFFRACTION98.4
1.9-2.090.27171330.24072879X-RAY DIFFRACTION97.95
2.09-2.390.24181470.20782877X-RAY DIFFRACTION98.34
2.39-3.010.24641550.20342884X-RAY DIFFRACTION98.32
3.01-42.220.19241530.17082885X-RAY DIFFRACTION97.4
Refinement TLS params.Method: refined / Origin x: 19.4165495118 Å / Origin y: -15.3404773765 Å / Origin z: 8.88570450093 Å
111213212223313233
T0.236355944676 Å2-0.00999899809154 Å2-0.00639757802766 Å2-0.257055447765 Å2-0.0168990327147 Å2--0.259050985065 Å2
L0.0660914748603 °2-0.56721605633 °2-0.136131190126 °2-1.63054510735 °20.143871447744 °2--0.100593473299 °2
S0.0104407663418 Å °-0.0133737388699 Å °0.0506645871705 Å °-0.116299003256 Å °0.0415953839277 Å °-0.186568242542 Å °-0.0262642231492 Å °0.0545178103545 Å °3.08331155602E-5 Å °
Refinement TLS groupSelection details: all

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