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- PDB-9qm9: TMEM55B tandem RING-like domains in complex with RILPL1 C-termina... -

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Basic information

Entry
Database: PDB / ID: 9qm9
TitleTMEM55B tandem RING-like domains in complex with RILPL1 C-terminal peptide
Components
  • RILP-like protein 1
  • Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
KeywordsMEMBRANE PROTEIN / complex / PP4P1 / lysosome
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 / protein transport from ciliary membrane to plasma membrane / response to sterol depletion / Synthesis of PIPs in the nucleus / phosphatidylinositol dephosphorylation / lysosome localization / epithelial cell morphogenesis / dynein light intermediate chain binding ...phosphatidylinositol-4,5-bisphosphate 4-phosphatase / phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity / proton-transporting V-type ATPase complex assembly / protein transport from ciliary membrane to plasma membrane / response to sterol depletion / Synthesis of PIPs in the nucleus / phosphatidylinositol dephosphorylation / lysosome localization / epithelial cell morphogenesis / dynein light intermediate chain binding / PI5P Regulates TP53 Acetylation / nitric oxide mediated signal transduction / cilium assembly / cholesterol metabolic process / phospholipid metabolic process / centriole / positive regulation of TORC1 signaling / regulation of signal transduction by p53 class mediator / small GTPase binding / phagocytic vesicle membrane / late endosome membrane / protein dimerization activity / ciliary basal body / cilium / lysosomal membrane / centrosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphatidylinositol 4,5-bisphosphate 4-phosphatase / Transmembrane protein 55A / Rab interacting lysosomal protein, dimerization domain / : / Rab interacting lysosomal protein / RH1 domain / RH2 domain / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile.
Similarity search - Domain/homology
RILP-like protein 1 / Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWaschbuesch, D. / Khan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation IrelandSFI-20/FFP-A/8446 Ireland
CitationJournal: To Be Published
Title: TMEM55B tandem RING-like domains in complex with RILPL1 C-terminal peptide
Authors: Waschbuesch, D. / Khan, A.R.
History
DepositionMar 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
D: RILP-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3587
Polymers21,0963
Non-polymers2624
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-11 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.514, 48.442, 79.992
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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 / Mutation: C136S, C140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4P1, C14orf9, TMEM55B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q86T03, phosphatidylinositol-4,5-bisphosphate 4-phosphatase
#2: Protein/peptide RILP-like protein 1 / Rab-interacting lysosomal-like protein 1


Mass: 1474.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: synthetic peptide corresponding to the C-terminal residues (391-403) of human RILPL1
Source: (gene. exp.) Homo sapiens (human) / Gene: RILPL1, RLP1 / Production host: synthetic construct (others) / References: UniProt: Q5EBL4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.91 Å3/Da / Density % sol: 35.48 % / Description: rod
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.05M KSCN 0.1M Tris pH 8.5 18% PEG5000/MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2023
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.55→79.99 Å / Num. obs: 24054 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 15.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Χ2: 1 / Net I/σ(I): 8.9
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 2.242 / Num. measured all: 7789 / Num. unique obs: 1163 / CC1/2: 0.536 / Rpim(I) all: 0.917 / Rrim(I) all: 2.426 / Χ2: 0.94 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→41.44 Å / SU ML: 0.1845 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 28.7649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 2255 5.02 %
Rwork0.2047 42675 -
obs0.2067 24054 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.11 Å2
Refinement stepCycle: LAST / Resolution: 1.55→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 4 127 1397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721296
X-RAY DIFFRACTIONf_angle_d1.01371754
X-RAY DIFFRACTIONf_chiral_restr0.062202
X-RAY DIFFRACTIONf_plane_restr0.0121227
X-RAY DIFFRACTIONf_dihedral_angle_d5.7453182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.4061430.32452603X-RAY DIFFRACTION98.6
1.58-1.620.33961480.31742649X-RAY DIFFRACTION98.62
1.62-1.660.32131280.30152650X-RAY DIFFRACTION98.58
1.66-1.710.32611570.26632678X-RAY DIFFRACTION99.79
1.71-1.760.28991430.25132617X-RAY DIFFRACTION98.96
1.76-1.810.27271530.24932696X-RAY DIFFRACTION99.2
1.81-1.880.26811100.2482727X-RAY DIFFRACTION99.65
1.88-1.950.241180.22622658X-RAY DIFFRACTION99.39
1.95-2.040.28491500.20672669X-RAY DIFFRACTION99.61
2.04-2.150.24591650.20262641X-RAY DIFFRACTION99.79
2.15-2.280.24191740.19642664X-RAY DIFFRACTION99.75
2.28-2.460.22851140.18892714X-RAY DIFFRACTION99.68
2.46-2.710.21941240.19432676X-RAY DIFFRACTION99.93
2.71-3.10.25281470.20492690X-RAY DIFFRACTION99.79
3.1-3.90.2321140.18092683X-RAY DIFFRACTION99.36
3.91-41.440.19721670.16152660X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: -24.9941070496 Å / Origin y: -2.48360926412 Å / Origin z: 8.07940072605 Å
111213212223313233
T0.117679095479 Å20.0047832443656 Å20.00582776773263 Å2-0.107118804245 Å2-0.0213515501376 Å2--0.112608002964 Å2
L0.920088567475 °20.131056005226 °20.100854716995 °2-0.52475523358 °20.441810163122 °2--0.859034910483 °2
S-0.0217434707488 Å °-0.101174923127 Å °0.105325209334 Å °-0.00213424830077 Å °0.0206547703895 Å °0.00458404124738 Å °-0.0690011637092 Å °0.0556586804475 Å °-0.00745250091602 Å °
Refinement TLS groupSelection details: all

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