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- PDB-9jtz: Crystal structure of Nir2 C-terminal domain in complex with phosp... -

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Basic information

Entry
Database: PDB / ID: 9jtz
TitleCrystal structure of Nir2 C-terminal domain in complex with phosphatidic acid
ComponentsMembrane-associated phosphatidylinositol transfer protein 1
KeywordsLIPID BINDING PROTEIN / PLC signaling / PI cycle / Membrane contact site / lipid transfer / lipid binding
Function / homology
Function and homology information


Synthesis of PI / phosphatidylinositol transfer activity / phosphatidic acid binding / phosphatidylcholine binding / Golgi cisterna membrane / cleavage furrow / lipid droplet / phosphatidylinositol binding / receptor tyrosine kinase binding / phospholipid binding ...Synthesis of PI / phosphatidylinositol transfer activity / phosphatidic acid binding / phosphatidylcholine binding / Golgi cisterna membrane / cleavage furrow / lipid droplet / phosphatidylinositol binding / receptor tyrosine kinase binding / phospholipid binding / protein transport / cell body / midbody / calcium ion binding / endoplasmic reticulum membrane / cytosol
Similarity search - Function
DDHD domain / DDHD domain / PITM 1-3, LNS2 domain / PITM 1-3, beta-sandwich domain / DDHD domain profile. / DDHD / : / Phosphatidylinositol transfer protein / Phosphatidylinositol transfer protein / LNS2/PITP ...DDHD domain / DDHD domain / PITM 1-3, LNS2 domain / PITM 1-3, beta-sandwich domain / DDHD domain profile. / DDHD / : / Phosphatidylinositol transfer protein / Phosphatidylinositol transfer protein / LNS2/PITP / LNS2 / START-like domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / 2-oxidanylethanal / Membrane-associated phosphatidylinositol transfer protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKim, D. / Lee, C.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021M3A9G8022417 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1A2C2009550 Korea, Republic Of
CitationJournal: To Be Published
Title: Structure of Nir2 reveals a phosphatidic acid sensing mechanism at the ER-PM contact sites
Authors: Kim, D. / Lee, S. / Jun, Y. / Lee, C.
History
DepositionOct 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 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: Membrane-associated phosphatidylinositol transfer protein 1
B: Membrane-associated phosphatidylinositol transfer protein 1
C: Membrane-associated phosphatidylinositol transfer protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5806
Polymers92,1123
Non-polymers4683
Water4,161231
1
A: Membrane-associated phosphatidylinositol transfer protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1724
Polymers30,7041
Non-polymers4683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area12850 Å2
MethodPISA
2
B: Membrane-associated phosphatidylinositol transfer protein 1


Theoretical massNumber of molelcules
Total (without water)30,7041
Polymers30,7041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13180 Å2
MethodPISA
3
C: Membrane-associated phosphatidylinositol transfer protein 1


Theoretical massNumber of molelcules
Total (without water)30,7041
Polymers30,7041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.941, 108.764, 120.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Membrane-associated phosphatidylinositol transfer protein 1 / Drosophila retinal degeneration B homolog 1 / RdgB1 / Mpt-1 / Phosphatidylinositol transfer protein ...Drosophila retinal degeneration B homolog 1 / RdgB1 / Mpt-1 / Phosphatidylinositol transfer protein / membrane-associated 1 / PITPnm 1 / Pyk2 N-terminal domain-interacting receptor 2 / NIR-2


Mass: 30703.957 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pitpnm1, Dres9, Mpt1, Nir2, Pitpnm / Production host: Escherichia coli (E. coli) / References: UniProt: O35954
#2: Chemical ChemComp-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate


Mass: 368.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H29O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical ChemComp-DW3 / 2-oxidanylethanal


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9% Polyethylene glycol (PEG) 4000, 100mM HEPES pH 7.5, 1% Ethanol, 4mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 50504 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.35-2.394.90.55917270.7540.9270.2740.6240.52499.9
2.39-2.434.90.51716880.760.9290.2570.5790.54499.8
2.43-2.484.90.47116950.830.9520.2320.5270.55299.9
2.48-2.5350.41517070.8610.9620.2040.4630.65299.5
2.53-2.594.90.38216750.870.9650.1890.4280.68699.8
2.59-2.654.80.35117300.8850.9690.1750.3930.72799.9
2.65-2.714.80.32716820.9050.9750.1620.3660.83299.4
2.71-2.794.50.28616870.920.9790.1460.3220.90298.3
2.79-2.874.40.25216520.9330.9830.1310.2860.97195.6
2.87-2.965.10.23716940.9460.9860.1150.2641.1699.8
2.96-3.075.20.20617040.9570.9890.0990.2291.31199.9
3.07-3.195.20.18917260.9640.9910.0920.2111.51799.6
3.19-3.335.10.16617310.9690.9920.0810.1851.83599.7
3.33-3.5150.14217320.9760.9940.070.1592.20299.3
3.51-3.734.90.12216990.980.9950.0610.1372.40999.4
3.73-4.024.50.11217170.9820.9950.0590.1272.75698.6
4.02-4.424.50.09417020.9870.9970.0490.1063.04296.7
4.42-5.064.90.08417550.990.9970.0420.0942.95399.4
5.06-6.374.80.08117650.9920.9980.0410.0912.60298.4
6.37-504.40.0618720.9950.9990.0310.0682.49498.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→40.375 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.45 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 2000 3.96 %
Rwork0.2026 --
obs0.2048 50455 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→40.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5799 0 17 231 6047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125986
X-RAY DIFFRACTIONf_angle_d1.4258138
X-RAY DIFFRACTIONf_dihedral_angle_d12.0782116
X-RAY DIFFRACTIONf_chiral_restr0.059929
X-RAY DIFFRACTIONf_plane_restr0.0081046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1504-2.20410.37341380.33843347X-RAY DIFFRACTION98
2.2041-2.26370.35761410.30263416X-RAY DIFFRACTION99
2.2637-2.33030.31671400.28963393X-RAY DIFFRACTION99
2.3303-2.40550.34311400.27053403X-RAY DIFFRACTION99
2.4055-2.49150.311430.24553442X-RAY DIFFRACTION100
2.4915-2.59120.28331410.23633418X-RAY DIFFRACTION100
2.5912-2.70910.29361410.22523428X-RAY DIFFRACTION99
2.7091-2.85190.2371440.21243462X-RAY DIFFRACTION100
2.8519-3.03060.29911410.21173443X-RAY DIFFRACTION100
3.0306-3.26450.30461430.21593466X-RAY DIFFRACTION100
3.2645-3.59280.27041440.20133487X-RAY DIFFRACTION100
3.5928-4.11230.2391460.18573520X-RAY DIFFRACTION100
4.1123-5.17930.20961450.15843540X-RAY DIFFRACTION100
5.1793-40.3750.20821530.16793690X-RAY DIFFRACTION100

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