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- PDB-9jui: Crystal structure of FFAT motif of Nir2 bound to VAPB -

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Basic information

Entry
Database: PDB / ID: 9jui
TitleCrystal structure of FFAT motif of Nir2 bound to VAPB
Components
  • Nir2 FFAT motif
  • Vesicle-associated membrane protein-associated protein B
KeywordsLIPID BINDING PROTEIN / PLC signaling / PI cycle / Membrane contact site / lipid transfer / lipid binding
Function / homology
Function and homology information


Synthesis of PI / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / endoplasmic reticulum membrane organization / RHOC GTPase cycle / RAC2 GTPase cycle / phosphatidylinositol transfer activity / RHOD GTPase cycle / RHOA GTPase cycle / RHOG GTPase cycle ...Synthesis of PI / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / endoplasmic reticulum membrane organization / RHOC GTPase cycle / RAC2 GTPase cycle / phosphatidylinositol transfer activity / RHOD GTPase cycle / RHOA GTPase cycle / RHOG GTPase cycle / phosphatidic acid binding / phosphatidylcholine binding / Golgi cisterna membrane / IRE1-mediated unfolded protein response / cleavage furrow / lipid droplet / phosphatidylinositol binding / receptor tyrosine kinase binding / phospholipid binding / intracellular calcium ion homeostasis / protein transport / cell body / midbody / calcium ion binding / endoplasmic reticulum membrane / membrane / plasma 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 / Vesicle-associated membrane-protein-associated protein ...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 / Vesicle-associated membrane-protein-associated protein / LNS2/PITP / LNS2 / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / PapD-like superfamily / START-like domain superfamily / HAD superfamily / HAD-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Membrane-associated phosphatidylinositol transfer protein 1 / Vesicle-associated membrane protein-associated protein B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 8, 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

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Assembly

Deposited unit
A: Vesicle-associated membrane protein-associated protein B
B: Nir2 FFAT motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0745
Polymers15,8782
Non-polymers1963
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-77 kcal/mol
Surface area8190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.973, 52.973, 88.283
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Vesicle-associated membrane protein-associated protein B / VAMP-B / VAMP-associated protein B / VAP-B / VAMP-associated protein 33b


Mass: 14637.852 Da / Num. of mol.: 1 / Fragment: MSP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vapb / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QY76
#2: Protein/peptide Nir2 FFAT motif / 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: 1240.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: O35954
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 18% PEG 8000, 0.1M sodium cacodylate pH 6.5, 0.2M zinc acetate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 9386 / % possible obs: 99.3 % / Redundancy: 3.9 % / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.066 / Rrim(I) all: 0.132 / Χ2: 2.569 / Net I/σ(I): 9.3 / Num. measured all: 36942
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.05-2.094.10.5164510.7450.9240.290.5941.68399.8
2.09-2.124.20.4794770.8310.9530.2660.5491.672100
2.12-2.164.10.4364340.860.9620.2440.5011.864100
2.16-2.214.10.4034820.8220.950.2240.4631.802100
2.21-2.264.10.3844430.9090.9760.2140.4411.968100
2.26-2.314.20.3794760.9380.9840.210.4341.84299.8
2.31-2.374.10.3254620.9510.9870.1820.3731.839100
2.37-2.434.10.2714610.9470.9860.1510.3122.052100
2.43-2.54.10.2634750.9480.9870.1470.3031.974100
2.5-2.584.10.2424580.960.990.1370.2792.143100
2.58-2.684.10.1944630.9660.9910.1080.2232.243100
2.68-2.7840.1654830.9770.9940.0940.192.43100
2.78-2.9140.1514540.9820.9950.0850.1732.67199.8
2.91-3.0640.1214750.9860.9960.0690.142.94799.8
3.06-3.253.90.1044710.9860.9960.0610.1213.27499.8
3.25-3.513.80.0844790.9890.9970.0490.0983.33499.6
3.51-3.863.70.074760.9920.9980.0420.0823.62899
3.86-4.423.60.0654860.9930.9980.040.0774.36999
4.42-5.563.50.0614720.9920.9980.0380.0724.43697.1
5.56-5030.0665080.990.9970.0420.0794.56993

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.14refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→50 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.285 --
Rwork0.276 --
obs-8402 93.6 %
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 3 61 1124
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-ID
2.05-2.090.516451X-RAY DIFFRACTION
2.09-2.120.479477X-RAY DIFFRACTION
2.12-2.160.436434X-RAY DIFFRACTION
2.16-2.210.403482X-RAY DIFFRACTION
2.21-2.260.384443X-RAY DIFFRACTION
2.26-2.310.379476X-RAY DIFFRACTION
2.31-2.370.325462X-RAY DIFFRACTION
2.37-2.430.271461X-RAY DIFFRACTION
2.43-2.50.263475X-RAY DIFFRACTION
2.5-2.580.242458X-RAY DIFFRACTION
2.58-2.680.194463X-RAY DIFFRACTION
2.68-2.780.165483X-RAY DIFFRACTION
2.78-2.910.151454X-RAY DIFFRACTION
2.91-3.060.121475X-RAY DIFFRACTION
3.06-3.250.104471X-RAY DIFFRACTION
3.25-3.510.084479X-RAY DIFFRACTION
3.51-3.860.07476X-RAY DIFFRACTION
3.86-4.420.065486X-RAY DIFFRACTION
4.42-5.560.061472X-RAY DIFFRACTION
5.56-500.066508X-RAY DIFFRACTION

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