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- PDB-7x14: Crystal structure of phospho-FFAT motif of MIGA2 bound to VAPB -

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Basic information

Entry
Database: PDB / ID: 7x14
TitleCrystal structure of phospho-FFAT motif of MIGA2 bound to VAPB
Components
  • MIGA2 phospho FFAT motif
  • Vesicle-associated membrane protein-associated protein B
KeywordsLIPID TRANSPORT / FFAT / VAPB / MIGA2
Function / homology
Function and homology information


Sphingolipid de novo biosynthesis / negative regulation by virus of viral protein levels in host cell / endoplasmic reticulum membrane organization / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / modulation by host of viral RNA genome replication / RAC2 GTPase cycle / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle ...Sphingolipid de novo biosynthesis / negative regulation by virus of viral protein levels in host cell / endoplasmic reticulum membrane organization / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / modulation by host of viral RNA genome replication / RAC2 GTPase cycle / RHOC GTPase cycle / RHOD GTPase cycle / RHOA GTPase cycle / RHOG GTPase cycle / positive regulation by host of viral genome replication / suppression of viral release by host / COPII-coated vesicle budding / negative regulation by host of viral genome replication / endoplasmic reticulum organization / beta-tubulin binding / IRE1-mediated unfolded protein response / viral release from host cell / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of viral genome replication / endoplasmic reticulum unfolded protein response / intracellular calcium ion homeostasis / microtubule binding / membrane => GO:0016020 / protein heterodimerization activity / endoplasmic reticulum membrane / Golgi apparatus / enzyme binding / endoplasmic reticulum / protein homodimerization activity / membrane / plasma membrane / cytoplasm
Similarity search - Function
Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / PapD-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Vesicle-associated membrane protein-associated protein B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Mus musculoides (Temminck's mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.675 Å
AuthorsKim, H. / 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: Nat Commun / Year: 2022
Title: Structural basis for mitoguardin-2 mediated lipid transport at ER-mitochondrial membrane contact sites.
Authors: Kim, H. / Lee, S. / Jun, Y. / Lee, C.
History
DepositionFeb 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: MIGA2 phospho FFAT motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6023
Polymers15,5052
Non-polymers961
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-24 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.363, 44.507, 83.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 14226.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vapb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9QY76
#2: Protein/peptide MIGA2 phospho FFAT motif


Mass: 1279.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculoides (Temminck's mouse)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.01 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 1.8 M ammonium sulfate, 100 mM phosphae-citrate pH 4.2, 2% Iso-propanol

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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: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.675→26.695 Å / Num. obs: 14734 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.995 / Net I/σ(I): 25.9
Reflection shellResolution: 1.675→1.73 Å / Num. unique obs: 715 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IKK

3ikk


Resolution: 1.675→26.695 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 733 4.99 %
Rwork0.1864 13952 -
obs0.1885 14685 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.3 Å2 / Biso mean: 28.6134 Å2 / Biso min: 8.75 Å2
Refinement stepCycle: final / Resolution: 1.675→26.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 5 95 1126
Biso mean--20 41.28 -
Num. residues----128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6752-1.80450.25071340.2125253893
1.8045-1.98610.30441460.18932801100
1.9861-2.27330.23341460.18152798100
2.2733-2.86360.22351500.19512841100
2.8636-26.6950.20951570.17952974100
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)
10.80470.06540.29740.67960.16963.92610.0353-0.03610.0836-0.01970.0020.0629-0.2027-0.0469-0.0460.08930.0028-0.00070.06670.00020.13618.2914-0.0802-5.5841
23.4879-2.2368-0.26962.11421.21422.3009-0.0930.04710.98090.13180.0544-0.2341-0.5837-0.3394-0.09630.40230.03380.02510.25160.05430.33266.16066.803-0.919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 124 )A4 - 124
2X-RAY DIFFRACTION2chain 'B' and (resid 501 through 507 )C - B501 - 507

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