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- PDB-6tqu: The crystal structure of the MSP domain of human MOSPD2 in comple... -

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Basic information

Entry
Database: PDB / ID: 6tqu
TitleThe crystal structure of the MSP domain of human MOSPD2 in complex with the Phospho-FFAT motif of STARD3.
Components
  • Motile sperm domain-containing protein 2
  • StAR-related lipid transfer protein 3
KeywordsPROTEIN BINDING / Membrane contact sites / FFAT motif / MSP domain / Endoplasmic reticulum
Function / homology
Function and homology information


vesicle tethering to endoplasmic reticulum / endoplasmic reticulum-endosome membrane contact site / progesterone biosynthetic process / FFAT motif binding / lipid droplet formation / organelle membrane contact site / Pregnenolone biosynthesis / cholesterol transfer activity / cholesterol transport / RHOD GTPase cycle ...vesicle tethering to endoplasmic reticulum / endoplasmic reticulum-endosome membrane contact site / progesterone biosynthetic process / FFAT motif binding / lipid droplet formation / organelle membrane contact site / Pregnenolone biosynthesis / cholesterol transfer activity / cholesterol transport / RHOD GTPase cycle / positive regulation of neutrophil chemotaxis / positive regulation of monocyte chemotaxis / cholesterol binding / mitochondrial transport / steroid metabolic process / endomembrane system / specific granule membrane / cholesterol metabolic process / protein homooligomerization / lipid metabolic process / chemotaxis / late endosome membrane / endosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
MENTAL domain / StAR-related lipid transfer protein 3, C-terminal / Cholesterol-capturing domain / MENTAL domain profile. / Steroidogenic acute regulatory protein-like / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain ...MENTAL domain / StAR-related lipid transfer protein 3, C-terminal / Cholesterol-capturing domain / MENTAL domain profile. / Steroidogenic acute regulatory protein-like / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / PapD-like superfamily / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / START-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
StAR-related lipid transfer protein 3 / Motile sperm domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsMcEwen, A.G. / Poussin-Courmontagne, P. / Di Mattia, T. / Wendling, C. / Cavarelli, J. / Tomasetto, C. / Alpy, F.
Funding support France, 4items
OrganizationGrant numberCountry
French National Research AgencyANR-19-CE44-0003 France
French National Research AgencyANR-10-INSB-05-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-10-IDEX-0002-02. France
CitationJournal: Embo J. / Year: 2020
Title: FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts.
Authors: Di Mattia, T. / Martinet, A. / Ikhlef, S. / McEwen, A.G. / Nomine, Y. / Wendling, C. / Poussin-Courmontagne, P. / Voilquin, L. / Eberling, P. / Ruffenach, F. / Cavarelli, J. / Slee, J. / ...Authors: Di Mattia, T. / Martinet, A. / Ikhlef, S. / McEwen, A.G. / Nomine, Y. / Wendling, C. / Poussin-Courmontagne, P. / Voilquin, L. / Eberling, P. / Ruffenach, F. / Cavarelli, J. / Slee, J. / Levine, T.P. / Drin, G. / Tomasetto, C. / Alpy, F.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Motile sperm domain-containing protein 2
B: Motile sperm domain-containing protein 2
C: StAR-related lipid transfer protein 3
D: StAR-related lipid transfer protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6315
Polymers34,5354
Non-polymers961
Water1,60389
1
A: Motile sperm domain-containing protein 2
C: StAR-related lipid transfer protein 3


Theoretical massNumber of molelcules
Total (without water)17,2672
Polymers17,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-12 kcal/mol
Surface area7460 Å2
MethodPISA
2
B: Motile sperm domain-containing protein 2
D: StAR-related lipid transfer protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3633
Polymers17,2672
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-9 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.968, 87.968, 95.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-501-

SO4

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Components

#1: Protein Motile sperm domain-containing protein 2


Mass: 14833.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MSP domain / Source: (gene. exp.) Homo sapiens (human) / Gene: MOSPD2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NHP6
#2: Protein/peptide StAR-related lipid transfer protein 3 / Metastatic lymph node gene 64 protein / MLN 64 / Protein CAB1 / START domain-containing protein 3 / StARD3


Mass: 2434.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phospho-FFAT motif / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14849
#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.: 89 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 7.5% PEG 2000, 7.5% PEG 3350, 7.5% PEG 4000, 7.5% PEG 5000 MME, 0.05 M Magnesium sulfate, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 24, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.4→87.97 Å / Num. obs: 15203 / % possible obs: 100 % / Redundancy: 24.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.258 / Rpim(I) all: 0.053 / Rrim(I) all: 0.263 / Net I/σ(I): 9.1 / Num. measured all: 378156 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.4926.33.9764098415590.390.7864.0541100
8.98-87.9720.20.0873553640.9970.0180.08229.999.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.25 Å64.58 Å
Translation3.25 Å64.58 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PHENIXdev-3644refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TQT

6tqt


Resolution: 2.4→43.98 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.86
RfactorNum. reflection% reflection
Rfree0.24 716 4.73 %
Rwork0.1832 --
obs0.1861 15149 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 180.95 Å2 / Biso mean: 75.1558 Å2 / Biso min: 36.87 Å2
Refinement stepCycle: final / Resolution: 2.4→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 5 89 2140
Biso mean--58.21 67.71 -
Num. residues----268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.590.32911240.243528422966
2.59-2.850.27591140.238928482962
2.85-3.260.27551150.218328812996
3.26-4.10.23441900.166828333023
4.1-43.980.22341730.166630293202
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)
14.272-0.5620.73924.7680.46682.59760.08840.1778-0.0694-0.1902-0.0335-0.2529-0.20.0750.00010.4602-0.0018-0.04240.59490.04290.35915.125932.666530.7922
26.6146-1.00911.04594.62440.14663.28160.23660.7562-0.8799-0.4748-0.00420.60110.4521-0.12740.02820.47010.0031-0.09890.6004-0.0830.64518.151810.529533.2825
30.8548-0.3881-0.38780.923-0.17260.6252-0.1564-1.03720.05580.7451-0.0463-0.22620.26550.6477-0.00120.59770.0465-0.10040.75620.04360.5546-3.153133.89835.4357
41.1589-0.71280.55951.1795-0.62910.58280.27730.3915-0.74550.82310.7320.80341.1626-0.26340.05510.73060.12360.01070.7645-0.00490.657227.51019.424340.9738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' )A0
2X-RAY DIFFRACTION2(chain 'B' )B0
3X-RAY DIFFRACTION3(chain 'C' )C0
4X-RAY DIFFRACTION4(chain 'D' )D0

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