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

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Basic information

Entry
Database: PDB / ID: 6tqs
TitleThe crystal structure of the MSP domain of human MOSPD2 in complex with the conventional FFAT motif of ORP1.
Components
  • Motile sperm domain-containing protein 2
  • Oxysterol-binding protein-related protein 1
KeywordsPROTEIN BINDING / Membrane contact sites / FFAT motif / MSP domain / Endoplasmic reticulum
Function / homology
Function and homology information


endoplasmic reticulum-endosome membrane contact site / FFAT motif binding / lipid droplet formation / organelle membrane contact site / : / perinuclear endoplasmic reticulum / bile acid biosynthetic process / RHOD GTPase cycle / positive regulation of monocyte chemotaxis / positive regulation of neutrophil chemotaxis ...endoplasmic reticulum-endosome membrane contact site / FFAT motif binding / lipid droplet formation / organelle membrane contact site / : / perinuclear endoplasmic reticulum / bile acid biosynthetic process / RHOD GTPase cycle / positive regulation of monocyte chemotaxis / positive regulation of neutrophil chemotaxis / cholesterol binding / Synthesis of bile acids and bile salts / endomembrane system / specific granule membrane / vesicle-mediated transport / MHC class II antigen presentation / cholesterol metabolic process / protein homooligomerization / phospholipid binding / chemotaxis / late endosome / endosome / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain ...Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / trifluoroacetic acid / Motile sperm domain-containing protein 2 / Oxysterol-binding protein-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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: Motile sperm domain-containing protein 2
D: Motile sperm domain-containing protein 2
E: Motile sperm domain-containing protein 2
F: Motile sperm domain-containing protein 2
G: Oxysterol-binding protein-related protein 1
H: Oxysterol-binding protein-related protein 1
I: Oxysterol-binding protein-related protein 1
J: Oxysterol-binding protein-related protein 1
K: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,23330
Polymers157,22911
Non-polymers2,00519
Water4,864270
1
A: Motile sperm domain-containing protein 2
G: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1148
Polymers26,5922
Non-polymers5226
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-14 kcal/mol
Surface area8240 Å2
MethodPISA
2
B: Motile sperm domain-containing protein 2
H: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7984
Polymers26,5922
Non-polymers2062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-4 kcal/mol
Surface area8310 Å2
MethodPISA
3
C: Motile sperm domain-containing protein 2
I: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0006
Polymers26,5922
Non-polymers4084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-15 kcal/mol
Surface area8290 Å2
MethodPISA
4
D: Motile sperm domain-containing protein 2
J: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7063
Polymers26,5922
Non-polymers1141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-7 kcal/mol
Surface area8010 Å2
MethodPISA
5
E: Motile sperm domain-containing protein 2
K: Oxysterol-binding protein-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8985
Polymers26,5922
Non-polymers3063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-23 kcal/mol
Surface area7960 Å2
MethodPISA
6
F: Motile sperm domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7174
Polymers24,2691
Non-polymers4483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-16 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.874, 126.874, 184.449
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11F-629-

HOH

21F-646-

HOH

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Components

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Protein / Protein/peptide , 2 types, 11 molecules ABCDEFGHIJK

#1: Protein
Motile sperm domain-containing protein 2


Mass: 24268.594 Da / Num. of mol.: 6
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
Oxysterol-binding protein-related protein 1 / OSBP-related protein 1


Mass: 2323.427 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: FFAT motif / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXW6

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Non-polymers , 7 types, 289 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2HF3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M sodium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 25, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→109.88 Å / Num. obs: 42297 / % possible obs: 100 % / Redundancy: 36.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.04 / Rrim(I) all: 0.248 / Net I/σ(I): 11.3 / Num. measured all: 1549132 / 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
2.25-2.3227.75.31410585838150.5071.0235.4130.799.9
9-109.8832.40.0712599680310.0130.07234.4100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.3 Å47.2 Å
Translation2.3 Å47.2 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: 1WIC

1wic


Resolution: 2.25→70.64 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.81
RfactorNum. reflection% reflection
Rfree0.26 2057 4.88 %
Rwork0.2169 --
obs0.219 42193 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 170.97 Å2 / Biso mean: 63.0693 Å2 / Biso min: 28.73 Å2
Refinement stepCycle: final / Resolution: 2.25→70.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6299 0 121 270 6690
Biso mean--72.56 54.44 -
Num. residues----821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.30.41581310.322526222753100
2.3-2.360.33381500.302526272777100
2.36-2.420.32581300.28526002730100
2.42-2.50.32951250.265326612786100
2.5-2.580.33361280.269726152743100
2.58-2.670.31171510.263526312782100
2.67-2.770.33231320.263726582790100
2.77-2.90.33171390.276426512790100
2.9-3.050.33791180.264226692787100
3.05-3.240.28131440.233726612805100
3.25-3.50.2441430.212626672810100
3.5-3.850.23661260.195627062832100
3.85-4.40.191560.166827012857100
4.4-5.550.21881430.159627462889100
5.55-70.640.26361410.22992921306299
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)
10.29050.03110.34730.69210.40881.20210.011-0.03520.00120.0830.0095-0.0657-0.0847-0.0587-00.39270.03340.02560.3723-0.00190.334255.0672-24.309515.7628
20.6616-0.58090.18530.9922-0.29312.10860.8220.43531.6599-0.19580.1778-0.4685-0.5872-0.88611.93240.55370.33970.49150.21320.27661.27927.7948-13.703416.6672
30.67510.33760.33170.68360.35671.25760.0424-0.1057-0.0382-0.02920.10040.03940.0687-0.033500.3518-0.02320.00380.4086-0.00660.327546.7916-39.061343.8806
41.44410.2077-0.08690.8907-0.33141.16450.28091.03240.99620.03270.18940.4497-0.027-0.1950.37720.33550.09980.09390.5270.22880.513731.7442-17.8369-0.641
50.5824-0.1483-0.55011.0904-0.16960.69120.054-0.19090.17610.3197-0.05820.122-0.1315-0.0066-00.50790.01840.04530.39070.00510.3358-1.7237-37.976431.2861
61.77220.4880.34790.67030.11310.13140.0194-0.1773-0.113-0.1917-0.07240.09230.0087-0.0431-00.3946-0.0549-0.00650.4636-0.00760.308829.9239-56.238327.9458
70.0082-0.0028-0.01670.0047-0.0090.02490.0295-0.18340.06720.13240.08210.20060.161-0.0585-0.00021.34580.17480.24761.25480.19611.463363.9481-31.387512.1275
80.12720.12540.04990.12420.04560.01730.0049-0.01820.00460.12950.1377-0.1728-0.09-0.04740.03761.45450.18750.78920.6509-0.1082.0645.3878-3.238221.6055
90.0484-0.0663-0.02290.08130.03130.01420.38240.1207-0.1064-0.3432-0.1741-0.15570.01160.202-0.00130.6374-0.2427-0.06430.8968-0.09010.573457.5829-34.984139.96
100.0106-0.01260.02310.02190.01410.03020.29760.04220.46850.0020.1430.0990.09830.18750.00070.89330.2701-0.08871.32390.37460.950932.9921-12.177-10.2686
110.01660.002-0.0102-0.00190.00080.005-0.1897-0.2083-0.2260.3005-0.16050.0185-0.1464-0.21970.00041.41430.0165-0.04080.7775-0.03480.71312.5426-40.131241.4387
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
5X-RAY DIFFRACTION5(chain 'E' )E0
6X-RAY DIFFRACTION6(chain 'F' )F0
7X-RAY DIFFRACTION7(chain 'G' )G0
8X-RAY DIFFRACTION8(chain 'H' )H0
9X-RAY DIFFRACTION9(chain 'I' )I0
10X-RAY DIFFRACTION10(chain 'J' )J0
11X-RAY DIFFRACTION11(chain 'K' )K0

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