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- PDB-6tqr: The crystal structure of the MSP domain of human VAP-A in complex... -

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Basic information

Entry
Database: PDB / ID: 6tqr
TitleThe crystal structure of the MSP domain of human VAP-A in complex with the Phospho-FFAT motif of STARD3.
Components
  • StAR-related lipid transfer protein 3
  • Vesicle-associated membrane protein-associated protein A
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 / endoplasmic reticulum-plasma membrane tethering / organelle membrane contact site / ceramide transport / protein localization to endoplasmic reticulum / sphingomyelin biosynthetic process / sterol transport ...vesicle tethering to endoplasmic reticulum / endoplasmic reticulum-endosome membrane contact site / progesterone biosynthetic process / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / organelle membrane contact site / ceramide transport / protein localization to endoplasmic reticulum / sphingomyelin biosynthetic process / sterol transport / positive regulation by host of viral genome replication / COPII-coated vesicle budding / negative regulation by host of viral genome replication / Sphingolipid de novo biosynthesis / cholesterol transfer activity / Pregnenolone biosynthesis / phospholipid transport / cholesterol transport / cholesterol binding / azurophil granule membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondrial transport / steroid metabolic process / bicellular tight junction / viral release from host cell / endoplasmic reticulum to Golgi vesicle-mediated transport / cholesterol metabolic process / lipid metabolic process / neuron projection development / microtubule cytoskeleton / late endosome membrane / microtubule binding / positive regulation of canonical NF-kappaB signal transduction / nuclear membrane / vesicle / membrane fusion / endosome / cadherin binding / protein heterodimerization activity / lysosomal membrane / protein domain specific binding / Golgi membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / 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 / Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / in StAR and phosphatidylcholine transfer protein ...MENTAL domain / StAR-related lipid transfer protein 3, C-terminal / Cholesterol-capturing domain / MENTAL domain profile. / Steroidogenic acute regulatory protein-like / Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / PapD-like superfamily / START-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
StAR-related lipid transfer protein 3 / Vesicle-associated membrane protein-associated protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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: Vesicle-associated membrane protein-associated protein A
B: Vesicle-associated membrane protein-associated protein A
C: Vesicle-associated membrane protein-associated protein A
D: Vesicle-associated membrane protein-associated protein A
E: StAR-related lipid transfer protein 3
F: StAR-related lipid transfer protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,12813
Polymers101,8806
Non-polymers2487
Water5,170287
1
A: Vesicle-associated membrane protein-associated protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5854
Polymers24,4781
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-19 kcal/mol
Surface area7740 Å2
MethodPISA
2
B: Vesicle-associated membrane protein-associated protein A
E: StAR-related lipid transfer protein 3


Theoretical massNumber of molelcules
Total (without water)26,4622
Polymers26,4622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-22 kcal/mol
Surface area8750 Å2
MethodPISA
3
C: Vesicle-associated membrane protein-associated protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5493
Polymers24,4781
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area7860 Å2
MethodPISA
4
D: Vesicle-associated membrane protein-associated protein A
F: StAR-related lipid transfer protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5334
Polymers26,4622
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-23 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.140, 43.780, 83.640
Angle α, β, γ (deg.)89.460, 92.910, 105.130
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Vesicle-associated membrane protein-associated protein A / VAP-A / 33 kDa VAMP-associated protein / VAP-33


Mass: 24478.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: MSP domain / Source: (gene. exp.) Homo sapiens (human) / Gene: VAPA, VAP33 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P0L0
#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: 1983.762 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phospho-FFAT motif / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14849
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 2000 MME, 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: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→42.26 Å / Num. obs: 42485 / % possible obs: 92.8 % / Redundancy: 3.338 % / Biso Wilson estimate: 38.514 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.133 / Rrim(I) all: 0.248 / Χ2: 1.116 / Net I/σ(I): 4.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2% possible allRmerge(I) obsMean I/σ(I) obsRrim(I) all
1.85-1.92.45619360.79357.1
1.9-1.952.47825240.78875.91.4710.41.872
1.95-2.012.84531020.12197.14.3570.275.4
2.01-2.073.00830550.16297.72.5680.523.141
2.07-2.143.26729610.28998.61.9590.742.349
2.14-2.213.57729070.43298.91.8240.862.141
2.21-2.293.1823140.62280.9
2.29-2.393.70426580.62999.41.1281.381.318
2.39-2.493.56325560.71398.80.8831.71.039
2.49-2.613.6125070.83498.90.652.420.761
2.61-2.763.54123410.89199.20.4443.410.522
2.76-2.923.71222020.94499.50.3344.620.389
2.92-3.133.61320990.97299.60.2126.750.249
3.13-3.383.70619520.98699.30.1389.610.162
3.38-3.73.42616640.98393.50.13410.770.158
3.7-4.133.56416230.9999.40.09314.330.109
4.13-4.773.65114290.99499.50.06518.570.076
4.77-5.853.45312110.99599.30.06218.750.074
5.85-8.273.6569320.99499.70.06418.290.075
8.27-42.263.495120.9971000.04325.580.051

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXdev-3699refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z9O

1z9o


Resolution: 1.85→42.26 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 34.68
RfactorNum. reflection% reflection
Rfree0.2543 1237 5.05 %
Rwork0.2043 --
obs0.2068 24512 53.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.49 Å2 / Biso mean: 36.8225 Å2 / Biso min: 8.91 Å2
Refinement stepCycle: final / Resolution: 1.85→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 7 289 4425
Biso mean--45.82 36.41 -
Num. residues----522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.930.4167100.38882152254
1.93-2.010.3407330.328345048310
2.01-2.120.3412470.309786591218
2.12-2.250.3476660.31751505157131
2.25-2.430.31471290.29772512264152
2.43-2.670.29812130.28093617383076
2.67-3.060.29072490.25754601485096
3.06-3.850.25272570.18944694495197
3.85-42.260.19972330.14574816504999
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)
11.75290.7684-0.28961.6985-0.02540.99230.00490.01-0.33950.0136-0.0043-0.04790.0292-0.0689-00.189-0.00150.00140.1630.01240.1863-4.8552-25.33694.0723
22.23750.8948-0.26711.30460.82572.4138-0.102-0.29460.04970.04-0.0652-0.1151-0.0165-0.1234-0.03460.22250.00650.03230.1474-0.00870.1538.8871-14.337423.0312
32.74910.3367-0.15360.8539-0.13930.9855-0.0116-0.3994-0.05050.08530.00820.07530.0617-0.02550.00350.1476-0.0079-0.00820.216-0.02640.13920.36962.997566.1222
42.0852-0.20121.29511.88081.5042.3032-0.07970.0605-0.16630.0221-0.0129-0.00230.03430.17710.00140.18180.01960.02880.23740.03140.15497.8169-5.079644.4827
51.32630.06170.62870.2372-0.32590.83660.1943-0.428-0.02340.10220.30580.18260.031-0.08033.0060.09730.05360.06170.3482-0.00930.6108-1.5359-24.202523.3679
61.35810.6232-0.82040.2934-0.34160.9766-0.70370.2906-0.83560.45990.2778-0.08030.2890.29670.00350.44610.0120.06770.59130.12370.367915.8374-12.59546.7826
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

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