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- PDB-6k9y: Crystal structure of human VAT-1 -

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Basic information

Entry
Database: PDB / ID: 6k9y
TitleCrystal structure of human VAT-1
ComponentsSynaptic vesicle membrane protein VAT-1 homolog
KeywordsOXIDOREDUCTASE / Phospholipid transfer protein
Function / homology
Function and homology information


negative regulation of mitochondrial fusion / Oxidoreductases / azurophil granule lumen / mitochondrial outer membrane / oxidoreductase activity / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region / membrane
Similarity search - Function
Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NITRATE ION / Synaptic vesicle membrane protein VAT-1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWatanabe, Y. / Endo, T.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis for interorganelle phospholipid transport mediated by VAT-1.
Authors: Watanabe, Y. / Tamura, Y. / Kakuta, C. / Watanabe, S. / Endo, T.
History
DepositionJun 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Synaptic vesicle membrane protein VAT-1 homolog
B: Synaptic vesicle membrane protein VAT-1 homolog
C: Synaptic vesicle membrane protein VAT-1 homolog
D: Synaptic vesicle membrane protein VAT-1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,35812
Polymers153,8624
Non-polymers4968
Water2,846158
1
A: Synaptic vesicle membrane protein VAT-1 homolog
B: Synaptic vesicle membrane protein VAT-1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1796
Polymers76,9312
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-14 kcal/mol
Surface area26270 Å2
MethodPISA
2
C: Synaptic vesicle membrane protein VAT-1 homolog
D: Synaptic vesicle membrane protein VAT-1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1796
Polymers76,9312
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-16 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.155, 131.720, 174.027
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
Synaptic vesicle membrane protein VAT-1 homolog


Mass: 38465.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99536, Oxidoreductases
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 78589 / % possible obs: 99.7 % / Redundancy: 6.7 % / Net I/σ(I): 12.45
Reflection shellResolution: 2.2→2.34 Å / Num. unique obs: 12336

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Processing

Software
NameVersionClassification
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A27

4a27


Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2548 7924 10 %
Rwork0.2224 --
obs-78589 99.2 %
Solvent computationBsol: 40.644 Å2
Displacement parametersBiso max: 114.24 Å2 / Biso mean: 58.5684 Å2 / Biso min: 27.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--4.824 Å20 Å2
3----5.603 Å2
Refinement stepCycle: final / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9985 0 32 158 10175
Biso mean--87.07 56.21 -
Num. residues----1328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.322
X-RAY DIFFRACTIONc_mcbond_it1.4691.5
X-RAY DIFFRACTIONc_scbond_it2.2132
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scangle_it3.3452.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.280.3786740.36346551722592.7
2.28-2.370.36087580.341170677825100
2.37-2.480.33967760.315870607836100
2.48-2.610.34948050.296870177822100
2.61-2.770.33628230.282370467869100
2.77-2.990.33327670.270670967863100
2.99-3.290.30378060.259671167922100
3.29-3.760.26627950.236271557950100
3.76-4.740.20368410.17667145798699.8
4.74-500.010.21138790.17987412829199.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6nitrate.paramnitrate.top

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