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- PDB-8r4y: Homotrimer for the lumenal domain of Vacuolar Sorting Receptor 1 ... -

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Basic information

Entry
Database: PDB / ID: 8r4y
TitleHomotrimer for the lumenal domain of Vacuolar Sorting Receptor 1 (VSR1)
ComponentsVacuolar-sorting receptor 1
KeywordsPROTEIN TRANSPORT / Vacuolar sorting receptor / membrane protein
Function / homology
Function and homology information


amino-terminal vacuolar sorting propeptide binding / Golgi to vacuole transport / vacuolar transport / clathrin-coated vesicle membrane / protein targeting to vacuole / trans-Golgi network / late endosome / Golgi membrane / calcium ion binding / endoplasmic reticulum ...amino-terminal vacuolar sorting propeptide binding / Golgi to vacuole transport / vacuolar transport / clathrin-coated vesicle membrane / protein targeting to vacuole / trans-Golgi network / late endosome / Golgi membrane / calcium ion binding / endoplasmic reticulum / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
: / Vacuolar sorting receptor thioredoxin-like domain / PA domain superfamily / PA domain / PA domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / EGF-like domain signature 2.
Similarity search - Domain/homology
alpha-D-mannopyranose / Vacuolar-sorting receptor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.51 Å
AuthorsBorges, R.J. / Eldahshoury, M.K. / Nettleship, J. / Bird, L. / An, J. / Levada, A.J.L. / Shah, N. / Thomson, M. / Fontes, M.R.M. / Owens, R. ...Borges, R.J. / Eldahshoury, M.K. / Nettleship, J. / Bird, L. / An, J. / Levada, A.J.L. / Shah, N. / Thomson, M. / Fontes, M.R.M. / Owens, R. / Denecke, J. / Postis, V. / Uson, I. / Goldman, A. / De Marcos Lousa, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustF/10 105/E United Kingdom
CitationJournal: To Be Published
Title: The crystal structure of Vacuolar Sorting Receptor 1 (VSR1) lumenal domain reveals a stable domain-swapped trimer and a potential new cargo binding site
Authors: Borges, R.J. / Eldahshoury, M.K. / Nettleship, J. / Bird, L. / An, J. / Levada, A.J.L. / Shah, N. / Thomson, M. / Fontes, M.R.M. / Owens, R. / Denecke, J. / Postis, V. / Uson, I. / Goldman, ...Authors: Borges, R.J. / Eldahshoury, M.K. / Nettleship, J. / Bird, L. / An, J. / Levada, A.J.L. / Shah, N. / Thomson, M. / Fontes, M.R.M. / Owens, R. / Denecke, J. / Postis, V. / Uson, I. / Goldman, A. / De Marcos Lousa, C.
History
DepositionNov 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar-sorting receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5735
Polymers60,2021
Non-polymers1,3714
Water00
1
A: Vacuolar-sorting receptor 1
hetero molecules

A: Vacuolar-sorting receptor 1
hetero molecules

A: Vacuolar-sorting receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,72015
Polymers180,6063
Non-polymers4,11412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11810 Å2
ΔGint6 kcal/mol
Surface area63540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.477, 141.477, 141.477
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

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Components

#1: Protein Vacuolar-sorting receptor 1 / AtVSR1 / BP80-like protein b / AtBP80b / Epidermal growth factor receptor-like protein 1 / AtELP / ...AtVSR1 / BP80-like protein b / AtBP80b / Epidermal growth factor receptor-like protein 1 / AtELP / AtELP1 / Spot 3 protein


Mass: 60202.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VSR1, BP80B, ELP, ELP1, At3g52850, F8J2.20 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P93026
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 8
Details: 0.1 M Tris pH 8.0, 20% v/v glycerol ethoxylate, 10% v/v tetrahydrofuran

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.9796
SYNCHROTRONDiamond I2323.024
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELJul 18, 2019
DECTRIS PILATUS 12M2PIXELJun 28, 2024
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
23.0241
ReflectionResolution: 3.51→49.96 Å / Num. obs: 12055 / % possible obs: 99.7 % / Redundancy: 16 % / Biso Wilson estimate: 137.53 Å2 / CC1/2: 0.999 / Net I/σ(I): 30.14
Reflection shellResolution: 3.51→3.72 Å / Redundancy: 28.8 % / Num. unique obs: 1908 / CC1/2: 0.301 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDS20180409data reduction
XDS20180409data scaling
Arcimboldophasing
Coot0.9.6model building
PHASERphasing
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.51→47.16 Å / SU ML: 0.6607 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.7215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2723 602 5 %
Rwork0.2558 11430 -
obs0.2566 12032 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 133.92 Å2
Refinement stepCycle: LAST / Resolution: 3.51→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 89 0 3454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263547
X-RAY DIFFRACTIONf_angle_d0.48854811
X-RAY DIFFRACTIONf_chiral_restr0.0416549
X-RAY DIFFRACTIONf_plane_restr0.0037614
X-RAY DIFFRACTIONf_dihedral_angle_d10.54991389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.51-3.860.43411460.36972784X-RAY DIFFRACTION98.52
3.86-4.420.30491500.32847X-RAY DIFFRACTION100
4.43-5.570.24531500.26262845X-RAY DIFFRACTION99.93
5.57-47.160.24681560.2192954X-RAY DIFFRACTION99.97

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