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- PDB-9l4o: Arabidopsis thaliana protease-associated domain of vacuolar sorti... -

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Basic information

Entry
Database: PDB / ID: 9l4o
TitleArabidopsis thaliana protease-associated domain of vacuolar sorting receptor 1 in complexed with vicilin-like seed storage protein 22 C-terminal pentapeptide SDRFV (pH 5.8)
Components
  • Vacuolar-sorting receptor 1
  • Vicilin-like seed storage protein C-terminal pentapeptide
KeywordsPROTEIN TRANSPORT / ligand binding domain vacuolar sorting determinant receptor-cargo interaction
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
DI(HYDROXYETHYL)ETHER / Vacuolar-sorting receptor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLui, S.N. / Wong, K.B.
Funding support Hong Kong, 2items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)CUHK 14118122 Hong Kong
The University Grants Committee, Research Grants Council (RGC)C4041-18E Hong Kong
CitationJournal: Febs J. / Year: 2025
Title: Structural insights into how vacuolar sorting receptor recognizes the C-terminal sorting determinant of a vicilin-like seed storage protein.
Authors: Lui, S.N. / Tsao, H.E. / Lo, A.H. / Jiang, L. / Wong, K.B.
History
DepositionDec 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar-sorting receptor 1
B: Vicilin-like seed storage protein C-terminal pentapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8015
Polymers18,4812
Non-polymers3203
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-2 kcal/mol
Surface area8270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.658, 60.384, 39.245
Angle α, β, γ (deg.)90.00, 113.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 17831.242 Da / Num. of mol.: 1 / Fragment: Protease associated domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VSR1, BP80B, ELP, ELP1, At3g52850, F8J2.20 / Production host: Escherichia coli (E. coli) / References: UniProt: P93026
#2: Protein/peptide Vicilin-like seed storage protein C-terminal pentapeptide


Mass: 649.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)

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Non-polymers , 4 types, 100 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 0.1 M MES pH 5.8 30% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5419 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.9→36.02 Å / Num. obs: 10890 / % possible obs: 98.2 % / Redundancy: 3.7 % / CC1/2: 0.999 / Net I/σ(I): 19
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2236 / CC1/2: 0.885

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Processing

Software
NameVersionClassification
PHENIX1.21 1-5286refinement
Aimlessdata scaling
XDSVERSION Jan 10, 2022 BUILT=20220820data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30.19 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 500 4.6 %
Rwork0.1687 --
obs0.1708 10867 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 20 97 1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.807
X-RAY DIFFRACTIONf_dihedral_angle_d12.027469
X-RAY DIFFRACTIONf_chiral_restr0.057199
X-RAY DIFFRACTIONf_plane_restr0.006218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.21971200.17342555X-RAY DIFFRACTION98
2.09-2.390.21941350.17112598X-RAY DIFFRACTION99
2.39-3.010.25361180.18482597X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -10.5681 Å / Origin y: 0.6299 Å / Origin z: -9.1589 Å
111213212223313233
T0.1372 Å20.0097 Å2-0.0046 Å2-0.1272 Å20.0122 Å2--0.1274 Å2
L2.0911 °20.2533 °20.127 °2-1.4767 °20.5401 °2--1.4366 °2
S-0.0228 Å °0.1471 Å °0.0018 Å °-0.096 Å °0.0188 Å °0.0424 Å °-0.0632 Å °0.0231 Å °0.0066 Å °
Refinement TLS groupSelection details: all

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