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- PDB-9l4p: Arabidopsis thaliana protease-associated domain of vacuolar sorti... -

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Basic information

Entry
Database: PDB / ID: 9l4p
TitleArabidopsis thaliana protease-associated domain of vacuolar sorting receptor 1 in complexed with vicilin-like seed storage protein 22 C-terminal pentapeptide SDRFV (pH 7.0)
Components
  • Vacuolar-sorting receptor 1
  • Vicilin-like seed storage protein 22
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
Vacuolar-sorting receptor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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

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Assembly

Deposited unit
A: Vacuolar-sorting receptor 1
B: Vicilin-like seed storage protein 22


Theoretical massNumber of molelcules
Total (without water)18,4812
Polymers18,4812
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-2 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.701, 60.435, 39.206
Angle α, β, γ (deg.)90.00, 113.29, 90.00
Int Tables number4
Space group name H-MP1211

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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: 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 22


Mass: 649.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.12 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MES pH 7.0 25% (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 / Wavelength: 1.5419 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.95→36.01 Å / Num. obs: 10101 / % possible obs: 98.1 % / Redundancy: 2.9 % / CC1/2: 0.996 / Net I/σ(I): 8.4
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 713 / CC1/2: 0.788

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30.22 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 477 4.73 %
Rwork0.1744 --
obs0.1773 10079 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 0 92 1290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.81
X-RAY DIFFRACTIONf_dihedral_angle_d11.794437
X-RAY DIFFRACTIONf_chiral_restr0.052197
X-RAY DIFFRACTIONf_plane_restr0.006214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.230.23771630.18063200X-RAY DIFFRACTION99
2.23-2.810.26461520.19713185X-RAY DIFFRACTION98
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)
10.55560.09060.22781.00270.15650.4753-0.00660.04680.1087-0.19240.0641-0.0341-0.03180.1215-0.00010.2185-0.00210.0140.21070.00950.1923-6.28456.9559-9.2374
20.52320.44360.15510.4188-0.15380.2643-0.0570.0557-0.20710.0682-0.0014-0.02980.0812-0.008500.18490.00190.00770.1739-0.02450.2015-13.406-5.206-7.4662
30.145-0.2519-0.26060.28920.24170.2965-0.1750.4692-0.4276-0.12890.10360.0012-0.0772-0.1015-0.01710.2301-0.0420.01880.334-0.03450.3128-16.5215-4.8817-19.6334
40.6050.3007-0.11580.42950.17880.49220.00720.02630.212-0.25880.17980.0066-0.1267-0.02510.00010.24420.00740.01340.21810.00930.1851-6.25594.8148-3.0855
51.3737-0.6343-0.73150.2950.32350.39020.51450.8290.5563-0.3035-0.3109-0.5594-0.17270.81140.01920.3611-0.02660.00340.61280.01820.2058-4.4285-5.6175-22.2557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 152 )
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 178 )
5X-RAY DIFFRACTION5chain 'B' and (resid 506 through 511 )

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