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- PDB-7f2d: Arabidopsis thaliana protease-associated domain of vacuolar-sorti... -

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Basic information

Entry
Database: PDB / ID: 7f2d
TitleArabidopsis thaliana protease-associated domain of vacuolar-sorting receptor 1 in complex with cruciferin 1 C-terminal pentapeptide RVAAA (pH9)
Components
  • Cruciferin 1 C-terminal peptide
  • Vacuolar-sorting receptor 1
KeywordsPROTEIN TRANSPORT / Ligand-binding domain Receptor-cargo interaction Cruciferin peptide
Function / homology
Function and homology information


amino-terminal vacuolar sorting propeptide binding / cellular response to abscisic acid stimulus / seed maturation / protein storage vacuole / Golgi to vacuole transport / response to abscisic acid / nutrient reservoir activity / clathrin-coated vesicle membrane / vacuolar transport / protein targeting to vacuole ...amino-terminal vacuolar sorting propeptide binding / cellular response to abscisic acid stimulus / seed maturation / protein storage vacuole / Golgi to vacuole transport / response to abscisic acid / nutrient reservoir activity / clathrin-coated vesicle membrane / vacuolar transport / protein targeting to vacuole / trans-Golgi network / late endosome / Golgi membrane / calcium ion binding / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / Cupin / Cupin 1 / Cupin / PA domain superfamily / PA domain / PA domain ...11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / Cupin / Cupin 1 / Cupin / PA domain superfamily / PA domain / PA domain / RmlC-like cupin domain superfamily / 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. / RmlC-like jelly roll fold
Similarity search - Domain/homology
12S seed storage protein CRA1 / Vacuolar-sorting receptor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLui, S.N. / Wong, K.B.
Funding support Hong Kong, 3items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)CUHK 14151416 Hong Kong
The University Grants Committee, Research Grants Council (RGC)C4041-18EF Hong Kong
The University Grants Committee, Research Grants Council (RGC)AoE/M-05/12 Hong Kong
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural insights into how vacuolar sorting receptors recognize the sorting determinants of seed storage proteins.
Authors: Tsao, H.E. / Lui, S.N. / Lo, A.H. / Chen, S. / Wong, H.Y. / Wong, C.K. / Jiang, L. / Wong, K.B.
History
DepositionJun 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar-sorting receptor 1
B: Cruciferin 1 C-terminal peptide


Theoretical massNumber of molelcules
Total (without water)18,3192
Polymers18,3192
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-3 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.680, 60.767, 40.594
Angle α, β, γ (deg.)90.000, 111.620, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 Cruciferin 1 C-terminal peptide


Mass: 487.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P15455
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M Bis-Tris, 30% w/v Polyethylene glycol monomethyl ether 2000

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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: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.45→37.74 Å / Num. obs: 5308 / % possible obs: 96.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.86 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 23.1
Reflection shellResolution: 2.45→2.55 Å / Rmerge(I) obs: 0.086 / Num. unique obs: 587

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TJX

4tjx


Resolution: 2.45→37.74 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 275 5.2 %
Rwork0.1839 5011 -
obs0.1866 5286 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.52 Å2 / Biso mean: 25.0438 Å2 / Biso min: 12.67 Å2
Refinement stepCycle: final / Resolution: 2.45→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1079 0 0 65 1144
Biso mean---26.67 -
Num. residues----148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.580.2654470.164468373095
2.58-2.740.2549400.204672676695
2.74-2.950.2527500.211869274296
2.95-3.250.2047310.208971174296
3.25-3.720.2361360.194171675297
3.72-4.680.224330.161374177497
4.69-37.740.2431380.167574278098
Refinement TLS params.Method: refined / Origin x: 5.7777 Å / Origin y: 33.3663 Å / Origin z: 8.1154 Å
111213212223313233
T0.1022 Å2-0.0131 Å2-0.0051 Å2-0.1264 Å2-0.0002 Å2--0.1017 Å2
L2.9094 °2-0.0076 °20.2216 °2-2.5389 °20.4027 °2--1.4224 °2
S-0.0504 Å °-0.0214 Å °-0.0356 Å °-0.002 Å °0.049 Å °0.0466 Å °0.0067 Å °0.0086 Å °0.0035 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 175
2X-RAY DIFFRACTION1allB1 - 5
3X-RAY DIFFRACTION1allS1 - 79

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