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- PDB-7o6t: Crystal structure of the polymerising VEL domain of VIN3 (R556D I... -

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Basic information

Entry
Database: PDB / ID: 7o6t
TitleCrystal structure of the polymerising VEL domain of VIN3 (R556D I575D mutant)
Components(Protein VERNALIZATION INSENSITIVE 3) x 2
KeywordsNUCLEAR PROTEIN / protein oligomerization / head-to-tail polymerization / domain swapping
Function / homology
Function and homology information


vernalization response / chromatin silencing complex / cellular response to cold / negative regulation of gene expression, epigenetic / response to cold / response to hypoxia / nuclear speck / DNA binding / zinc ion binding / nucleus
Similarity search - Function
VIN3-like, fibronectin type-III domain / Oberon, PHD finger domain / Vernalization insensitive 3-like / : / PHD - plant homeodomain finger protein / VIN3-like, C-terminal domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Protein VERNALIZATION INSENSITIVE 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsFiedler, M. / Franco-Echevarria, E. / Dean, C. / Bienz, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105192713 United Kingdom
Royal SocietyRP/R1/180002 United Kingdom
CitationJournal: Cell Rep / Year: 2022
Title: Head-to-tail polymerization by VEL proteins underpins cold-induced Polycomb silencing in flowering control.
Authors: Fiedler, M. / Franco-Echevarria, E. / Schulten, A. / Nielsen, M. / Rutherford, T.J. / Yeates, A. / Ahsan, B. / Dean, C. / Bienz, M.
History
DepositionApr 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein VERNALIZATION INSENSITIVE 3
B: Protein VERNALIZATION INSENSITIVE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4003
Polymers17,3752
Non-polymers241
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-41 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.423, 51.809, 85.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein VERNALIZATION INSENSITIVE 3


Mass: 8725.775 Da / Num. of mol.: 1 / Mutation: R556D I575D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VIN3, At5g57380, MSF19.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FIE3
#2: Protein Protein VERNALIZATION INSENSITIVE 3


Mass: 8649.657 Da / Num. of mol.: 1 / Mutation: R556D I575D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VIN3, At5g57380, MSF19.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FIE3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.06M Morpheus Divalents, 0.1M Morpheus Buffer System 2 pH 7.5, 10% w/v PEG 8K, 20% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.02→29.49 Å / Num. obs: 9677 / % possible obs: 99.7 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 36.2
Reflection shellResolution: 2.02→2.07 Å / Num. unique obs: 677 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.02→29.49 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 11.826 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23655 506 5.3 %RANDOM
Rwork0.20241 ---
obs-9131 99.71 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.648 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2--3.04 Å2-0 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.02→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 1 49 1223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0181193
X-RAY DIFFRACTIONr_bond_other_d0.0010.021127
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.8841602
X-RAY DIFFRACTIONr_angle_other_deg1.0992.7432599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9935139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.35121.54971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93415221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9951510
X-RAY DIFFRACTIONr_chiral_restr0.0630.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02279
X-RAY DIFFRACTIONr_mcbond_it2.7293.016562
X-RAY DIFFRACTIONr_mcbond_other2.7313.013561
X-RAY DIFFRACTIONr_mcangle_it3.5574.496699
X-RAY DIFFRACTIONr_mcangle_other3.5554.5700
X-RAY DIFFRACTIONr_scbond_it4.053.662631
X-RAY DIFFRACTIONr_scbond_other4.0493.663631
X-RAY DIFFRACTIONr_scangle_other6.3285.256903
X-RAY DIFFRACTIONr_long_range_B_refined7.84536.8181392
X-RAY DIFFRACTIONr_long_range_B_other7.85136.7231388
LS refinement shellResolution: 2.02→2.069 Å
RfactorNum. reflection% reflection
Rfree0.329 36 -
Rwork0.254 639 -
obs--96.43 %
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)
10.81121.0506-0.91063.5163-3.90955.78050.1135-0.040.05250.37030.12190.1053-0.3239-0.3363-0.23540.11950.00690.0580.03630.02110.101815.9656.38673.178
20.51230.5134-1.97412.4214-3.408610.34410.0431-0.0542-0.11050.10520.05260.09670.1680.1072-0.09570.1269-0.0235-0.05430.0250.01910.167624.5818.31864.682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A531 - 603
2X-RAY DIFFRACTION2B533 - 600

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