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- PDB-7oqv: Crystal structure of the polymerising VEL domain of VIN3 (I575D m... -

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Basic information

Entry
Database: PDB / ID: 7oqv
TitleCrystal structure of the polymerising VEL domain of VIN3 (I575D mutant)
ComponentsProtein VERNALIZATION INSENSITIVE 3
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: 2.4 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
DepositionJun 4, 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 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Protein VERNALIZATION INSENSITIVE 3
BBB: Protein VERNALIZATION INSENSITIVE 3
CCC: Protein VERNALIZATION INSENSITIVE 3
DDD: Protein VERNALIZATION INSENSITIVE 3


Theoretical massNumber of molelcules
Total (without water)35,3804
Polymers35,3804
Non-polymers00
Water68538
1
AAA: Protein VERNALIZATION INSENSITIVE 3
CCC: Protein VERNALIZATION INSENSITIVE 3


Theoretical massNumber of molelcules
Total (without water)17,6902
Polymers17,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-38 kcal/mol
Surface area8390 Å2
MethodPISA
2
BBB: Protein VERNALIZATION INSENSITIVE 3
DDD: Protein VERNALIZATION INSENSITIVE 3


Theoretical massNumber of molelcules
Total (without water)17,6902
Polymers17,6902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-34 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.498, 91.273, 98.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein VERNALIZATION INSENSITIVE 3


Mass: 8845.021 Da / Num. of mol.: 4 / Mutation: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 1M potassium phosphate monobasic, 3 % v/v 2 propanol, 0.1M sodium cacodylate pH6.5

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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: 2.4→29.07 Å / Num. obs: 11740 / % possible obs: 100 % / Redundancy: 8.7 % / CC1/2: 1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 11740 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.826 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.647 / ESU R Free: 0.303
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2695 590 5.044 %
Rwork0.2234 11107 -
all0.226 --
obs-11697 99.923 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 56.228 Å2
Baniso -1Baniso -2Baniso -3
1-7.125 Å20 Å20 Å2
2---4.445 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 0 38 2357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132361
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172213
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6393171
X-RAY DIFFRACTIONr_angle_other_deg1.3141.5845100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5435275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.29720.604149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.01715449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.541525
X-RAY DIFFRACTIONr_chiral_restr0.0710.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
X-RAY DIFFRACTIONr_nbd_refined0.2160.2581
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22029
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21136
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0760.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.214
X-RAY DIFFRACTIONr_nbd_other0.1770.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3740.26
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0720.21
X-RAY DIFFRACTIONr_mcbond_it4.3635.5021112
X-RAY DIFFRACTIONr_mcbond_other4.3645.5011111
X-RAY DIFFRACTIONr_mcangle_it6.328.2311383
X-RAY DIFFRACTIONr_mcangle_other6.3188.2321384
X-RAY DIFFRACTIONr_scbond_it5.8836.3641249
X-RAY DIFFRACTIONr_scbond_other5.886.3651250
X-RAY DIFFRACTIONr_scangle_it9.2249.2181788
X-RAY DIFFRACTIONr_scangle_other9.2229.2181789
X-RAY DIFFRACTIONr_lrange_it11.50364.5782729
X-RAY DIFFRACTIONr_lrange_other11.50264.5842729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.354460.328808X-RAY DIFFRACTION100
2.462-2.530.487460.308759X-RAY DIFFRACTION100
2.53-2.6030.272370.271774X-RAY DIFFRACTION100
2.603-2.6830.305360.277736X-RAY DIFFRACTION100
2.683-2.7710.364300.264720X-RAY DIFFRACTION100
2.771-2.8680.254430.248704X-RAY DIFFRACTION100
2.868-2.9760.317350.259661X-RAY DIFFRACTION100
2.976-3.0970.303330.251661X-RAY DIFFRACTION100
3.097-3.2350.304420.25610X-RAY DIFFRACTION100
3.235-3.3920.374350.221594X-RAY DIFFRACTION100
3.392-3.5750.252390.197571X-RAY DIFFRACTION100
3.575-3.7910.231200.19550X-RAY DIFFRACTION100
3.791-4.0520.217280.183510X-RAY DIFFRACTION100
4.052-4.3750.197250.156490X-RAY DIFFRACTION100
4.375-4.7910.196180.154448X-RAY DIFFRACTION100
4.791-5.3530.232240.207416X-RAY DIFFRACTION100
5.353-6.1750.17110.17378X-RAY DIFFRACTION100
6.175-7.5460.329140.265314X-RAY DIFFRACTION100
7.546-100.235150.21257X-RAY DIFFRACTION100
8-100.299130.266146X-RAY DIFFRACTION94.6429

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