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- PDB-7o6w: Crystal structure of (the) VEL1 VEL polymerising domain (I664D mutant) -

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Basic information

Entry
Database: PDB / ID: 7o6w
TitleCrystal structure of (the) VEL1 VEL polymerising domain (I664D mutant)
ComponentsVIN3-like protein 2
KeywordsNUCLEAR PROTEIN / protein oligomerization / head-to-tail polymerization
Function / homology
Function and homology information


regulation of short-day photoperiodism, flowering / : / vernalization response / vegetative to reproductive phase transition of meristem / flower development / PcG protein complex / plasmodesma / chromatin silencing complex / epigenetic regulation of gene expression / methylated histone binding ...regulation of short-day photoperiodism, flowering / : / vernalization response / vegetative to reproductive phase transition of meristem / flower development / PcG protein complex / plasmodesma / chromatin silencing complex / epigenetic regulation of gene expression / methylated histone binding / response to cold / circadian regulation of gene expression / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
Oberon, PHD finger domain / Vernalization insensitive 3-like / PHD - plant homeodomain finger protein / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / VIN3-like protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 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 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VIN3-like protein 2
B: VIN3-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3513
Polymers16,2572
Non-polymers951
Water1086
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-6 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.259, 79.259, 59.957
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein VIN3-like protein 2 / Vernalization5/VIN3-like protein 1


Mass: 8128.257 Da / Num. of mol.: 2 / Mutation: I664D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VIL2, VEL1, At4g30200, F9N11.50 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SUM4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.25M (NH4)H2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.64→27.49 Å / Num. obs: 6333 / % possible obs: 98.8 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.011 / Rrim(I) all: 0.069 / Net I/σ(I): 37
Reflection shell

Diffraction-ID: 1 / Redundancy: 15 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.64-2.771.0457820.8420.183192
8-100.03318610.050.03397.2

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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: 2.64→27.49 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 28.814 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.604 / ESU R Free: 0.309 / 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
Rfree0.24916 631 10 %RANDOM
Rwork0.21157 ---
obs0.21527 5671 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.726 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å2-0.72 Å20 Å2
2---1.43 Å2-0 Å2
3---4.65 Å2
Refinement stepCycle: LAST / Resolution: 2.64→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1140 0 5 6 1151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0181164
X-RAY DIFFRACTIONr_bond_other_d0.0010.021104
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.8671568
X-RAY DIFFRACTIONr_angle_other_deg1.0082.7522536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3325136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30821.94472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32615216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4661510
X-RAY DIFFRACTIONr_chiral_restr0.0530.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
X-RAY DIFFRACTIONr_mcbond_it0.7566.63550
X-RAY DIFFRACTIONr_mcbond_other0.7516.631549
X-RAY DIFFRACTIONr_mcangle_it1.2559.945684
X-RAY DIFFRACTIONr_mcangle_other1.2569.945685
X-RAY DIFFRACTIONr_scbond_it0.7776.776614
X-RAY DIFFRACTIONr_scbond_other0.7776.714610
X-RAY DIFFRACTIONr_scangle_other1.31410.038879
X-RAY DIFFRACTIONr_long_range_B_refined5.87577.221320
X-RAY DIFFRACTIONr_long_range_B_other5.87377.2341321
LS refinement shellResolution: 2.643→2.711 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 39 -
Rwork0.382 377 -
obs--87.76 %
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)
15.65240.28162.01639.1471-3.08967.08250.0792-0.10190.23290.67460.05830.5013-0.6920.3309-0.13750.16960.02180.00810.0721-0.02820.0626-21.438-19.9960.431
28.5484-0.87245.05236.4635-0.59878.22580.1352-0.2384-0.43530.24880.2557-0.0359-0.591-0.1746-0.39090.10260.03570.00430.1624-0.00490.0282-8.617-28.00915.407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A621 - 689
2X-RAY DIFFRACTION2B621 - 689

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