[English] 日本語
Yorodumi
- PDB-7o6v: Crystal structure of the VEL1 VEL polymerising domain (R643A K645... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o6v
TitleCrystal structure of the VEL1 VEL polymerising domain (R643A K645D 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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VIN3-like protein 2
B: VIN3-like protein 2
C: VIN3-like protein 2
D: VIN3-like protein 2


Theoretical massNumber of molelcules
Total (without water)35,4364
Polymers35,4364
Non-polymers00
Water1629
1
A: VIN3-like protein 2


Theoretical massNumber of molelcules
Total (without water)8,8591
Polymers8,8591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VIN3-like protein 2


Theoretical massNumber of molelcules
Total (without water)8,8591
Polymers8,8591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: VIN3-like protein 2


Theoretical massNumber of molelcules
Total (without water)8,8591
Polymers8,8591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: VIN3-like protein 2


Theoretical massNumber of molelcules
Total (without water)8,8591
Polymers8,8591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.066, 58.053, 119.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 8858.979 Da / Num. of mol.: 4
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 (E. coli) / References: UniProt: Q9SUM4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20% PEG 3350, 2M Sodium malonate pH7

-
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: 2.5→29.04 Å / Num. obs: 13183 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.99 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 1481 / CC1/2: 0.84

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→29.04 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.951 / SU B: 20.883 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.457 / ESU R Free: 0.263 / 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
Rfree0.2407 649 4.9 %RANDOM
Rwork0.21358 ---
obs0.21492 13134 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.134 Å2
Baniso -1Baniso -2Baniso -3
1-4.14 Å20 Å20 Å2
2---1.2 Å20 Å2
3----2.94 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 0 9 2302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0182340
X-RAY DIFFRACTIONr_bond_other_d0.0010.022177
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.8673162
X-RAY DIFFRACTIONr_angle_other_deg1.1022.7765011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3865280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84322.908141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2411516
X-RAY DIFFRACTIONr_chiral_restr0.0690.2360
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022636
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02552
X-RAY DIFFRACTIONr_mcbond_it0.7664.4971129
X-RAY DIFFRACTIONr_mcbond_other0.7664.4961128
X-RAY DIFFRACTIONr_mcangle_it1.2756.741406
X-RAY DIFFRACTIONr_mcangle_other1.2746.7411407
X-RAY DIFFRACTIONr_scbond_it0.8184.6011211
X-RAY DIFFRACTIONr_scbond_other0.8184.6011211
X-RAY DIFFRACTIONr_scangle_other1.3846.8611757
X-RAY DIFFRACTIONr_long_range_B_refined2.11552.512640
X-RAY DIFFRACTIONr_long_range_B_other2.11452.5112640
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 52 -
Rwork0.305 906 -
obs--100 %
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)
13.4787-0.4386-0.38764.8915-2.05696.2176-0.07780.0625-0.0697-0.13580.0205-0.17910.25460.29380.05730.0140.0086-0.00960.0199-0.00440.1734-8.709-2.7118.17
25.476-1.5832-0.5057.1154-1.1375.3645-0.0554-0.10780.2990.1710.08790.2108-0.2221-0.2745-0.03250.02960.0446-0.00850.0747-0.00840.2193-24.57211.16510.331
35.3745-0.3983-1.50134.81820.72645.48720.00070.1493-0.19550.0396-0.04870.03880.1236-0.10340.0480.02250.0152-0.00310.03220.0260.2132-40.11621.94722.486
45.7725-1.881-0.00425.4472-1.09945.64710.0417-0.1530.0897-0.14480.0891-0.216-0.1866-0.0648-0.13080.08690.04340.0380.05720.0410.2682-46.77341.618.855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A620 - 690
2X-RAY DIFFRACTION2B620 - 689
3X-RAY DIFFRACTION3C619 - 689
4X-RAY DIFFRACTION4D620 - 689

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more