[English] 日本語
Yorodumi
- PDB-5nqs: Structure of the Arabidopsis Thaliana TOPLESS N-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nqs
TitleStructure of the Arabidopsis Thaliana TOPLESS N-terminal domain
ComponentsProtein TOPLESS
KeywordsTRANSCRIPTION / TOPLESS / Transcription Factor / Plant / Auxin
Function / homology
Function and homology information


primary shoot apical meristem specification / xylem and phloem pattern formation / jasmonic acid mediated signaling pathway / response to auxin / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity / identical protein binding / nucleus
Similarity search - Function
Topless family / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. ...Topless family / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsNanao, M.H. / Arevalillo, M.R. / Vinos-Poyo, T. / Parcy, F. / Dumas, R.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of the Arabidopsis TOPLESS corepressor provides insight into the evolution of transcriptional repression.
Authors: Martin-Arevalillo, R. / Nanao, M.H. / Larrieu, A. / Vinos-Poyo, T. / Mast, D. / Galvan-Ampudia, C. / Brunoud, G. / Vernoux, T. / Dumas, R. / Parcy, F.
History
DepositionApr 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein TOPLESS
B: Protein TOPLESS


Theoretical massNumber of molelcules
Total (without water)50,5862
Polymers50,5862
Non-polymers00
Water55831
1
A: Protein TOPLESS


Theoretical massNumber of molelcules
Total (without water)25,2931
Polymers25,2931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein TOPLESS


Theoretical massNumber of molelcules
Total (without water)25,2931
Polymers25,2931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.681, 72.681, 181.147
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

-
Components

#1: Protein Protein TOPLESS / WUS-interacting protein 1


Mass: 25292.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TPL, WSIP1, At1g15750, F7H2.9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta De3 / References: UniProt: Q94AI7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Na2HPO4-Citrate 0.2 M pH 4.2, 2-propanol 10% v/v and Lithium sulfate 0.3 M

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 21, 2014 / Details: KB
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.61→100 Å / Num. obs: 16949 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 75.29 Å2 / Rsym value: 0.105 / Net I/σ(I): 12.2
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 6.48 % / Mean I/σ(I) obs: 1.79 / Num. unique obs: 10538 / CC1/2: 0.672 / Rsym value: 0.89 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDS(VERSION January 10, 2014data reduction
XSCALE(VERSION January 10, 2014data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: partially built MAD model

Resolution: 2.61→24.91 Å / Cor.coef. Fo:Fc: 0.9403 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.422 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.399 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.274
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 859 5.07 %RANDOM
Rwork0.2003 ---
obs0.2027 16929 99.71 %-
Displacement parametersBiso mean: 62.22 Å2
Baniso -1Baniso -2Baniso -3
1--5.2725 Å20 Å20 Å2
2---5.2725 Å20 Å2
3---10.5449 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å
Refinement stepCycle: 1 / Resolution: 2.61→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 0 31 3060
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013087HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094140HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1168SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes429HARMONIC5
X-RAY DIFFRACTIONt_it3087HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion20.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion381SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3421SEMIHARMONIC4
LS refinement shellResolution: 2.61→2.77 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2862 132 4.91 %
Rwork0.2383 2554 -
all0.2406 2686 -
obs--99.71 %

+
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://pdbjlvh1.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