[English] 日本語
Yorodumi
- PDB-6to5: Crystal structure of the oligomerisation domain of the transcript... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6to5
TitleCrystal structure of the oligomerisation domain of the transcription factor PHOSPHATE STARVATION RESPONSE 1 from Arabidopsis.
ComponentsProtein PHOSPHATE STARVATION RESPONSE 1
KeywordsTRANSCRIPTION / phosphate starvation / myb domain / coiled-coil domain / inositol pyrophosphate / plant nutrition
Function / homology
Function and homology information


response to arsenite ion / sulfate ion homeostasis / cellular response to high light intensity / regulation of monoatomic ion transmembrane transport / cellular response to phosphate starvation / circadian rhythm / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
MYB-CC type transcription factor, LHEQLE-containing domain / : / MYB-CC type transfactor, LHEQLE motif / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Protein PHOSPHATE STARVATION RESPONSE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHothorn, M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
European Research Council (ERC)818696/INSPIRE Switzerland
Swiss National Science FoundationCRSII5_170925 Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: Inositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis.
Authors: Ried, M.K. / Wild, R. / Zhu, J. / Pipercevic, J. / Sturm, K. / Broger, L. / Harmel, R.K. / Abriata, L.A. / Hothorn, L.A. / Fiedler, D. / Hiller, S. / Hothorn, M.
History
DepositionDec 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 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
AAAA: Protein PHOSPHATE STARVATION RESPONSE 1
AAAB: Protein PHOSPHATE STARVATION RESPONSE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6563
Polymers18,6312
Non-polymers241
Water28816
1
AAAA: Protein PHOSPHATE STARVATION RESPONSE 1
AAAB: Protein PHOSPHATE STARVATION RESPONSE 1
hetero molecules

AAAA: Protein PHOSPHATE STARVATION RESPONSE 1
AAAB: Protein PHOSPHATE STARVATION RESPONSE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3116
Polymers37,2634
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area10470 Å2
ΔGint-78 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.400, 70.400, 148.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein Protein PHOSPHATE STARVATION RESPONSE 1 / AtPHR1


Mass: 9315.647 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHR1, At4g28610, T5F17.60 / Plasmid: pMH-HT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q94CL7
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M phosphate citrate pH 4.2, 0.2 M NaCl, 20% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→47.18 Å / Num. obs: 16576 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 20.8 % / Biso Wilson estimate: 48.58 Å2 / CC1/2: 1 / Rrim(I) all: 0.189 / Net I/σ(I): 14.9
Reflection shellResolution: 2.38→2.52 Å / Mean I/σ(I) obs: 1.48 / Num. unique obs: 2262 / CC1/2: 0.69 / Rrim(I) all: 2.21 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IIT

5iit


Resolution: 2.38→47.17 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0838
RfactorNum. reflection% reflection
Rfree0.2294 826 4.99 %
Rwork0.2144 --
obs0.2153 16560 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.43 Å2
Refinement stepCycle: LAST / Resolution: 2.38→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 1 16 957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037947
X-RAY DIFFRACTIONf_angle_d0.59991260
X-RAY DIFFRACTIONf_chiral_restr0.0314139
X-RAY DIFFRACTIONf_plane_restr0.0031165
X-RAY DIFFRACTIONf_dihedral_angle_d7.8492603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.530.28731350.27682617X-RAY DIFFRACTION99.24
2.53-2.720.27871380.24682617X-RAY DIFFRACTION99.93
2.72-30.26671350.24122617X-RAY DIFFRACTION100
3-3.430.28391370.22632627X-RAY DIFFRACTION100
3.43-4.320.18521380.19222631X-RAY DIFFRACTION100
4.32-47.170.21621430.20262625X-RAY DIFFRACTION100

+
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