[English] 日本語
Yorodumi
- PDB-5b3g: The crystal structure of the heterodimer of SHORT-ROOT and SCAREC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b3g
TitleThe crystal structure of the heterodimer of SHORT-ROOT and SCARECROW GRAS domains
Components
  • Protein SCARECROW
  • Protein SHORT-ROOT
KeywordsTRANSCRIPTION / Transcription cofactor
Function / homology
Function and homology information


bundle sheath cell fate specification / radial pattern formation / regulation of hormone metabolic process / gravitropism / asymmetric cell division / leaf development / root development / maintenance of protein location in nucleus / negative regulation of mitotic cell cycle / cell redox homeostasis ...bundle sheath cell fate specification / radial pattern formation / regulation of hormone metabolic process / gravitropism / asymmetric cell division / leaf development / root development / maintenance of protein location in nucleus / negative regulation of mitotic cell cycle / cell redox homeostasis / recycling endosome / late endosome / sequence-specific DNA binding / transcription cis-regulatory region binding / early endosome / DNA-binding transcription factor activity / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Transcription factor GRAS / GRAS domain family / GRAS family profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Protein SCARECROW / Protein SHORT-ROOT
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHirano, Y. / Nakagawa, M. / Hakoshima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology25440025 Japan
Ministry of Education, Culture, Sports, Science and Technology22121002 Japan
CitationJournal: Nat Plants / Year: 2017
Title: Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD
Authors: Hirano, Y. / Nakagawa, M. / Suyama, T. / Murase, K. / Shirakawa, M. / Takayama, S. / Sun, T.P. / Hakoshima, T.
History
DepositionFeb 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein SCARECROW
B: Protein SHORT-ROOT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8489
Polymers95,2482
Non-polymers6007
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-9 kcal/mol
Surface area31850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.700, 84.428, 89.797
Angle α, β, γ (deg.)90.00, 92.66, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Protein SCARECROW / AtSCR / GRAS family protein 20 / AtGRAS-20 / Protein SHOOT GRAVITROPISM 1


Mass: 42212.922 Da / Num. of mol.: 1 / Fragment: UNP residues 274-653
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SCR, SGR1, At3g54220, F24B22.180 / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9M384
#2: Protein Protein SHORT-ROOT / AtSHR / GRAS family protein 26 / AtGRAS-26 / Protein SHOOT GRAVITROPISM 7


Mass: 53035.047 Da / Num. of mol.: 1 / Fragment: UNP residues 59-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHR, SGR7, At4g37650, F19F18.140 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9SZF7

-
Non-polymers , 4 types, 293 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsSEQUENCE CONFLICT P233S IS BASED ON REFERENCE 4 (AAL69513) ACCORDING TO DATABASE Q9SZF7 (SHR_ARATH)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: phosphate buffer (pH 7.0), polyethylene glycol (PEG) 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 26, 2011
RadiationMonochromator: Rotated-inclined double-crystal monochromator , Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 56799 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rsym value: 0.072 / Net I/σ(I): 28.1
Reflection shellResolution: 2→2.07 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→33.101 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.63 / Phase error: 23.8
RfactorNum. reflection% reflection
Rfree0.2296 2875 5.06 %
Rwork0.1835 --
obs0.1859 56799 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→33.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 38 286 6393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076256
X-RAY DIFFRACTIONf_angle_d0.9788472
X-RAY DIFFRACTIONf_dihedral_angle_d14.4472266
X-RAY DIFFRACTIONf_chiral_restr0.055936
X-RAY DIFFRACTIONf_plane_restr0.0041097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03280.31111250.23772497X-RAY DIFFRACTION97
2.0328-2.06780.30591110.22482544X-RAY DIFFRACTION99
2.0678-2.10540.26731410.21412563X-RAY DIFFRACTION99
2.1054-2.14590.27261240.20512520X-RAY DIFFRACTION99
2.1459-2.18970.27221300.20542575X-RAY DIFFRACTION99
2.1897-2.23730.27861150.20712600X-RAY DIFFRACTION99
2.2373-2.28930.25511400.22272540X-RAY DIFFRACTION99
2.2893-2.34660.23681560.1892564X-RAY DIFFRACTION100
2.3466-2.410.23311450.18632571X-RAY DIFFRACTION100
2.41-2.48090.27251410.18982588X-RAY DIFFRACTION100
2.4809-2.56090.27391160.18982554X-RAY DIFFRACTION100
2.5609-2.65240.21251440.18732582X-RAY DIFFRACTION100
2.6524-2.75860.22451350.19792563X-RAY DIFFRACTION100
2.7586-2.88410.26421310.19282593X-RAY DIFFRACTION100
2.8841-3.0360.25391430.19922562X-RAY DIFFRACTION100
3.036-3.22610.23061460.20432583X-RAY DIFFRACTION100
3.2261-3.47490.20761310.18682584X-RAY DIFFRACTION100
3.4749-3.82420.21411530.16312598X-RAY DIFFRACTION100
3.8242-4.37640.21981410.1542581X-RAY DIFFRACTION100
4.3764-5.50970.19921480.15432599X-RAY DIFFRACTION100
5.5097-33.10590.20271590.17892563X-RAY DIFFRACTION97

+
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