[English] 日本語
Yorodumi
- PDB-5b3h: The crystal structure of the JACKDAW/IDD10 bound to the heterodim... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b3h
TitleThe crystal structure of the JACKDAW/IDD10 bound to the heterodimeric SHR-SCR complex
Components
  • Protein SCARECROW
  • Protein SHORT-ROOT
  • Zinc finger protein JACKDAW
KeywordsTRANSCRIPTION / Transcription factor
Function / homology
Function and homology information


bundle sheath cell fate specification / radial pattern formation / regulation of hormone metabolic process / regulation of meristem growth / gravitropism / asymmetric cell division / leaf development / root development / regulation of epidermal cell differentiation / maintenance of protein location in nucleus ...bundle sheath cell fate specification / radial pattern formation / regulation of hormone metabolic process / regulation of meristem growth / gravitropism / asymmetric cell division / leaf development / root development / regulation of epidermal cell differentiation / maintenance of protein location in nucleus / regulation of cell division / negative regulation of mitotic cell cycle / protein localization to nucleus / cell redox homeostasis / recycling endosome / late endosome / sequence-specific DNA binding / early endosome / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / BIRD-IDD transcription factor, fourth C2HC zinc finger / BIRD-IDD transcription factor, third C2HC zinc finger / BIRD-IDD transcription factor, second C2H2 zinc finger / Transcription factor GRAS / GRAS domain family / GRAS family profile. ...: / : / : / : / BIRD-IDD transcription factor, fourth C2HC zinc finger / BIRD-IDD transcription factor, third C2HC zinc finger / BIRD-IDD transcription factor, second C2H2 zinc finger / Transcription factor GRAS / GRAS domain family / GRAS family profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger protein JACKDAW / Protein SCARECROW / Protein SHORT-ROOT
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHirano, Y. / Suyama, T. / Nakagawa, M. / Hakoshima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Grant-in-Aid for Scientific Research (C)50452529 Japan
Grant-in-Aid for Scientific Research on Innovative Areas22121002 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 1.2Nov 8, 2023Group: 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 SCARECROW
B: Protein SHORT-ROOT
D: Protein SCARECROW
E: Protein SHORT-ROOT
C: Zinc finger protein JACKDAW
F: Zinc finger protein JACKDAW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,24610
Polymers194,9846
Non-polymers2624
Water19811
1
A: Protein SCARECROW
B: Protein SHORT-ROOT
C: Zinc finger protein JACKDAW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6235
Polymers97,4923
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Protein SCARECROW
E: Protein SHORT-ROOT
F: Zinc finger protein JACKDAW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6235
Polymers97,4923
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.668, 203.389, 88.451
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 42055.730 Da / Num. of mol.: 2 / Fragment: UNP residues 275-653
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: 47279.145 Da / Num. of mol.: 2 / Fragment: UNP residues 112-531
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
#3: Protein Zinc finger protein JACKDAW / ID1-like zinc finger protein 3 / Protein indeterminate-domain 10


Mass: 8157.245 Da / Num. of mol.: 2 / Fragment: UNP residues 155-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: JKD, IDD10, IDZ3, At5g03150, F15A17.180 / Plasmid: pET49b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q700D2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: tris-HCl (pH 8.0) buffer, 8% w/v 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: Jul 4, 2013
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: 2.7→50 Å / Num. obs: 54886 / % possible obs: 98.9 % / Redundancy: 3.1 % / Net I/σ(I): 14.2
Reflection shellResolution: 2.7→2.75 Å / Rsym value: 0.08

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B3G

5b3g


Resolution: 2.7→39.438 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 2781 5.07 %
Rwork0.2077 --
obs0.2096 54886 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→39.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12772 0 4 11 12787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813049
X-RAY DIFFRACTIONf_angle_d0.96817688
X-RAY DIFFRACTIONf_dihedral_angle_d14.0854639
X-RAY DIFFRACTIONf_chiral_restr0.0521972
X-RAY DIFFRACTIONf_plane_restr0.0042280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74650.3371280.30642499X-RAY DIFFRACTION94
2.7465-2.79650.35851380.28322563X-RAY DIFFRACTION99
2.7965-2.85020.35121360.27632653X-RAY DIFFRACTION99
2.8502-2.90840.33261340.27642595X-RAY DIFFRACTION99
2.9084-2.97160.321450.26682588X-RAY DIFFRACTION99
2.9716-3.04070.29441280.2672666X-RAY DIFFRACTION99
3.0407-3.11670.33841430.26122578X-RAY DIFFRACTION99
3.1167-3.2010.34731530.26072653X-RAY DIFFRACTION99
3.201-3.29510.26251360.24792579X-RAY DIFFRACTION99
3.2951-3.40140.26121670.22632613X-RAY DIFFRACTION99
3.4014-3.52290.26191240.22292610X-RAY DIFFRACTION99
3.5229-3.66390.22511360.20712585X-RAY DIFFRACTION99
3.6639-3.83050.26661420.20632624X-RAY DIFFRACTION99
3.8305-4.03230.20161360.19232622X-RAY DIFFRACTION99
4.0323-4.28460.23941330.17372587X-RAY DIFFRACTION99
4.2846-4.6150.19711260.16232651X-RAY DIFFRACTION99
4.615-5.07850.20831690.1772582X-RAY DIFFRACTION99
5.0785-5.81140.23111430.20452646X-RAY DIFFRACTION99
5.8114-7.31410.22981270.20992640X-RAY DIFFRACTION99
7.3141-39.44180.19031370.15922571X-RAY DIFFRACTION96

+
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