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- PDB-5b3h: The crystal structure of the JACKDAW/IDD10 bound to the heterodim... -

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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 meristem growth / regulation of hormone metabolic process / 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 meristem growth / regulation of hormone metabolic process / gravitropism / asymmetric cell division / leaf development / root development / regulation of epidermal cell differentiation / maintenance of protein location in nucleus / negative regulation of mitotic cell cycle / regulation of cell division / 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 / zinc ion binding / nucleus
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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)

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Experimental details

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Experiment

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

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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

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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

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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

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