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- PDB-5c6v: Crystal structure of the rice Topless related protein 2 (TPR2) N-... -

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Basic information

Entry
Database: PDB / ID: 5c6v
TitleCrystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis NINJA peptide
Components
  • AFP homolog 2
  • ASPR2 protein
KeywordsTRANSCRIPTION / transcriptional corepressor / alpha-helical structure / tetrameric protein / plant transcriptional repression / Plant development
Function / homology
Function and homology information


positive regulation of pattern recognition receptor signaling pathway / regulation of leaf morphogenesis / jasmonic acid mediated signaling pathway / response to jasmonic acid / protein sequestering activity / defense response / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / nucleus / plasma membrane
Similarity search - Function
Ninja family / Tify domain binding domain / Tify domain binding domain / Topless family / : / : / TOPLESS, zinc finger domain / TPR1-like, CTLH-containing domain / : / LisH-like dimerisation domain ...Ninja family / Tify domain binding domain / Tify domain binding domain / Topless family / : / : / TOPLESS, zinc finger domain / TPR1-like, CTLH-containing domain / : / LisH-like dimerisation domain / 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 / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein TPR1 / AFP homolog 2
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKe, J. / Ma, H. / Gu, X. / Brunzelle, J.S. / Xu, H.E. / Melcher, K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104212 United States
CitationJournal: Sci Adv / Year: 2015
Title: Structural basis for recognition of diverse transcriptional repressors by the TOPLESS family of corepressors.
Authors: Ke, J. / Ma, H. / Gu, X. / Thelen, A. / Brunzelle, J.S. / Li, J. / Xu, H.E. / Melcher, K.
History
DepositionJun 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: ASPR2 protein
B: ASPR2 protein
C: ASPR2 protein
D: ASPR2 protein
E: AFP homolog 2
F: AFP homolog 2
G: AFP homolog 2
H: AFP homolog 2


Theoretical massNumber of molelcules
Total (without water)104,0838
Polymers104,0838
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.743, 65.042, 107.735
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ASPR2 protein / Os01g0254100 protein / Putative CTV.2 / Uncharacterized protein


Mass: 24903.611 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 1-209)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: P0705D01.10-1, ASPR2, Os01g0254100, OsJ_01134 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5NBT9
#2: Protein/peptide
AFP homolog 2 / Ninja-family protein At4g28910 / Novel interactor of JAZ


Mass: 1117.210 Da / Num. of mol.: 4 / Fragment: UNP residues 4-14 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SV55
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% w/v PEG 3,350, 0.2 M NaCl, 0.1 M BIS-TRIS pH 5.5, 3.0% w/v D-(+)-glucose monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2014
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 20063 / Num. obs: 20063 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 5.9
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHE

4zhe


Resolution: 3.1→48.495 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 34.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 1863 4.84 %Random selection
Rwork0.2323 ---
obs0.2349 20020 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6880 0 0 34 6914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087002
X-RAY DIFFRACTIONf_angle_d1.4119388
X-RAY DIFFRACTIONf_dihedral_angle_d16.372655
X-RAY DIFFRACTIONf_chiral_restr0.0651046
X-RAY DIFFRACTIONf_plane_restr0.0071178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.18390.38341370.32452815X-RAY DIFFRACTION100
3.1839-3.27760.39451500.30112822X-RAY DIFFRACTION99
3.2776-3.38330.33641560.28782822X-RAY DIFFRACTION99
3.3833-3.50420.33481600.27072783X-RAY DIFFRACTION99
3.5042-3.64450.30421240.25022846X-RAY DIFFRACTION99
3.6445-3.81030.30631810.23972794X-RAY DIFFRACTION99
3.8103-4.01110.24381450.21742807X-RAY DIFFRACTION99
4.0111-4.26220.24991290.21512812X-RAY DIFFRACTION99
4.2622-4.59110.26161660.20172829X-RAY DIFFRACTION99
4.5911-5.05270.29471110.20472879X-RAY DIFFRACTION100
5.0527-5.78280.26431310.2282826X-RAY DIFFRACTION99
5.7828-7.28170.32341520.24582836X-RAY DIFFRACTION100
7.2817-48.50140.2261210.19682789X-RAY DIFFRACTION98

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