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- PDB-5c7f: Crystal structure of the rice Topless related protein 2 (TPR2) N-... -

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Basic information

Entry
Database: PDB / ID: 5c7f
TitleCrystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis IAA1 peptide
Components
  • ASPR2 protein
  • Auxin-responsive protein IAA1
KeywordsTRANSCRIPTION / transcriptional corepressor / alpha-helical structure / tetrameric protein / plant transcriptional repression / Plant development / auxin signaling
Function / homology
Function and homology information


positive regulation of pattern recognition receptor signaling pathway / response to auxin / auxin-activated signaling pathway / protein sequestering activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding / nucleus / plasma membrane
Similarity search - Function
AUX/IAA protein / Topless family / : / : / TOPLESS, zinc finger domain / TPR1-like, CTLH-containing domain / AUX/IAA domain / AUX/IAA family / : / LisH-like dimerisation domain ...AUX/IAA protein / Topless family / : / : / TOPLESS, zinc finger domain / TPR1-like, CTLH-containing domain / AUX/IAA domain / AUX/IAA family / : / LisH-like dimerisation domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / : / PB1 domain 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
Auxin-responsive protein IAA1 / Protein TPR1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 24, 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: Auxin-responsive protein IAA1
F: Auxin-responsive protein IAA1
G: Auxin-responsive protein IAA1
H: Auxin-responsive protein IAA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,54710
Polymers104,4168
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14980 Å2
ΔGint-92 kcal/mol
Surface area40860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.509, 129.284, 79.171
Angle α, β, γ (deg.)90.00, 110.11, 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
Auxin-responsive protein IAA1 / Indoleacetic acid-induced protein 1


Mass: 1200.386 Da / Num. of mol.: 4 / Fragment: UNP residues 10-20 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P49677
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 56.3 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2014
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 30324 / Num. obs: 30324 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 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: 2.7→41.863 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 30.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 3072 5.15 %Random selection
Rwork0.2226 ---
obs0.2243 59696 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→41.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6839 0 2 0 6841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086963
X-RAY DIFFRACTIONf_angle_d1.2999341
X-RAY DIFFRACTIONf_dihedral_angle_d16.5632627
X-RAY DIFFRACTIONf_chiral_restr0.0591038
X-RAY DIFFRACTIONf_plane_restr0.0061176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74220.42391360.37482541X-RAY DIFFRACTION100
2.7422-2.78720.42871350.35162625X-RAY DIFFRACTION100
2.7872-2.83520.33251280.33062540X-RAY DIFFRACTION100
2.8352-2.88680.32791450.32192555X-RAY DIFFRACTION100
2.8868-2.94230.27951250.30252619X-RAY DIFFRACTION100
2.9423-3.00230.31021510.27932593X-RAY DIFFRACTION100
3.0023-3.06760.32991410.30012594X-RAY DIFFRACTION100
3.0676-3.13890.35521560.30092501X-RAY DIFFRACTION100
3.1389-3.21740.37531120.2832626X-RAY DIFFRACTION100
3.2174-3.30440.33691200.28292607X-RAY DIFFRACTION100
3.3044-3.40150.29911620.26432527X-RAY DIFFRACTION100
3.4015-3.51130.31271290.25052592X-RAY DIFFRACTION100
3.5113-3.63670.2911570.24392582X-RAY DIFFRACTION100
3.6367-3.78220.25421270.22152561X-RAY DIFFRACTION100
3.7822-3.95420.2511300.20882589X-RAY DIFFRACTION100
3.9542-4.16250.19611500.19192599X-RAY DIFFRACTION100
4.1625-4.42310.20531530.18632513X-RAY DIFFRACTION100
4.4231-4.76410.21141390.18572599X-RAY DIFFRACTION100
4.7641-5.24280.251340.18252588X-RAY DIFFRACTION100
5.2428-5.99950.25871280.21032588X-RAY DIFFRACTION100
5.9995-7.55150.21941630.20772557X-RAY DIFFRACTION100
7.5515-41.86850.19071510.15742528X-RAY DIFFRACTION99

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