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- PDB-5c7e: Crystal structure of the rice Topless related protein 2 (TPR2) N-... -

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Basic information

Entry
Database: PDB / ID: 5c7e
TitleCrystal structure of the rice Topless related protein 2 (TPR2) N-terminal domain (1-209) in complex with Arabidopsis IAA10 peptide
Components
  • ASPR2 protein
  • Auxin-responsive protein IAA10
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 / 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 IAA10 / Protein TPR1
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 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: ASPR2 protein
F: ASPR2 protein
G: Auxin-responsive protein IAA10
H: Auxin-responsive protein IAA10
I: Auxin-responsive protein IAA10
J: Auxin-responsive protein IAA10
K: Auxin-responsive protein IAA10
L: Auxin-responsive protein IAA10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,77618
Polymers156,38312
Non-polymers3926
Water41423
1
A: ASPR2 protein
B: ASPR2 protein
C: ASPR2 protein
D: ASPR2 protein
G: Auxin-responsive protein IAA10
H: Auxin-responsive protein IAA10
I: Auxin-responsive protein IAA10
J: Auxin-responsive protein IAA10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,51712
Polymers104,2568
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: ASPR2 protein
F: ASPR2 protein
K: Auxin-responsive protein IAA10
L: Auxin-responsive protein IAA10
hetero molecules

E: ASPR2 protein
F: ASPR2 protein
K: Auxin-responsive protein IAA10
L: Auxin-responsive protein IAA10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,51712
Polymers104,2568
Non-polymers2624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Unit cell
Length a, b, c (Å)162.668, 162.668, 157.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 24903.611 Da / Num. of mol.: 6 / 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 IAA10 / Indoleacetic acid-induced protein 10


Mass: 1160.273 Da / Num. of mol.: 6 / Fragment: UNP residues 41-51 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q38828
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 4 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 3,350, 0.2 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07818 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 15, 2014
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07818 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 44008 / Num. obs: 44008 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.3
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 7.6 % / 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: 3.1→44.995 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 4287 5.09 %Random selection
Rwork0.1961 ---
obs0.1977 43939 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→44.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10629 0 6 23 10658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810834
X-RAY DIFFRACTIONf_angle_d1.43614561
X-RAY DIFFRACTIONf_dihedral_angle_d17.0814120
X-RAY DIFFRACTIONf_chiral_restr0.061624
X-RAY DIFFRACTIONf_plane_restr0.0081838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.13530.45681650.35272673X-RAY DIFFRACTION100
3.1353-3.17220.35881570.36162587X-RAY DIFFRACTION100
3.1722-3.21080.37651120.35022688X-RAY DIFFRACTION100
3.2108-3.25150.29821430.33572717X-RAY DIFFRACTION100
3.2515-3.29420.35411650.30152601X-RAY DIFFRACTION100
3.2942-3.33930.34131390.2972703X-RAY DIFFRACTION100
3.3393-3.3870.30331370.30122652X-RAY DIFFRACTION100
3.387-3.43760.34521390.28592700X-RAY DIFFRACTION100
3.4376-3.49130.3281630.27152639X-RAY DIFFRACTION100
3.4913-3.54850.26931330.26772705X-RAY DIFFRACTION100
3.5485-3.60960.27471260.25432678X-RAY DIFFRACTION100
3.6096-3.67530.32541190.23992650X-RAY DIFFRACTION100
3.6753-3.74590.29311530.24732675X-RAY DIFFRACTION100
3.7459-3.82230.24161560.22442682X-RAY DIFFRACTION100
3.8223-3.90540.27481360.2152638X-RAY DIFFRACTION100
3.9054-3.99620.19381330.20312667X-RAY DIFFRACTION100
3.9962-4.09610.28061200.20782738X-RAY DIFFRACTION100
4.0961-4.20670.23461500.20162657X-RAY DIFFRACTION100
4.2067-4.33040.2351450.18252650X-RAY DIFFRACTION100
4.3304-4.47010.2221480.18192672X-RAY DIFFRACTION100
4.4701-4.62970.23051290.17952740X-RAY DIFFRACTION100
4.6297-4.81490.231520.17942670X-RAY DIFFRACTION100
4.8149-5.03370.22511520.16542660X-RAY DIFFRACTION100
5.0337-5.29870.21261350.17582622X-RAY DIFFRACTION100
5.2987-5.63010.24751580.19292683X-RAY DIFFRACTION100
5.6301-6.06390.19571280.19692659X-RAY DIFFRACTION100
6.0639-6.67230.23431530.18462680X-RAY DIFFRACTION100
6.6723-7.63380.17211590.16292631X-RAY DIFFRACTION100
7.6338-9.60230.15881410.12222686X-RAY DIFFRACTION100
9.6023-44.99960.141410.14292612X-RAY DIFFRACTION97

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