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- PDB-5j9k: Crystal structure of the rice Topless related protein 2 (TPR2) N-... -

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Basic information

Entry
Database: PDB / ID: 5j9k
TitleCrystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) in complex with rice D53 repressor EAR peptide motif
Components
  • Protein TPR1
  • rice D53 peptide 794-808
KeywordsTRANSCRIPTION / TRANSCRIPTION REPRESSION / TRANSCRIPTIONAL COREPRESSOR TOPLESS / ALPHA-HELICAL STRUCTURE / TETRAMER / TRANSCRIPTIONAL REPRESSOR D53
Function / homology
Function and homology information


positive regulation of pattern recognition receptor signaling pathway / response to strigolactone / protein sequestering activity / regulation of DNA-templated transcription / nucleus / plasma membrane
Similarity search - Function
: / TOPLESS, zinc finger domain / Topless family / 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 / Clp repeat (R) domain profile. ...: / TOPLESS, zinc finger domain / Topless family / 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 / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein DWARF 53 / Protein TPR1
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 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
Citation
Journal: Sci Adv / Year: 2017
Title: A D53 repression motif induces oligomerization of TOPLESS corepressors and promotes assembly of a corepressor-nucleosome complex.
Authors: Ma, H. / Duan, J. / Ke, J. / He, Y. / Gu, X. / Xu, T.H. / Yu, H. / Wang, Y. / Brunzelle, J.S. / Jiang, Y. / Rothbart, S.B. / Xu, H.E. / Li, J. / Melcher, K.
#1: Journal: 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
DepositionApr 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein TPR1
B: Protein TPR1
C: rice D53 peptide 794-808
D: rice D53 peptide 794-808
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6686
Polymers53,5374
Non-polymers1312
Water1,56787
1
A: Protein TPR1
B: Protein TPR1
C: rice D53 peptide 794-808
D: rice D53 peptide 794-808
hetero molecules

A: Protein TPR1
B: Protein TPR1
C: rice D53 peptide 794-808
D: rice D53 peptide 794-808
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,33612
Polymers107,0748
Non-polymers2624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14940 Å2
ΔGint-87 kcal/mol
Surface area43540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.718, 59.638, 171.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein TPR1 / Aberrant spikelet and panicle1-related 2 / Protein ASP1-RELATED 2 / OsASPR2 / Topless-related ...Aberrant spikelet and panicle1-related 2 / Protein ASP1-RELATED 2 / OsASPR2 / Topless-related protein 1 / Topless-related protein 2 / OsTPR2


Mass: 24903.611 Da / Num. of mol.: 2 / Fragment: N-terminal topless domain (UNP residues 1-209)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice)
Gene: TPR1, ASPR2, TPR2, Os01g0254100, LOC_Os01g15020, OsJ_01134, OSNPB_010254100, P0705D01.10-1
Production host: Escherichia coli (E. coli) / References: UniProt: Q5NBT9
#2: Protein/peptide rice D53 peptide 794-808


Mass: 1864.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DNLIYLDLNLQ / Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Production host: Escherichia coli (E. coli) / References: UniProt: Q2RBP2*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% w/v Polyethylene glycol 3350, 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 19882 / % possible obs: 99.4 % / Redundancy: 8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.6
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.55→34.377 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1890 5.12 %
Rwork0.2147 --
obs0.2166 36936 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→34.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3551 0 2 87 3640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063617
X-RAY DIFFRACTIONf_angle_d0.984855
X-RAY DIFFRACTIONf_dihedral_angle_d15.8911380
X-RAY DIFFRACTIONf_chiral_restr0.033540
X-RAY DIFFRACTIONf_plane_restr0.003612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.61380.38491140.35192521X-RAY DIFFRACTION98
2.6138-2.68440.36241580.32622475X-RAY DIFFRACTION100
2.6844-2.76340.35561570.30842480X-RAY DIFFRACTION99
2.7634-2.85250.31981160.29772497X-RAY DIFFRACTION99
2.8525-2.95440.33251270.28542516X-RAY DIFFRACTION100
2.9544-3.07260.29051400.26932518X-RAY DIFFRACTION99
3.0726-3.21240.31181470.24992488X-RAY DIFFRACTION99
3.2124-3.38160.30361300.23792488X-RAY DIFFRACTION99
3.3816-3.59330.30451490.22892513X-RAY DIFFRACTION99
3.5933-3.87040.20721360.21042501X-RAY DIFFRACTION100
3.8704-4.25920.21370.17562527X-RAY DIFFRACTION99
4.2592-4.8740.21641290.17582514X-RAY DIFFRACTION100
4.874-6.13510.23441250.20562495X-RAY DIFFRACTION99
6.1351-34.38010.21581250.17232513X-RAY DIFFRACTION99

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