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

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Basic information

Entry
Database: PDB / ID: 5jgc
TitleCrystal structure of the rice Topless related protein 2 (TPR2) N-terminal topless domain (1-209) L111A, L130A, L179A and I195A mutant
ComponentsProtein TPR1
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 / protein sequestering activity / regulation of DNA-templated transcription / 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 / Quinoprotein alcohol dehydrogenase-like superfamily ...: / 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 / 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
Similarity search - Domain/homology
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.08 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 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8012
Polymers24,7351
Non-polymers651
Water1,26170
1
A: Protein TPR1
hetero molecules

A: Protein TPR1
hetero molecules

A: Protein TPR1
hetero molecules

A: Protein TPR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2038
Polymers98,9414
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area10520 Å2
ΔGint-217 kcal/mol
Surface area40830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.516, 57.516, 174.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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: 24735.291 Da / Num. of mol.: 1 / 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) / Strain (production host): BL21 / References: UniProt: Q5NBT9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% w/v Polyethylene glycol 4000, 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2015
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 18565 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.1
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 12 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.08→27.319 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.04
RfactorNum. reflection% reflection
Rfree0.2457 1601 4.76 %
Rwork0.2098 --
obs0.2115 18499 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.08→27.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 1 70 1711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051670
X-RAY DIFFRACTIONf_angle_d0.8152243
X-RAY DIFFRACTIONf_dihedral_angle_d14.63628
X-RAY DIFFRACTIONf_chiral_restr0.033249
X-RAY DIFFRACTIONf_plane_restr0.003284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0801-2.14720.32441390.30292916X-RAY DIFFRACTION100
2.1472-2.22390.29441660.26032901X-RAY DIFFRACTION100
2.2239-2.31290.22631410.24752899X-RAY DIFFRACTION100
2.3129-2.41810.28671500.25092919X-RAY DIFFRACTION100
2.4181-2.54550.2931800.24422876X-RAY DIFFRACTION100
2.5455-2.70490.28911280.24672945X-RAY DIFFRACTION100
2.7049-2.91350.33581560.25192907X-RAY DIFFRACTION100
2.9135-3.20630.25421440.23842924X-RAY DIFFRACTION100
3.2063-3.66930.261070.22042949X-RAY DIFFRACTION100
3.6693-4.61930.20741510.16252905X-RAY DIFFRACTION100
4.6193-27.32170.1991390.17552916X-RAY DIFFRACTION99

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