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- PDB-4zhe: Crystal structure of the SeMet substituted Topless related protei... -

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Basic information

Entry
Database: PDB / ID: 4zhe
TitleCrystal structure of the SeMet substituted Topless related protein 2 (TPR2) N-terminal domain (1-209) from rice
ComponentsASPR2 protein
KeywordsTRANSCRIPTION / transcriptional corepressor / alpha-helical structure / tetrameric protein / plant transcriptional repression
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 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. ...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 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 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 General Medical Sciences (NIH/NIGMS)GM102545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104212 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK071662 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
DepositionApr 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 6, 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 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)100,3654
Polymers100,3654
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.149, 111.882, 144.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.998117, -0.059449, 0.015136), (-0.05754, 0.992806, 0.105004), (-0.021269, 0.103935, -0.994357)144.17496, -3.28844, 151.92398
3given(0.956945, 0.036661, 0.287945), (0.034421, -0.999325, 0.012841), (0.288222, -0.002377, -0.957561)-22.73504, 129.01103, 133.67032
4given(-0.952287, 0.008421, -0.305089), (0.027886, -0.993037, -0.114452), (-0.303928, -0.117499, 0.945421)161.3271, 139.50212, 33.99967

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Components

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


Mass: 25091.193 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 subsp. japonica (Japanese 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57 % / Description: Rod shaped.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% w/v PEG 3,350, 0.2 M Magnesium chloride, 0.1 M BIS-TRIS, pH 6.5, 19.6 mM 5-Methyl-6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. all: 43276 / Num. obs: 43276 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 19.1
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 15 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→44.283 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 3871 5.08 %RANDOM
Rwork0.1994 ---
obs0.2016 40217 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→44.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6804 0 0 378 7182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126942
X-RAY DIFFRACTIONf_angle_d1.4599320
X-RAY DIFFRACTIONf_dihedral_angle_d14.6212650
X-RAY DIFFRACTIONf_chiral_restr0.0651026
X-RAY DIFFRACTIONf_plane_restr0.0071178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53050.31811380.28112599X-RAY DIFFRACTION100
2.5305-2.56250.2681530.27532541X-RAY DIFFRACTION100
2.5625-2.59630.27751400.24762641X-RAY DIFFRACTION100
2.5963-2.63180.28781390.24632523X-RAY DIFFRACTION100
2.6318-2.66940.28441200.24622590X-RAY DIFFRACTION100
2.6694-2.70930.3191200.23892607X-RAY DIFFRACTION100
2.7093-2.75160.26831840.23862541X-RAY DIFFRACTION100
2.7516-2.79670.26051420.23642615X-RAY DIFFRACTION100
2.7967-2.84490.32651040.22682620X-RAY DIFFRACTION100
2.8449-2.89660.25981390.23662571X-RAY DIFFRACTION100
2.8966-2.95230.28211680.23822559X-RAY DIFFRACTION100
2.9523-3.01260.26071130.21832626X-RAY DIFFRACTION100
3.0126-3.07810.35811230.22392563X-RAY DIFFRACTION100
3.0781-3.14970.31751450.22452625X-RAY DIFFRACTION100
3.1497-3.22840.28521540.22132522X-RAY DIFFRACTION100
3.2284-3.31570.24731360.21592617X-RAY DIFFRACTION100
3.3157-3.41320.29341350.22422569X-RAY DIFFRACTION100
3.4132-3.52330.26411260.2112598X-RAY DIFFRACTION100
3.5233-3.64920.25311430.1952581X-RAY DIFFRACTION100
3.6492-3.79520.20381390.17852564X-RAY DIFFRACTION100
3.7952-3.96780.19271230.16812602X-RAY DIFFRACTION100
3.9678-4.17690.20051600.16872572X-RAY DIFFRACTION100
4.1769-4.43840.21721380.1632601X-RAY DIFFRACTION100
4.4384-4.78070.20991250.17162578X-RAY DIFFRACTION100
4.7807-5.26110.19771450.1762576X-RAY DIFFRACTION100
5.2611-6.02070.24381370.21592589X-RAY DIFFRACTION100
6.0207-7.57930.25691240.21322600X-RAY DIFFRACTION100
7.5793-44.29040.20871580.16732551X-RAY DIFFRACTION99

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