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- PDB-8yey: TRIP4 ASCH domain in complex with ssDNA-1 -

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Basic information

Entry
Database: PDB / ID: 8yey
TitleTRIP4 ASCH domain in complex with ssDNA-1
Components
  • Activating signal cointegrator 1
  • DNA (5'-D(*GP*TP*TP*TP*C)-3')
KeywordsDNA BINDING PROTEIN / ASCH Domain / Complex
Function / homology
Function and homology information


RQC-trigger complex / regulation of myoblast differentiation / ribosome disassembly / ribosome-associated ubiquitin-dependent protein catabolic process / histone acetyltransferase binding / ubiquitin-like protein ligase binding / estrogen receptor signaling pathway / rescue of stalled ribosome / nuclear receptor binding / nuclear estrogen receptor binding ...RQC-trigger complex / regulation of myoblast differentiation / ribosome disassembly / ribosome-associated ubiquitin-dependent protein catabolic process / histone acetyltransferase binding / ubiquitin-like protein ligase binding / estrogen receptor signaling pathway / rescue of stalled ribosome / nuclear receptor binding / nuclear estrogen receptor binding / neuromuscular junction / protease binding / transcription coactivator activity / nuclear body / centrosome / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
TRIP4, third domain / TRI4 N-terminal domain / Zinc finger, C2HC5-type / Activating signal cointegrator 1-like / Putative zinc finger motif, C2HC5-type / ASCH / ASCH domain / ASCH domain / PUA-like superfamily
Similarity search - Domain/homology
DNA / Activating signal cointegrator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDing, J. / Yang, H. / Hu, C.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030305 China
CitationJournal: Structure / Year: 2024
Title: Biochemical and structural characterization of the DNA-binding properties of human TRIP4 ASCH domain reveals insights into its functional role.
Authors: Hu, C. / Chen, Z. / Wang, G. / Yang, H. / Ding, J.
History
DepositionFeb 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Activating signal cointegrator 1
D: DNA (5'-D(*GP*TP*TP*TP*C)-3')
A: Activating signal cointegrator 1
B: DNA (5'-D(*GP*TP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)36,8194
Polymers36,8194
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.077, 29.438, 126.462
Angle α, β, γ (deg.)90.00, 89.91, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11C-666-

HOH

21A-674-

HOH

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Components

#1: Protein Activating signal cointegrator 1 / ASC-1 / Thyroid receptor-interacting protein 4 / TR-interacting protein 4 / TRIP-4


Mass: 16923.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIP4, RQT4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q15650
#2: DNA chain DNA (5'-D(*GP*TP*TP*TP*C)-3')


Mass: 1486.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bicine (pH 8.5) and 20% (w/v) PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19378 / % possible obs: 99 % / Redundancy: 5.1 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.058 / Rrim(I) all: 0.133 / Χ2: 1.357 / Net I/σ(I): 6.1 / Num. measured all: 98282
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.034.10.438690.7990.9420.230.4910.80992.9
2.03-2.074.80.3489480.9220.9790.1720.390.82399.9
2.07-2.114.80.33410230.920.9790.1660.3740.86699.6
2.11-2.1550.3449100.9170.9780.1670.3840.89298.7
2.15-2.24.90.2929690.9540.9880.1450.3281.04599.4
2.2-2.254.80.2899700.9230.980.1430.3231.00898.5
2.25-2.3150.3069430.9340.9830.150.3421.07799.7
2.31-2.375.10.2669650.9590.990.1270.2961.08899.9
2.37-2.444.90.2439590.9470.9860.120.2721.14698.4
2.44-2.525.20.249600.9620.990.1150.2671.21799.7
2.52-2.615.30.2349610.9610.990.1090.2591.28799.7
2.61-2.715.30.1919850.9750.9940.0910.2121.32299.6
2.71-2.845.30.1739700.9840.9960.0830.1921.33199.3
2.84-2.995.20.1599600.9840.9960.0760.1771.53798.6
2.99-3.175.30.1299790.9890.9970.0610.1431.64499.9
3.17-3.425.40.1129760.9870.9970.0530.1251.59199.6
3.42-3.765.50.09510020.990.9980.0440.1051.804100
3.76-4.315.20.0819930.9930.9980.0390.091.8399.9
4.31-5.435.30.0739960.9910.9980.0360.0821.8199.6
5.43-504.90.08910400.9870.9970.0480.1022.5397.9

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Processing

SoftwareName: PHENIX / Version: (1.17.1_3660: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.154 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 962 4.97 %
Rwork0.2014 --
obs0.2042 19373 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 196 0 192 2752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072652
X-RAY DIFFRACTIONf_angle_d0.9293622
X-RAY DIFFRACTIONf_dihedral_angle_d14.4591584
X-RAY DIFFRACTIONf_chiral_restr0.049382
X-RAY DIFFRACTIONf_plane_restr0.006430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.09950.2971300.21892476X-RAY DIFFRACTION94
2.0995-2.2310.28891380.21722585X-RAY DIFFRACTION99
2.231-2.40330.28071390.22772648X-RAY DIFFRACTION99
2.4033-2.64510.2711360.22862620X-RAY DIFFRACTION100
2.6451-3.02770.26411400.22982633X-RAY DIFFRACTION99
3.0277-3.81420.26541420.17992673X-RAY DIFFRACTION100
3.8142-42.150.2241370.1842776X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.4993 Å / Origin y: -15.9208 Å / Origin z: 31.6214 Å
111213212223313233
T0.168 Å2-0.0068 Å2-0.0036 Å2-0.1503 Å20.0376 Å2--0.1863 Å2
L0.3144 °2-0.0351 °20.0142 °2-0.3245 °20.4472 °2--0.838 °2
S-0.0739 Å °-0.0179 Å °0.0253 Å °-0.0086 Å °0.0198 Å °0.0156 Å °-0.0012 Å °0.0446 Å °0.0523 Å °
Refinement TLS groupSelection details: all

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