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- PDB-8yxw: TRIP4 ASCH domain in complex with a 12bp dsDNA (5'-TGAGGTACCTCC-3') -

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Basic information

Entry
Database: PDB / ID: 8yxw
TitleTRIP4 ASCH domain in complex with a 12bp dsDNA (5'-TGAGGTACCTCC-3')
Components
  • Activating signal cointegrator 1
  • DNA (5'-D(*GP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*A)-3')
  • DNA (5'-D(*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*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 estrogen receptor binding / nuclear 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 estrogen receptor binding / nuclear receptor binding / neuromuscular junction / protease binding / transcription coactivator activity / nuclear body / centrosome / protein kinase binding / regulation of DNA-templated transcription / 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 / DNA (> 10) / Activating signal cointegrator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionApr 3, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,8324
Polymers39,8324
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.597, 66.597, 199.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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: 16252.862 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*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*A)-3')


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*C)-3')


Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate 0.1 M BIS-TRIS pH 5.5 25% w/v Polyethylene glycol 3,350

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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 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29191 / % possible obs: 100 % / Redundancy: 15.7 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.039 / Rrim(I) all: 0.154 / Χ2: 0.67 / Net I/σ(I): 3 / Num. measured all: 456895
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.1414.30.80614400.8950.9720.2240.8370.53100
2.14-2.18150.72914930.9250.980.1930.7540.551100
2.18-2.22150.65314490.9290.9810.1730.6760.561100
2.22-2.26150.59714470.940.9840.1620.6190.552100
2.26-2.31150.51114560.960.990.1370.5290.579100
2.31-2.37150.49314520.9580.9890.1290.510.567100
2.37-2.42150.41414360.9740.9930.1080.4280.59100
2.42-2.49150.38214510.9730.9930.10.3950.591100
2.49-2.56150.3414940.9850.9960.090.3520.609100
2.56-2.65150.2814460.9810.9950.0750.290.628100
2.65-2.74150.25514460.9810.9950.0690.2640.678100
2.74-2.85150.21914410.9870.9970.0570.2260.684100
2.85-2.98150.19114470.9880.9970.0510.1980.722100
2.98-3.14150.16714630.9910.9980.0430.1730.738100
3.14-3.33150.13614930.9930.9980.0350.140.811100
3.33-3.59150.12114470.9940.9980.0320.1250.838100
3.59-3.95150.1114680.9940.9990.0290.1140.89199.9
3.95-4.52150.114610.9950.9990.0260.1030.832100
4.52-5.7150.09814680.9960.9990.0250.1010.759100
5.7-5015.20.0914930.9950.9990.0240.0940.67299.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.83 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 1455 5.06 %
Rwork0.1943 --
obs0.1965 28780 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 486 0 282 3052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082892
X-RAY DIFFRACTIONf_angle_d0.9754010
X-RAY DIFFRACTIONf_dihedral_angle_d19.2821126
X-RAY DIFFRACTIONf_chiral_restr0.055426
X-RAY DIFFRACTIONf_plane_restr0.011428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.261400.23212679X-RAY DIFFRACTION97
2.17-2.260.33331450.22652702X-RAY DIFFRACTION98
2.26-2.360.24311480.22342706X-RAY DIFFRACTION98
2.37-2.490.31661390.2182699X-RAY DIFFRACTION98
2.49-2.650.25581500.22662741X-RAY DIFFRACTION99
2.65-2.850.22761430.22432734X-RAY DIFFRACTION99
2.85-3.140.2611470.21862751X-RAY DIFFRACTION100
3.14-3.590.2441470.17482774X-RAY DIFFRACTION100
3.59-4.520.1871530.15992766X-RAY DIFFRACTION100
4.52-32.830.23561430.18552773X-RAY DIFFRACTION100

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