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

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Basic information

Entry
Database: PDB / ID: 8yxx
TitleTRIP4 ASCH domain in complex with a 12bp dsDNA (5'-TGAGGTACCTCG-3')
Components
  • Activating signal cointegrator 1
  • DNA (5'-D(*CP*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*G)-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 / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
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: 2.65 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(*CP*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*G)-3')


Theoretical massNumber of molelcules
Total (without water)39,8324
Polymers39,8324
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.897, 66.897, 203.101
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(*CP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*A)-3')


Mass: 3647.393 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*G)-3')


Mass: 3678.403 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.: 119 / 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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Succinic acid pH 7.0 0.1 M BICINE pH 8.5 30% v/v Polyethylene glycol monomethyl ether 550

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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: 2.65→50 Å / Num. obs: 14939 / % possible obs: 100 % / Redundancy: 20.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.037 / Rrim(I) all: 0.17 / Χ2: 0.551 / Net I/σ(I): 3.1 / Num. measured all: 306032
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.65-2.719.80.7967540.9360.9830.1830.8170.493100
2.7-2.7419.20.7567380.9540.9880.1770.7760.50199.7
2.74-2.817.70.6287470.9490.9870.1540.6470.452100
2.8-2.8521.20.6217390.9730.9930.1370.6360.497100
2.85-2.9221.60.5297560.980.9950.1150.5420.525100
2.92-2.9821.50.4847190.9860.9960.1060.4950.523100
2.98-3.0621.20.447710.9850.9960.0970.450.545100
3.06-3.1421.10.3367260.9920.9980.0740.3440.556100
3.14-3.2321.10.2937380.9920.9980.0650.3010.605100
3.23-3.34210.2347690.9940.9990.0520.240.653100
3.34-3.4620.70.1827230.9970.9990.0410.1870.667100
3.46-3.618.80.1697440.9960.9990.040.1740.64100
3.6-3.7619.80.1387560.9980.9990.0320.1410.601100
3.76-3.9621.80.1337540.9970.9990.0290.1360.616100
3.96-4.2121.50.1157390.99810.0250.1180.585100
4.21-4.5321.10.0967410.99810.0210.0990.553100
4.53-4.9920.60.0917480.9960.9990.0210.0930.511100
4.99-5.7118.90.0947480.99810.0220.0970.477100
5.71-7.1921.60.0987580.99810.0210.10.481100
7.19-5019.40.0637710.9960.9990.0150.0650.51999.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→44.02 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 740 5.02 %
Rwork0.2113 --
obs0.2128 14729 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 486 0 119 2889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082892
X-RAY DIFFRACTIONf_angle_d0.9614010
X-RAY DIFFRACTIONf_dihedral_angle_d20.3011126
X-RAY DIFFRACTIONf_chiral_restr0.054426
X-RAY DIFFRACTIONf_plane_restr0.01428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.860.32371460.26272774X-RAY DIFFRACTION98
2.86-3.140.24421510.23572784X-RAY DIFFRACTION99
3.14-3.60.25721510.22222802X-RAY DIFFRACTION99
3.6-4.530.20551490.18112824X-RAY DIFFRACTION100
4.54-44.020.23821430.20582805X-RAY DIFFRACTION98

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