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

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Basic information

Entry
Database: PDB / ID: 8yfi
TitleTRIP4 ASCH domain in complex with a 12bp dsDNA (5'-TGAGGTACCTCA-3')
Components
  • Activating signal cointegrator 1
  • DNA (5'-D(*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*A)-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 / DNA (> 10) / Activating signal cointegrator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Aug 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(*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)20,5862
Polymers20,5862
Non-polymers00
Water2,000111
1
A: Activating signal cointegrator 1
B: DNA (5'-D(*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*A)-3')

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


Theoretical massNumber of molelcules
Total (without water)41,1724
Polymers41,1724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)66.263, 66.263, 199.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

21B-123-

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.: 1
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(*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*CP*A)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 2.0 M (NH4)2SO4

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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: 2.02→50 Å / Num. obs: 17897 / % possible obs: 99.7 % / Redundancy: 6.1 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Χ2: 0.436 / Net I/σ(I): 4.3 / Num. measured all: 109981
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.02-2.056.40.718660.8580.9610.3010.7730.44699.8
2.05-2.096.50.5788620.90.9730.2420.6290.48699.8
2.09-2.136.40.4868680.9120.9770.2050.5290.43599.9
2.13-2.186.40.4188640.930.9820.1760.4540.448100
2.18-2.226.20.388820.9490.9870.1630.4150.445100
2.22-2.2760.3088700.9590.990.1340.3370.49399.9
2.27-2.336.20.2628650.9690.9920.1120.2860.45799.7
2.33-2.396.30.2318810.9780.9940.0990.2510.44999.9
2.39-2.476.10.2048810.9760.9940.0890.2230.465100
2.47-2.546.30.1728740.9870.9970.0740.1880.46299.9
2.54-2.646.40.148840.9910.9980.0590.1520.457100
2.64-2.746.30.1348920.9920.9980.0570.1460.5100
2.74-2.876.20.18810.9940.9990.0430.1090.476100
2.87-3.026.10.0819050.9950.9990.0360.0890.45100
3.02-3.216.20.0618880.99810.0260.0670.442100
3.21-3.456.10.0489110.99810.0210.0520.462100
3.45-3.86.30.0449150.99810.0190.0480.44100
3.8-4.355.80.0359290.99910.0150.0380.373100
4.35-5.485.80.039480.99910.0130.0330.29399.2
5.48-505.20.02510310.99910.0120.0280.23296.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→33.131 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 893 5 %
Rwork0.2039 --
obs0.2061 17846 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→33.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 243 0 111 1496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081446
X-RAY DIFFRACTIONf_angle_d0.9772005
X-RAY DIFFRACTIONf_dihedral_angle_d12.763829
X-RAY DIFFRACTIONf_chiral_restr0.057213
X-RAY DIFFRACTIONf_plane_restr0.006214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.14640.28731450.25512742X-RAY DIFFRACTION100
2.1464-2.31210.27521430.23312736X-RAY DIFFRACTION100
2.3121-2.54470.29511470.23492784X-RAY DIFFRACTION100
2.5447-2.91280.26821470.23522797X-RAY DIFFRACTION100
2.9128-3.6690.24971510.19312851X-RAY DIFFRACTION100
3.669-33.130.22031600.1823043X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.051 Å / Origin y: -23.1232 Å / Origin z: -5.5993 Å
111213212223313233
T0.2229 Å2-0.0261 Å2-0.0204 Å2-0.2657 Å20.0716 Å2--0.2429 Å2
L1.4062 °20.3427 °2-0.0001 °2-0.9646 °20.2361 °2--1.9353 °2
S0.0265 Å °-0.3081 Å °-0.2435 Å °-0.0239 Å °-0.0207 Å °-0.05 Å °0.2225 Å °-0.1575 Å °-0.0097 Å °
Refinement TLS groupSelection details: all

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