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- PDB-8yew: TRIP4 ASCH domain in unliganded form -

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Basic information

Entry
Database: PDB / ID: 8yew
TitleTRIP4 ASCH domain in unliganded form
ComponentsActivating signal cointegrator 1
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 cytosolic 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 cytosolic 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 / 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
Activating signal cointegrator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
A: Activating signal cointegrator 1


Theoretical massNumber of molelcules
Total (without water)16,9241
Polymers16,9241
Non-polymers00
Water1,63991
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)29.387, 67.487, 73.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Li2SO4, 0.1 M Tris HCl (pH 8.5), and 30% (w/v) polyethylene glycol (PEG) 4,000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→49.56 Å / Num. obs: 11259 / % possible obs: 94.9 % / Redundancy: 2.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.079 / Rrim(I) all: 0.147 / Χ2: 0.35 / Net I/σ(I): 5.7 / Num. measured all: 33045
Reflection shellResolution: 1.9→2 Å / % possible obs: 96.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.546 / Num. measured all: 4942 / Num. unique obs: 1656 / CC1/2: 0.735 / Rpim(I) all: 0.344 / Rrim(I) all: 0.649 / Χ2: 0.29 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30.63 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 535 4.76 %
Rwork0.2069 --
obs0.2091 11230 93.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 0 91 1273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081214
X-RAY DIFFRACTIONf_angle_d0.9011639
X-RAY DIFFRACTIONf_dihedral_angle_d13.559465
X-RAY DIFFRACTIONf_chiral_restr0.052171
X-RAY DIFFRACTIONf_plane_restr0.008209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.090.31011210.23252715X-RAY DIFFRACTION96
2.09-2.390.29151360.21562665X-RAY DIFFRACTION96
2.39-3.020.2931470.2192668X-RAY DIFFRACTION94
3.02-30.60.20781310.19052647X-RAY DIFFRACTION89

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