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- PDB-9kyl: Crystal structure of human TRIP4 in complex with 11bp dsDNA -

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Basic information

Entry
Database: PDB / ID: 9kyl
TitleCrystal structure of human TRIP4 in complex with 11bp dsDNA
Components
  • Activating signal cointegrator 1
  • DNA (5'-D(*AP*GP*AP*AP*AP*TP*AP*CP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*TP*AP*AP*TP*TP*CP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / ASCH domain / dsDNA / complex / DNA BINDING PROTEIN-DNA 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 / Activating signal cointegrator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGuo, W.T. / Meng, C.Y. / Wen, Y. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural analysis of ASCH domain-containing proteins and their implications for nucleotide processing.
Authors: Meng, C. / Shi, X. / Guo, W. / Jian, X. / Zhao, J. / Wen, Y. / Wang, R. / Li, Y. / Xu, S. / Chen, H. / Zhang, J. / Chen, M. / Chen, H. / Wu, B.
History
DepositionDec 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activating signal cointegrator 1
C: DNA (5'-D(*CP*GP*GP*TP*AP*AP*TP*TP*CP*T)-3')
D: DNA (5'-D(*AP*GP*AP*AP*AP*TP*AP*CP*CP*G)-3')
B: Activating signal cointegrator 1


Theoretical massNumber of molelcules
Total (without water)45,5924
Polymers45,5924
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.339, 74.798, 73.304
Angle α, β, γ (deg.)90.000, 102.608, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 434 through 520 or (resid 521...
d_2ens_1(chain "B" and (resid 434 through 567 or (resid 568...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 434 - 571 / Label seq-ID: 25 - 162

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BD

NCS oper: (Code: givenMatrix: (-0.868638088938, -0.495447132024, 9.90734408269E-5), (-0.491590185714, 0.861850996126, -0.124707456819), (0.0617005652791, -0.108374350498, -0.992193549867)Vector: 15. ...NCS oper: (Code: given
Matrix: (-0.868638088938, -0.495447132024, 9.90734408269E-5), (-0.491590185714, 0.861850996126, -0.124707456819), (0.0617005652791, -0.108374350498, -0.992193549867)
Vector: 15.7533405384, 8.45295611763, 67.2702712789)

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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: 19747.652 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(DE3) (bacteria) / References: UniProt: Q15650
#2: DNA chain DNA (5'-D(*CP*GP*GP*TP*AP*AP*TP*TP*CP*T)-3')


Mass: 3035.003 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*AP*AP*AP*TP*AP*CP*CP*G)-3')


Mass: 3062.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M L-Proline, 0.1 M HEPES pH 7.5, 10% 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: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 21150 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.065 / Rrim(I) all: 0.154 / Net I/σ(I): 3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2072 / CC1/2: 0.918 / Rpim(I) all: 0.232 / Rrim(I) all: 0.516 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→29.83 Å / SU ML: 0.2593 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 28.5026
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 936 5.15 %
Rwork0.2142 17251 -
obs0.2167 18187 85.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.77 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 405 0 162 2806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952757
X-RAY DIFFRACTIONf_angle_d1.16973813
X-RAY DIFFRACTIONf_chiral_restr0.0668403
X-RAY DIFFRACTIONf_plane_restr0.0111418
X-RAY DIFFRACTIONf_dihedral_angle_d26.62591062
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.920594485762 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.270.334790.22331691X-RAY DIFFRACTION58.42
2.27-2.410.27581110.23881962X-RAY DIFFRACTION68.24
2.41-2.60.27361250.25332256X-RAY DIFFRACTION79.42
2.6-2.860.30911420.25922673X-RAY DIFFRACTION92.9
2.86-3.270.28561510.23772890X-RAY DIFFRACTION99.67
3.27-4.120.28031610.19682856X-RAY DIFFRACTION99.47
4.12-29.830.21021670.18342923X-RAY DIFFRACTION99.58

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