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- PDB-8tly: Human ASCC1 Phosphodiesterase/Ligase Domain -

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Basic information

Entry
Database: PDB / ID: 8tly
TitleHuman ASCC1 Phosphodiesterase/Ligase Domain
ComponentsActivating signal cointegrator 1 complex subunit 1
KeywordsRNA BINDING PROTEIN / alkylation response / RNA damage / KH domain / phosphoesterase domain / RNA ligase domain
Function / homology
Function and homology information


ALKBH3 mediated reversal of alkylation damage / DNA alkylation repair / DNA repair complex / DNA duplex unwinding / neuromuscular junction / transcription regulator complex / nuclear speck / regulation of DNA-templated transcription / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Activating signal cointegrator 1 complex subunit 1 / : / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Cyclic phosphodiesterase / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily
Similarity search - Domain/homology
Activating signal cointegrator 1 complex subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTsutakawa, S.E. / Tainer, J.A. / Arvai, A.S. / Thapar, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220430 United States
Cancer Prevention and Research Institute of Texas (CPRIT) United States
Citation
Journal: J.Biol.Chem. / Year: 2024
Title: ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase.
Authors: Chinnam, N.B. / Thapar, R. / Arvai, A.S. / Sarker, A.H. / Soll, J.M. / Paul, T. / Syed, A. / Rosenberg, D.J. / Hammel, M. / Bacolla, A. / Katsonis, P. / Asthana, A. / Tsai, M.S. / Ivanov, I. ...Authors: Chinnam, N.B. / Thapar, R. / Arvai, A.S. / Sarker, A.H. / Soll, J.M. / Paul, T. / Syed, A. / Rosenberg, D.J. / Hammel, M. / Bacolla, A. / Katsonis, P. / Asthana, A. / Tsai, M.S. / Ivanov, I. / Lichtarge, O. / Silverman, R.H. / Mosammaparast, N. / Tsutakawa, S.E. / Tainer, J.A.
#1: Journal: Proteins / Year: 2021
Title: Target highlights in CASP14: Analysis of models by structure providers.
Authors: Alexander, L.T. / Lepore, R. / Kryshtafovych, A. / Adamopoulos, A. / Alahuhta, M. / Arvin, A.M. / Bomble, Y.J. / Bottcher, B. / Breyton, C. / Chiarini, V. / Chinnam, N.B. / Chiu, W. / ...Authors: Alexander, L.T. / Lepore, R. / Kryshtafovych, A. / Adamopoulos, A. / Alahuhta, M. / Arvin, A.M. / Bomble, Y.J. / Bottcher, B. / Breyton, C. / Chiarini, V. / Chinnam, N.B. / Chiu, W. / Fidelis, K. / Grinter, R. / Gupta, G.D. / Hartmann, M.D. / Hayes, C.S. / Heidebrecht, T. / Ilari, A. / Joachimiak, A. / Kim, Y. / Linares, R. / Lovering, A.L. / Lunin, V.V. / Lupas, A.N. / Makbul, C. / Michalska, K. / Moult, J. / Mukherjee, P.K. / Nutt, W.S. / Oliver, S.L. / Perrakis, A. / Stols, L. / Tainer, J.A. / Topf, M. / Tsutakawa, S.E. / Valdivia-Delgado, M. / Schwede, T.
#2: Journal: Methods Mol.Biol. / Year: 2022
Title: Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights.
Authors: Chinnam, N.B. / Syed, A. / Burnett, K.H. / Hura, G.L. / Tainer, J.A. / Tsutakawa, S.E.
#3: Journal: Methods Enzymol. / Year: 2023
Title: Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution.
Authors: Chinnam, N.B. / Syed, A. / Hura, G.L. / Hammel, M. / Tainer, J.A. / Tsutakawa, S.E.
History
DepositionJul 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Activating signal cointegrator 1 complex subunit 1
B: Activating signal cointegrator 1 complex subunit 1


Theoretical massNumber of molelcules
Total (without water)56,2502
Polymers56,2502
Non-polymers00
Water2,828157
1
A: Activating signal cointegrator 1 complex subunit 1


Theoretical massNumber of molelcules
Total (without water)28,1251
Polymers28,1251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Activating signal cointegrator 1 complex subunit 1


Theoretical massNumber of molelcules
Total (without water)28,1251
Polymers28,1251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.879, 62.105, 136.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Activating signal cointegrator 1 complex subunit 1 / ASC-1 complex subunit p50 / Trip4 complex subunit p50


Mass: 28124.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASCC1, CGI-18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N9N2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 12.5% MPEG 2K, 200 mM imidizole/malate (I/M) pH 5.0, 5% saturated KCl at room temperature. For cryoprotection, 25% ethylene glycol added to the mother liquor
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→35.73 Å / Num. obs: 12679 / % possible obs: 99.6 % / Redundancy: 1.72 % / Biso Wilson estimate: 44.18 Å2 / CC1/2: 0.988 / Net I/σ(I): 9.71
Reflection shellResolution: 2.8→2.97 Å / Num. unique obs: 1990 / CC1/2: 0.796

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35.73 Å / SU ML: 0.2378 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 24.292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2556 600 4.93 %
Rwork0.2061 11574 -
obs0.2086 12174 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 0 157 3685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233604
X-RAY DIFFRACTIONf_angle_d0.4954840
X-RAY DIFFRACTIONf_chiral_restr0.0402520
X-RAY DIFFRACTIONf_plane_restr0.003633
X-RAY DIFFRACTIONf_dihedral_angle_d16.05921349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.080.34061340.26612703X-RAY DIFFRACTION91.75
3.08-3.520.22781450.21762852X-RAY DIFFRACTION96.18
3.52-4.440.25241650.17882936X-RAY DIFFRACTION97.89
4.44-35.730.24421560.20393083X-RAY DIFFRACTION98.24

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