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- PDB-6yxq: Crystal structure of a DNA repair complex ASCC3-ASCC2 -

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Basic information

Entry
Database: PDB / ID: 6yxq
TitleCrystal structure of a DNA repair complex ASCC3-ASCC2
Components
  • Activating signal cointegrator 1 complex subunit 2
  • Activating signal cointegrator 1 complex subunit 3
KeywordsSTRUCTURAL PROTEIN / DNA alkylation damage / DNA repair / ubiquitin binding / helicase
Function / homology
Function and homology information


ALKBH3 mediated reversal of alkylation damage / activating signal cointegrator 1 complex / DNA alkylation repair / ribosome disassembly / ribosome-associated ubiquitin-dependent protein catabolic process / DNA repair complex / DNA duplex unwinding / 3'-5' DNA helicase activity / K63-linked polyubiquitin modification-dependent protein binding / cytosolic ribosome ...ALKBH3 mediated reversal of alkylation damage / activating signal cointegrator 1 complex / DNA alkylation repair / ribosome disassembly / ribosome-associated ubiquitin-dependent protein catabolic process / DNA repair complex / DNA duplex unwinding / 3'-5' DNA helicase activity / K63-linked polyubiquitin modification-dependent protein binding / cytosolic ribosome / rescue of stalled ribosome / ubiquitin binding / DNA helicase / cell population proliferation / nuclear speck / regulation of DNA-templated transcription / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Activating signal cointegrator 1 complex subunit 2, CUE domain / : / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Sec63 Brl domain / : / Sec63 domain / Sec63 Brl domain ...Activating signal cointegrator 1 complex subunit 2, CUE domain / : / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Sec63 Brl domain / : / Sec63 domain / Sec63 Brl domain / UBA-like superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / C2 domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Activating signal cointegrator 1 complex subunit 3 / Activating signal cointegrator 1 complex subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsJia, J. / Absmeier, E. / Holton, N. / Bohnsack, K.E. / Pietrzyk-Brzezinska, A.J. / Bohnsack, M.T. / Wahl, M.C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)QBI-FUB Collaborative Integrative Structural Biology Initiative Germany
German Research Foundation (DFG)BO3442/1-2 Germany
CitationJournal: Nat Commun / Year: 2020
Title: The interaction of DNA repair factors ASCC2 and ASCC3 is affected by somatic cancer mutations.
Authors: Jia, J. / Absmeier, E. / Holton, N. / Pietrzyk-Brzezinska, A.J. / Hackert, P. / Bohnsack, K.E. / Bohnsack, M.T. / Wahl, M.C.
History
DepositionMay 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI
Revision 1.3Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activating signal cointegrator 1 complex subunit 3
B: Activating signal cointegrator 1 complex subunit 2


Theoretical massNumber of molelcules
Total (without water)74,4752
Polymers74,4752
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-30 kcal/mol
Surface area28150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.108, 158.108, 69.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Activating signal cointegrator 1 complex subunit 3 / ASC-1 complex subunit p200 / ASC1p200 / Helicase / ATP binding 1 / Trip4 complex subunit p200


Mass: 23926.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASCC3, HELIC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N3C0, DNA helicase
#2: Protein Activating signal cointegrator 1 complex subunit 2 / ASC-1 complex subunit p100 / Trip4 complex subunit p100


Mass: 50548.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASCC2, ASC1P100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H1I8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: MES-NaOH, pH 6.5, polyethylene glycol 3350, 2-methyl-2,4-pentanediol and methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97957 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.7→41.964 Å / Num. obs: 45845 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 86.11 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.89
Reflection shellResolution: 2.7→2.86 Å / Num. unique obs: 7271 / CC1/2: 0.139

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→41.96 Å / SU ML: 0.5619 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 32.1721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2474 2107 4.6 %
Rwork0.2044 43732 -
obs0.2063 45839 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.04 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4729 0 0 55 4784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074836
X-RAY DIFFRACTIONf_angle_d0.90716535
X-RAY DIFFRACTIONf_chiral_restr0.0465727
X-RAY DIFFRACTIONf_plane_restr0.0056839
X-RAY DIFFRACTIONf_dihedral_angle_d18.6053620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.34781340.33452812X-RAY DIFFRACTION95.4
2.76-2.830.3711460.35132948X-RAY DIFFRACTION99.36
2.83-2.910.36141370.32982886X-RAY DIFFRACTION98.76
2.91-2.990.37381410.3562936X-RAY DIFFRACTION99.45
2.99-3.090.43451360.37752889X-RAY DIFFRACTION99.18
3.09-3.20.31331400.32882917X-RAY DIFFRACTION98.58
3.2-3.330.33851430.2882950X-RAY DIFFRACTION99.2
3.33-3.480.30951420.26452913X-RAY DIFFRACTION99.32
3.48-3.660.33611340.22632941X-RAY DIFFRACTION99.16
3.66-3.890.23631450.20232914X-RAY DIFFRACTION99.48
3.89-4.190.25341390.17222893X-RAY DIFFRACTION99.28
4.19-4.610.21071430.1522942X-RAY DIFFRACTION99.48
4.61-5.270.17831400.14182938X-RAY DIFFRACTION99.55
5.28-6.640.25411400.21022928X-RAY DIFFRACTION99.42
6.65-41.960.17881470.15872925X-RAY DIFFRACTION99.48
Refinement TLS params.Method: refined / Origin x: 110.979427718 Å / Origin y: 47.2515114336 Å / Origin z: 52.785622842 Å
111213212223313233
T0.505901204675 Å20.0211857696055 Å2-0.0192107133979 Å2-0.53551948501 Å2-0.052810426049 Å2--0.478122983775 Å2
L1.93311930622 °22.04573114544 °2-0.373583110195 °2-2.16507782041 °2-0.34811940853 °2--0.280085255746 °2
S0.181125484854 Å °-0.25564628402 Å °0.183660066002 Å °0.076278989577 Å °-0.17307857332 Å °0.284475826028 Å °-0.0597671557271 Å °0.0663315416836 Å °-0.0203021471521 Å °
Refinement TLS groupSelection details: all

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