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- PDB-6edb: Crystal structure of SRY.hcGAS-21bp dsDNA complex -

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Basic information

Entry
Database: PDB / ID: 6edb
TitleCrystal structure of SRY.hcGAS-21bp dsDNA complex
Components
  • DNA (5'-D(*CP*GP*AP*TP*CP*CP*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3')
  • DNA (5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*CP*GP*GP*AP*TP*C)-3')
  • Sex-determining region Y protein,Cyclic GMP-AMP synthase
KeywordsTransferase/DNA / SRY human cGAS DNA complex / Transferase-DNA complex
Function / homology
Function and homology information


positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / 2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / male sex determination / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production ...positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / 2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / male sex determination / STING mediated induction of host immune responses / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / pattern recognition receptor signaling pathway / : / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / positive regulation of type I interferon production / negative regulation of double-strand break repair via homologous recombination / : / nucleosome binding / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / determination of adult lifespan / Deactivation of the beta-catenin transactivating complex / molecular condensate scaffold activity / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / calmodulin binding / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / DNA repair / DNA damage response / chromatin binding / positive regulation of gene expression / chromatin / GTP binding / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Transcription factor SRY / : / Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / High mobility group box domain / DNA Binding (I), subunit A / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like ...Transcription factor SRY / : / Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / High mobility group box domain / DNA Binding (I), subunit A / Poly(a)-polymerase, middle domain / Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Sex-determining region Y protein / Cyclic GMP-AMP synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.209 Å
AuthorsXie, W. / Lama, L. / Adura, C. / Glickman, J.F. / Tuschl, T. / Patel, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Human cGAS catalytic domain has an additional DNA-binding interface that enhances enzymatic activity and liquid-phase condensation.
Authors: Xie, W. / Lama, L. / Adura, C. / Tomita, D. / Glickman, J.F. / Tuschl, T. / Patel, D.J.
History
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sex-determining region Y protein,Cyclic GMP-AMP synthase
B: Sex-determining region Y protein,Cyclic GMP-AMP synthase
C: DNA (5'-D(*CP*GP*AP*TP*CP*CP*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3')
D: DNA (5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*CP*GP*GP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0035
Polymers120,9384
Non-polymers651
Water00
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)90.307, 115.827, 159.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Sex-determining region Y protein,Cyclic GMP-AMP synthase / Testis-determining factor / h-cGAS / 2'3'-cGAMP synthase / Mab-21 domain-containing protein 1


Mass: 53716.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRY, TDF, CGAS, C6orf150, MB21D1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q05066, UniProt: Q8N884, cyclic GMP-AMP synthase
#2: DNA chain DNA (5'-D(*CP*GP*AP*TP*CP*CP*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3')


Mass: 6745.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*CP*GP*GP*AP*TP*C)-3')


Mass: 6758.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 1.72 Å3/Da / Density % sol: 28.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M L-proline, 0.1 M HEPES, pH 7.5, 8% PEG3350 (v/v), 10 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→30.008 Å / Num. obs: 12639 / % possible obs: 60.4 % / Redundancy: 5.4 % / CC1/2: 0.98 / Rpim(I) all: 0.051 / Net I/σ(I): 13.4
Reflection shellResolution: 3.2→3.32 Å / Num. unique obs: 833 / CC1/2: 0.722 / Rpim(I) all: 0.338

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K96

4k96


Resolution: 3.209→30.008 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.93
RfactorNum. reflection% reflection
Rfree0.3016 1263 10 %
Rwork0.2553 --
obs0.2598 12629 90.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.209→30.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 855 1 0 4379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194586
X-RAY DIFFRACTIONf_angle_d0.5686331
X-RAY DIFFRACTIONf_dihedral_angle_d21.6232653
X-RAY DIFFRACTIONf_chiral_restr0.037679
X-RAY DIFFRACTIONf_plane_restr0.003661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
3.2094-3.33770.3646940.320384882762
3.3377-3.48940.35871160.3199104376
3.4894-3.67310.3411260.3352114484
3.6731-3.90270.37551430.3126127392
3.9027-4.20330.32541520.2892136799
4.2033-4.6250.321540.28041392100
4.625-5.2910.31121560.26351401100
5.291-6.65410.35421570.29691417100
6.6541-30.00890.24891650.20321481100

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