6EDB | pdb_00006edb

Crystal structure of SRY.hcGAS-21bp dsDNA complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	HMG-box	8036768	3001368	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PAP/OAS1 substrate-binding domain-like	8055833	3000941	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotidyltransferase-like	8055835	3000129	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	NUDIX	e6edbB1	A: alpha bundles	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: NUDIX	ECOD (develop294)
A	NUDIX	e6edbA1	A: alpha bundles	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: NUDIX	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.30.10	Mainly Alpha	Orthogonal Bundle	DNA Binding (I), subunit A	High mobility group box domain	CATH (utative)
A	1.10.1410.40	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain		CATH (utative)
A	3.30.460.90	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03281	Mab-21 protein nucleotidyltransferase domain (Mab-21)	Mab-21 protein nucleotidyltransferase domain	This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development [2-3].	Domain
A, B	PF20266	Mab-21 protein HhH/H2TH-like domain (Mab-21_C)	Mab-21 protein HhH/H2TH-like domain	This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development [2-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	DNA (5'-D(GPCPAPTPTPGPTPTPTPAPGPAPTPCPCPCPGPGPAPTP*C)-3')	-	-	-
C	DNA (5'-D(CPGPAPTPCPCPGPGPGPAPTPCPTPAPAPAPCPAPAPTP*G)-3')	-	-	-
A, B	Sex-determining region Y protein,Cyclic GMP-AMP synthase	DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity transcription factor binding protein binding DNA-binding transcription factor binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity transcription factor binding protein binding DNA-binding transcription factor binding sequence-specific DNA binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding calmodulin binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity chromatin binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding adenyl ribonucleotide binding adenyl nucleotide binding ATP binding identical protein binding protein homodimerization activity protein dimerization activity ADP-D-ribose modification-dependent protein binding poly-ADP-D-ribose modification-dependent protein binding modification-dependent protein binding cyclic GMP-AMP synthase activity transferase activity 2',3'-cyclic GMP-AMP synthase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding metal ion binding protein-containing complex binding nucleosome binding	developmental process cellular developmental process cell differentiation cellular process reproductive process sex differentiation developmental process involved in reproduction multicellular organism development multicellular organismal process sex determination male sex determination anatomical structure development regulation of biosynthetic process regulation of biological process developmental process cellular developmental process cell differentiation cellular process reproductive process sex differentiation developmental process involved in reproduction multicellular organism development multicellular organismal process sex determination male sex determination anatomical structure development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process positive regulation of DNA-templated transcription RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of developmental process regulation of gonad development regulation of reproductive process male gonad development positive regulation of developmental process male sex differentiation development of primary male sexual characteristics development of primary sexual characteristics positive regulation of male gonad development reproductive structure development regulation of multicellular organismal process regulation of male gonad development system development positive regulation of reproductive process gonad development reproductive system development animal organ development positive regulation of gonad development positive regulation of multicellular organismal process transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II cellular response to stimulus cytoplasmic pattern recognition receptor signaling pathway regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus intracellular receptor signaling pathway signaling response to biotic stimulus intracellular signal transduction cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cellular response to stress DNA damage response regulation of DNA recombination regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process negative regulation of DNA repair negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair negative regulation of response to stimulus negative regulation of metabolic process DNA recombination DNA metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination negative regulation of DNA metabolic process regulation of DNA metabolic process cellular response to nitrogen compound cellular response to dsRNA cellular response to exogenous dsRNA response to dsRNA response to nitrogen compound response to exogenous dsRNA cellular response to chemical stimulus response to chemical cell-cell signaling paracrine signaling cGAS/STING signaling pathway determination of adult lifespan production of molecular mediator of immune response regulation of immune effector process immunoglobulin production immune effector process regulation of immunoglobulin production regulation of production of molecular mediator of immune response regulation of leukocyte activation cell activation regulation of cell activation regulation of T cell activation lymphocyte activation leukocyte activation T cell activation regulation of lymphocyte activation regulation of cellular senescence cellular senescence positive regulation of cellular senescence regulation of defense response to virus defense response to virus positive regulation of defense response to virus by host regulation of defense response to virus by host response to virus regulation of signal transduction negative regulation of cGAS/STING signaling pathway regulation of pattern recognition receptor signaling pathway negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication regulation of intracellular signal transduction regulation of signaling negative regulation of signal transduction negative regulation of immune system process regulation of cell communication cytokine production regulation of cytokine production positive regulation of type I interferon production type I interferon production positive regulation of cytokine production regulation of type I interferon production	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytoplasm chromatin chromosome cytosol cell periphery plasma membrane membrane site of double-strand break site of DNA damage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050140	SRY-related HMG-box transcription factor-like	Family
A, B	IPR017253	Transcription factor SRY	Family
A, B	IPR009071	High mobility group box domain	Domain
A, B	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
A, B	IPR024810	MAB21L/Cyclic GMP-AMP synthase-like receptor	Family
A, B	IPR046906	Mab-21-like, HhH/H2TH-like domain	Domain
A, B	IPR046903	Mab-21-like, nucleotidyltransferase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q8N884	46,XY complete gonadal dysgenesis 46,XX sex reversal 1 46,XX ovotesticular disorder of sex development 46,XY sex reversal 1 46,XY partial gonadal dysgenesis gonadal dysgenesis mixed gonadal dysgenesis True Hermaphroditism (disorder) intellectual disability 46,XX testicular disorder of sex development large cell medulloblastoma acute myeloid leukemia chronic obstructive pulmonary disease lung carcinoma Aicardi-Goutieres syndrome 46,XY complete gonadal dysgenesis 46,XX sex reversal 1 46,XX ovotesticular disorder of sex development 46,XY sex reversal 1 46,XY partial gonadal dysgenesis gonadal dysgenesis mixed gonadal dysgenesis True Hermaphroditism (disorder) intellectual disability 46,XX testicular disorder of sex development large cell medulloblastoma acute myeloid leukemia chronic obstructive pulmonary disease lung carcinoma Aicardi-Goutieres syndrome glioblastoma psoriasis breast cancer head and neck cancer ulcerative colitis

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.