8SJD

Cryo-EM structure of the Hermes transposase bound to two right-ends of its DNA transposon.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth C]	SCOP2B Superfamily	Hermes dimerisation domain	8038725	3002013	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Ribonuclease H-like	8038724	3000143	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Hermes dimerisation domain	8038725	3002013	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Ribonuclease H-like	8038724	3000143	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8038724	3000143	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Hermes dimerisation domain	8038725	3002013	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Hermes dimerisation domain	8038725	3002013	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8038724	3000143	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)
A [auth C]	PF10683	e8sjdC2	A: alpha duplicates or obligate multimers	X: Hermes dimerisation domain (From Topology)	H: Hermes dimerisation domain (From Topology)	T: Hermes dimerisation domain	F: PF10683	ECOD (1.6)
A [auth C]	PF05699	e8sjdC1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF05699	ECOD (1.6)
B [auth D]	PF10683	e8sjdD1	A: alpha duplicates or obligate multimers	X: Hermes dimerisation domain (From Topology)	H: Hermes dimerisation domain (From Topology)	T: Hermes dimerisation domain	F: PF10683	ECOD (1.6)
B [auth D]	PF05699	e8sjdD2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF05699	ECOD (1.6)
C [auth B]	PF10683	e8sjdB2	A: alpha duplicates or obligate multimers	X: Hermes dimerisation domain (From Topology)	H: Hermes dimerisation domain (From Topology)	T: Hermes dimerisation domain	F: PF10683	ECOD (1.6)
C [auth B]	PF05699	e8sjdB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF05699	ECOD (1.6)
D [auth A]	PF10683	e8sjdA2	A: alpha duplicates or obligate multimers	X: Hermes dimerisation domain (From Topology)	H: Hermes dimerisation domain (From Topology)	T: Hermes dimerisation domain	F: PF10683	ECOD (1.6)
D [auth A]	PF05699	e8sjdA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF05699	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth D], C [auth B], D [auth A]	PF05699	hAT family C-terminal dimerisation region (Dimer_Tnp_hAT)	hAT family C-terminal dimerisation region	This dimerisation region is found at the C terminus of the transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerisation region forms extremely stable dimers in vitro [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D], C [auth B], D [auth A]	Hermes transposase	DNA binding binding organic cyclic compound binding nucleic acid binding protein binding protein dimerization activity cation binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
E [auth J], G	DNA (55-MER)	-	-	-
F [auth I], J [auth F]	DNA (46-MER)	-	-	-
H, I [auth E]	DNA (8-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth D], C [auth B], D [auth A]	IPR018473	Hermes trasposase, DNA-binding domain	Domain
A [auth C], B [auth D], C [auth B], D [auth A]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A [auth C], B [auth D], C [auth B], D [auth A]	IPR003656	Zinc finger, BED-type	Domain
A [auth C], B [auth D], C [auth B], D [auth A]	IPR008906	HAT, C-terminal dimerisation domain	Domain

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 R01GM133198.