4B3G | pdb_00004b3g

crystal structure of Ighmbp2 helicase in complex with RNA

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)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8090883	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Upf1 beta-barrel domain-like	8090882	3002168	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8090884	3002019	SCOP2B (2022-06-29)
B	SCOP2 Family	UPF1 beta-barrel domain-like	8048215	4007598	SCOP2 (2022-06-29)
B	SCOP2 Family	Tandem AAA-ATPase domain	8048222	4000282	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Upf1 beta-barrel domain-like	8090882	3002168	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RecA-like P-loop NTPases	8090883	3002019	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RecA-like P-loop NTPases	8090884	3002019	SCOP2 (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	SNase	e4b3gA3	A: a/b three-layered sandwiches	X: HAMP domain	H: Metalloproteases (zincins) catalytic domain	T: Metalloproteases (zincins) catalytic domain	F: SNase	ECOD (v294.1)
A	V-set	e4b3gA6	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (v294.1)
B	PI3K_C2	e4b3gB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: PI3K_C2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	2.40.30.270	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	2.40.30.270	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13086	AAA domain (AAA_11)	AAA domain	This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.	Domain
A, B	PF13087	AAA domain (AAA_12)	AAA domain	This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.	Domain
A, B	PF21138	Helicase SMUBP-2/HCS1, 1B domain (SMUBP-2_HCS1_1B)	Helicase SMUBP-2/HCS1, 1B domain	Proteins in this entry belong to the DNA2/NAM7 helicase family and includes SMUBP-2 (also known as IGHMBP2) from mammals and HCS1 (also known as DNA polymerase alpha-associated DNA helicase A) from yeasts. This entry represents the 1B domain consisti ...	Proteins in this entry belong to the DNA2/NAM7 helicase family and includes SMUBP-2 (also known as IGHMBP2) from mammals and HCS1 (also known as DNA polymerase alpha-associated DNA helicase A) from yeasts. This entry represents the 1B domain consisting of a short alpha-helix and a beta-barrel. This domain forms the RNA-binding channel together with 1A, 2A and 1C domains [1]. Domains 1B and 1C directly interact with the 3'-end of RNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA-BINDING PROTEIN SMUBP-2	nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity transcription factor binding protein binding binding nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity transcription factor binding protein binding binding general transcription initiation factor binding RNA binding nucleic acid binding single-stranded RNA binding tRNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding ATP-dependent activity, acting on RNA ribonucleoprotein complex binding protein-containing complex binding ribosome binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity, acting on RNA RNA helicase activity 5'-3' RNA helicase activity cation binding transition metal ion binding zinc ion binding metal ion binding identical protein binding single-stranded DNA binding double-stranded DNA helicase activity	-	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol growth cone axon cell projection distal axon neuron projection plasma membrane bounded cell projection site of polarized growth membrane-bounded organelle nucleus cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol growth cone axon cell projection distal axon neuron projection plasma membrane bounded cell projection site of polarized growth membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex ribonucleoprotein complex intracellular membraneless organelle nuclear body membraneless organelle
C [auth G], D [auth H]	RNA (5'-(APAPAPAPAPAPAPAPAP)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR041677	DNA2/NAM7 helicase, helicase domain	Domain
A, B	IPR050534	Coronaviruses polyprotein 1ab	Family
A, B	IPR034072	DNA-binding protein SMUBP-2, R3H domain	Domain
A, B	IPR048761	Helicase SMUBP-2/HCS1, 1B domain	Domain
A, B	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
A, B	IPR001374	R3H domain	Domain
A, B	IPR003593	AAA+ ATPase domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR000058	Zinc finger, AN1-type	Domain
A, B	IPR004483	Helicase SMUBP-2/Hcs1-like	Family
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR035896	AN1-like Zinc finger	Homologous Superfamily
A, B	IPR036867	R3H domain superfamily	Homologous Superfamily
A, B	IPR047187	Upf1-like, C-terminal helicase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P38935	autosomal recessive distal spinal muscular atrophy 1 Charcot-Marie-Tooth disease axonal type 2S Charcot-Marie-Tooth disease peripheral neuropathy arthrogryposis motor peripheral neuropathy intellectual disability neurodegenerative disease psoriasis malignant mesothelioma peripheral nervous system disease spinal muscular atrophy, type 1

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.