1M8V | pdb_00001m8v

Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
U [auth N]	d1m8vn_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
T [auth M]	d1m8vm_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
S [auth L]	d1m8vl_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
R [auth K]	d1m8vk_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
Q [auth J]	d1m8vj_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
P [auth I]	d1m8vi_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
O [auth H]	d1m8vh_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
N [auth G]	d1m8vg_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
M [auth F]	d1m8vf_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
L [auth E]	d1m8ve_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
K [auth D]	d1m8vd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
J [auth C]	d1m8vc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
I [auth B]	d1m8vb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
H [auth A]	d1m8va1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)
H [auth A]	d1m8va2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Pyrococcus abyssi ) [TaxId: 29292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
U [auth N]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
T [auth M]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
S [auth L]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
R [auth K]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
Q [auth J]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
P [auth I]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
O [auth H]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
N [auth G]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
M [auth F]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
L [auth E]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
K [auth D]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
J [auth C]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
I [auth B]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	SCOP2B (2022-06-29)
H [auth A]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8042422	3000419	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)
U [auth N]	MS_channel_2nd	e1m8vN1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
T [auth M]	MS_channel_2nd	e1m8vM1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
S [auth L]	MS_channel_2nd	e1m8vL1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
R [auth K]	MS_channel_2nd	e1m8vK1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
Q [auth J]	MS_channel_2nd	e1m8vJ1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
P [auth I]	MS_channel_2nd	e1m8vI1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
O [auth H]	MS_channel_2nd	e1m8vH1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
N [auth G]	MS_channel_2nd	e1m8vG1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
M [auth F]	MS_channel_2nd	e1m8vF1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
L [auth E]	MS_channel_2nd	e1m8vE1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
K [auth D]	MS_channel_2nd	e1m8vD1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
J [auth C]	MS_channel_2nd	e1m8vC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
I [auth B]	MS_channel_2nd	e1m8vB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)
H [auth A]	MS_channel_2nd	e1m8vA1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: MS_channel_2nd	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
U [auth N]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
T [auth M]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
S [auth L]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
R [auth K]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
Q [auth J]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
P [auth I]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
O [auth H]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
N [auth G]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
M [auth F]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
L [auth E]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
K [auth D]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
J [auth C]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I [auth B]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
H [auth A]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N]	PUTATIVE SNRNP SM-LIKE PROTEIN	RNA binding binding nucleic acid binding	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing	protein-containing complex ribonucleoprotein complex
A [auth O], B [auth P], C [auth Q], D [auth R], E [auth S], A [auth O], B [auth P], C [auth Q], D [auth R], E [auth S], F [auth T], G [auth U]	5'-R(PUPUPUPUPUPUP*U)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N]	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N]	IPR016487	Sm-like protein Lsm6/SmF	Family
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N]	IPR010920	LSM domain superfamily	Homologous Superfamily
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N]	IPR047575	Sm domain	Domain
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth K], S [auth L], T [auth M], U [auth N]	IPR022901	snRNP Sm-like, putative, archaea	Family

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.