1LOJ | pdb_00001loj

Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
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)
A	d1loja1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
A	d1loja2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
B	d1lojb1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
B	d1lojb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
C	d1lojc1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
C	d1lojc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
D	d1lojd1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
D	d1lojd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
E	d1loje1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
E	d1loje2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
F	d1lojf1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
F	d1lojf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
G	d1lojg1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
G	d1lojg2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
H	d1lojh1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
H	d1lojh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
I	d1loji1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
I	d1loji2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
J	d1lojj1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
J	d1lojj2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
K	d1lojk1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
K	d1lojk2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
L	d1lojl1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
L	d1lojl2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
M	d1lojm1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
M	d1lojm2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
N	d1lojn1	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)
N	d1lojn2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanothermobacter thermautotrophicus str. Delta H ) [TaxId: 187420 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	3000419	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Sm-like ribonucleoproteins	8043542	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)
A	LSM	e1lojA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B	LSM	e1lojB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e1lojC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e1lojD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e1lojE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e1lojF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e1lojG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H	LSM	e1lojH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
I	LSM	e1lojI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J	LSM	e1lojJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K	LSM	e1lojK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
L	LSM	e1lojL1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
M	LSM	e1lojM1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
N	LSM	e1lojN1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
B	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
C	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
D	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
E	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
F	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
G	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
H	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
I	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
J	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
K	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
L	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
M	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
N	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	PF01423	LSM domain (LSM)	LSM domain	The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ...	The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	small nuclear ribonucleoprotein homolog (Sm-like)	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 Sm-like protein family complex

InterPro: Protein Family Classification InterPro Database Homepage

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