1I4K | pdb_00001i4k

CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS AT 2.5A RESOLUTION

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)
Z	d1i4kz_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
Y	d1i4ky_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
X	d1i4kx_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
W	d1i4kw_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
V	d1i4kv_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
U	d1i4ku_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
T	d1i4kt_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
S	d1i4ks_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
R	d1i4kr_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
Q	d1i4kq_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
P	d1i4kp_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
O	d1i4ko_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
N	d1i4kn_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
M	d1i4km_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
L	d1i4kl_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
K	d1i4kk_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
J	d1i4kj_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
I	d1i4ki_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
H	d1i4kh_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
G	d1i4kg_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
F	d1i4kf_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
E	d1i4ke_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
D	d1i4kd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
C	d1i4kc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
BA [auth 2]	d1i4k2_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
B	d1i4kb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
AA [auth 1]	d1i4k1_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
A	d1i4ka_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	Sm motif of small nuclear ribonucleoproteins, SNRNP	Archaeal homoheptameric Sm protein	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
Z	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
Y	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
X	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
BA [auth 2]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
AA [auth 1]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8033644	3000419	SCOP2B (2022-06-29)
A	SCOP2 Family	Sm motif of small nuclear ribonucleoproteins, SNRNP	8021264	4001809	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sm-like ribonucleoproteins	8033644	3000419	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)
Z	LSM	e1i4kZ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
Y	LSM	e1i4kY1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
X	LSM	e1i4kX1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
W	LSM	e1i4kW1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
V	LSM	e1i4kV1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
U	LSM	e1i4kU1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
T	LSM	e1i4kT1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
S	LSM	e1i4kS1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
R	LSM	e1i4kR1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
Q	LSM	e1i4kQ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
P	LSM	e1i4kP1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
O	LSM	e1i4kO1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
N	LSM	e1i4kN1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
M	LSM	e1i4kM1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
L	LSM	e1i4kL1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K	LSM	e1i4kK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J	LSM	e1i4kJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
I	LSM	e1i4kI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H	LSM	e1i4kH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e1i4kG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e1i4kF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e1i4kE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e1i4kD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e1i4kC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
BA [auth 2]	LSM	e1i4k21	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B	LSM	e1i4kB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
AA [auth 1]	LSM	e1i4k11	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
A	LSM	e1i4kA1	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)
Z	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
Y	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
X	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
W	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
V	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
U	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
T	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
S	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
R	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
Q	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
P	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
O	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)
M	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)
K	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)
I	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)
G	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)
E	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)
C	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
BA [auth 2]	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)
AA [auth 1]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (4.3.0)
A	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, AA [auth 1], B, BA [auth 2], C, A, AA [auth 1], B, BA [auth 2], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	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, AA [auth 1], B, BA [auth 2], C, A, AA [auth 1], B, BA [auth 2], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	PUTATIVE SNRNP SM-LIKE PROTEIN	RNA binding binding nucleic acid binding	-	protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, AA [auth 1], B, BA [auth 2], C, A, AA [auth 1], B, BA [auth 2], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
A, AA [auth 1], B, BA [auth 2], C, A, AA [auth 1], B, BA [auth 2], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR010920	LSM domain superfamily	Homologous Superfamily
A, AA [auth 1], B, BA [auth 2], C, A, AA [auth 1], B, BA [auth 2], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR047575	Sm domain	Domain
A, AA [auth 1], B, BA [auth 2], C, A, AA [auth 1], B, BA [auth 2], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR022901	snRNP Sm-like, putative, archaea	Family
A, AA [auth 1], B, BA [auth 2], C, A, AA [auth 1], B, BA [auth 2], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	IPR044641	Sm-like protein Lsm7/SmG	Family