1N9R - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A HEPTAMERIC RING COMPLEX OF YEAST SMF IN SPACEGROUP P4122

Authors :   B. M. Collins, L. Cubeddu, N. Naidoo, S. J. Harrop, G. D. Kornfeld, I. W. D P. M. G. Curmi, B. C. Mabbutt

Date :   26 Nov 02 (Deposition) - 13 Dec 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B,C,D,E,F,G  (1x)
Biol. Unit 2: A,B,C,D,E,F,G  (2x)

Keywords :   Snrnp, Sm Protein, Heptamer, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. M. Collins, L. Cubeddu, N. Naidoo, S. J. Harrop, G. D. Kornfeld, I. W. Dawes, P. M. G. Curmi, B. C. Mabbutt
Homomeric Ring Assemblies Of Eukaryotic Sm Proteins Have Affinity For Both Rna And Dna: Crystal Structure Of An Oligomeric Complex Of Yeast Smf
J. Biol. Chem. V. 278 17291 2003
PubMed-ID: 12618433 | Reference-DOI: 10.1074/JBC.M211826200

Molecule 1 - SMALL NUCLEAR RIBONUCLEOPROTEIN F
	Chains	:	A, B, C, D, E, F, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	SMF; SM-LIKE SNRNP PROTEIN; SNRNP-F; SM PROTEIN F; SM-F

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	E	F	G
Biological Unit 1 (1x)	:	A	B	C	D	E	F	G
Biological Unit 2 (2x)	:	A	B	C	D	E	F	G

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1N9R)

(no "Site" information available for 1N9R)

(no "SS Bond" information available for 1N9R)

(no "Cis Peptide Bond" information available for 1N9R)

(no "SAP(SNP)/Variant" information available for 1N9R)

(no "PROSITE Motif" information available for 1N9R)

Asymmetric Unit (1, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YPR182W	1	YPR182W.1	XVI:900190-900450	261	RUXF_YEAST	1-86	86	7	A:19-86 B:18-86 C:19-86 D:19-86 E:19-86 F:18-86 G:19-86	68 69 68 68 68 69 68

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:68
 aligned with RUXF_YEAST | P54999 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:68
                                    28        38        48        58        68        78        
            RUXF_YEAST   19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
               SCOP domains d1n9ra_ A: Small nuclear ribonucleoprotein F, Smf                    SCOP domains
               CATH domains 1n9rA00 A:19-86  [code=2.30.30.100, no name defined]                 CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeeeee....eeeeeeeee......eeeeeeeeee..eeeee..........eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:19-86 UniProt: 1-86 [INCOMPLETE]                    Transcript 1
                  1n9r A 19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
                                    28        38        48        58        68        78

Chain B from PDB  Type:PROTEIN  Length:69
 aligned with RUXF_YEAST | P54999 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:69
                                    27        37        47        57        67        77         
            RUXF_YEAST   18 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
               SCOP domains d1n9rb_ B: Small nuclear ribonucleoprotein F, Smf                     SCOP domains
               CATH domains 1n9rB00 B:18-86  [code=2.30.30.100, no name defined]                  CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee....eeeeeeeee......eeeeeeeeee..........eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:18-86 UniProt: 1-86 [INCOMPLETE]                     Transcript 1
                  1n9r B 18 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
                                    27        37        47        57        67        77

Chain C from PDB  Type:PROTEIN  Length:68
 aligned with RUXF_YEAST | P54999 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:68
                                    28        38        48        58        68        78        
            RUXF_YEAST   19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
               SCOP domains d1n9rc_ C: Small nuclear ribonucleoprotein F, Smf                    SCOP domains
               CATH domains 1n9rC00 C:19-86  [code=2.30.30.100, no name defined]                 CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeeeee....eeeeeeeee......eeeeeeeeee..eeeee...eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:19-86 UniProt: 1-86 [INCOMPLETE]                    Transcript 1
                  1n9r C 19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
                                    28        38        48        58        68        78

Chain D from PDB  Type:PROTEIN  Length:68
 aligned with RUXF_YEAST | P54999 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:68
                                    28        38        48        58        68        78        
            RUXF_YEAST   19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
               SCOP domains d1n9rd_ D: Small nuclear ribonucleoprotein F, Smf                    SCOP domains
               CATH domains 1n9rD00 D:19-86  [code=2.30.30.100, no name defined]                 CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeeeee....eeeeeeeee......eeeeeeeeee..eeeee...eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:19-86 UniProt: 1-86 [INCOMPLETE]                    Transcript 1
                  1n9r D 19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
                                    28        38        48        58        68        78

Chain E from PDB  Type:PROTEIN  Length:68
 aligned with RUXF_YEAST | P54999 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:68
                                    28        38        48        58        68        78        
            RUXF_YEAST   19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
               SCOP domains d1n9re_ E: Small nuclear ribonucleoprotein F, Smf                    SCOP domains
               CATH domains 1n9rE00 E:19-86  [code=2.30.30.100, no name defined]                 CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....eeeeeeeee......eeeeeeeeee..eeeee...eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: E:19-86 UniProt: 1-86 [INCOMPLETE]                    Transcript 1
                  1n9r E 19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
                                    28        38        48        58        68        78

Chain F from PDB  Type:PROTEIN  Length:69
 aligned with RUXF_YEAST | P54999 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:69
                                    27        37        47        57        67        77         
            RUXF_YEAST   18 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
               SCOP domains d1n9rf_ F: Small nuclear ribonucleoprotein F, Smf                     SCOP domains
               CATH domains 1n9rF00 F:18-86  [code=2.30.30.100, no name defined]                  CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeeeee....eeeeeeeee......eeeeeeeeee..eeeee...eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: F:18-86 UniProt: 1-86 [INCOMPLETE]                     Transcript 1
                  1n9r F 18 FLKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
                                    27        37        47        57        67        77

Chain G from PDB  Type:PROTEIN  Length:68
 aligned with RUXF_YEAST | P54999 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:68
                                    28        38        48        58        68        78        
            RUXF_YEAST   19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
               SCOP domains d1n9rg_ G: Small nuclear ribonucleoprotein F, Smf                    SCOP domains
               CATH domains 1n9rG00 G:19-86  [code=2.30.30.100, no name defined]                 CATH domains
           Pfam domains (1) LSM-1n9rG01 G:19-83                                              --- Pfam domains (1)
           Pfam domains (2) LSM-1n9rG02 G:19-83                                              --- Pfam domains (2)
           Pfam domains (3) LSM-1n9rG03 G:19-83                                              --- Pfam domains (3)
           Pfam domains (4) LSM-1n9rG04 G:19-83                                              --- Pfam domains (4)
           Pfam domains (5) LSM-1n9rG05 G:19-83                                              --- Pfam domains (5)
           Pfam domains (6) LSM-1n9rG06 G:19-83                                              --- Pfam domains (6)
           Pfam domains (7) LSM-1n9rG07 G:19-83                                              --- Pfam domains (7)
         Sec.struct. author hhhhh..eeeeee....eeeeeeeeeee...eeeeeeeeeee..eeeee...eee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: G:19-86 UniProt: 1-86 [INCOMPLETE]                    Transcript 1
                  1n9r G 19 LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEIFIRCNNVLYIRELPN 86
                                    28        38        48        58        68        78

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Sm-like fold (103)

Superfamily: Sm-like ribonucleoproteins (95)

Family: Sm motif of small nuclear ribonucleoproteins, SNRNP (31)

Protein domain: Small nuclear ribonucleoprotein F, Smf (2)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d1n9ra_	A:
1b	d1n9rb_	B:
1c	d1n9rc_	C:
1d	d1n9rd_	D:
1e	d1n9re_	E:
1f	d1n9rf_	F:
1g	d1n9rg_	G:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.100, no name defined] (40)

Baker's yeast (Saccharomyces cerevisiae) (3)

1a	1n9rB00	B:18-86
1b	1n9rF00	F:18-86
1c	1n9rA00	A:19-86
1d	1n9rC00	C:19-86
1e	1n9rD00	D:19-86
1f	1n9rE00	E:19-86
1g	1n9rG00	G:19-86

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Sm-like (17)

Family: LSM (13)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (2)

1a	LSM-1n9rG01	G:19-83
1b	LSM-1n9rG02	G:19-83
1c	LSM-1n9rG03	G:19-83
1d	LSM-1n9rG04	G:19-83
1e	LSM-1n9rG05	G:19-83
1f	LSM-1n9rG06	G:19-83
1g	LSM-1n9rG07	G:19-83

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G (RUXF_YEAST | P54999)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
cellular component
	GO:0005685	U1 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U1.
	GO:0046540	U4/U6 x U5 tri-snRNP complex	A ribonucleoprotein complex formed by the association of the U4/U6 and U5 small nuclear ribonucleoproteins.
	GO:0005682	U5 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U5.
	GO:0071013	catalytic step 2 spliceosome	A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005732	small nucleolar ribonucleoprotein complex	A ribonucleoprotein complex that contains an RNA molecule of the small nucleolar RNA (snoRNA) family and associated proteins. Most are involved in a step of processing of rRNA: cleavage, 2'-O-methylation, or pseudouridylation. The majority, though not all, fall into one of two classes, box C/D type or box H/ACA type.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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	1n9r
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	RUXF_YEAST \| P54999	:	1n9s 3jcm 5gam 5gan 5gao 5gm6 5gmk 5lj3 5lj5 5lqw 5mps 5mq0 5wsg

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