2F9D - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   2.5 ANGSTROM RESOLUTION STRUCTURE OF THE SPLICEOSOMAL PROTEIN P14 BOUND TO REGION OF SF3B155

Authors :   M. J. Schellenberg, R. A. Edwards, D. B. Ritchie, J. N. M. Glover, A. M. Ma

Date :   05 Dec 05 (Deposition) - 24 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,P,Q
Biol. Unit 1: A,P  (1x)
Biol. Unit 2: B,Q  (1x)

Keywords :   P14 Sf3Bp14 Sf3B155 Sap155 Rrm, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Schellenberg, R. A. Edwards, D. B. Ritchie, O. A. Kent, M. M. Golas H. Stark, J. N. M. Glover, A. M. Macmillan
Crystal Structure Of A Core Spliceosomal Protein Interface
Proc. Natl. Acad. Sci. Usa V. 103 1266 2006
PubMed-ID: 16432215 | Reference-DOI: 10.1073/PNAS.0508048103

Molecule 1 - PRE-MRNA BRANCH SITE PROTEIN P14
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PMALC2X
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	SF3B14
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SF3B 14 KDA SUBUNIT

Molecule 2 - SPLICING FACTOR 3B SUBUNIT 1
	Chains	:	P, Q
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES: 373-415
	Gene	:	SF3B1, SAP155
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SPLICEOSOME ASSOCIATED PROTEIN 155, SAP 155, SF3B155, PRE- MRNA SPLICING FACTOR SF3B 155 KDA SUBUNIT

		1	2	3	4
Asymmetric Unit	:	A	B	P	Q
Biological Unit 1 (1x)	:	A		P
Biological Unit 2 (1x)	:		B		Q

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2F9D)

(no "SS Bond" information available for 2F9D)

(no "Cis Peptide Bond" information available for 2F9D)

(no "SAP(SNP)/Variant" information available for 2F9D)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SF3B6_HUMAN	19-94	2	A:19-94 B:19-94

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SF3B6_HUMAN	19-94	1	A:19-94 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	SF3B6_HUMAN	19-94	1	- B:19-94

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000233468	1a	ENSE00001034726	chr2:24299313-24299070	244	SF3B6_HUMAN	1-10	10	0	-	-
1.2a	ENST00000233468	2a	ENSE00000721455	chr2:24297064-24296946	119	SF3B6_HUMAN	11-50	40	2	A:12-50 B:12-50	39 39
1.3	ENST00000233468	3	ENSE00000721450	chr2:24291329-24291191	139	SF3B6_HUMAN	50-96	47	2	A:50-96 B:50-96	47 47
1.4	ENST00000233468	4	ENSE00000808827	chr2:24290721-24290454	268	SF3B6_HUMAN	97-125	29	2	A:97-125 B:97-125	29 29

2.1a	ENST00000335508	1a	ENSE00001858642	chr2:198299815-198299696	120	SF3B1_HUMAN	1-10	10	0	-	-
2.2b	ENST00000335508	2b	ENSE00001005134	chr2:198288698-198288532	167	SF3B1_HUMAN	10-65	56	0	-	-
2.3	ENST00000335508	3	ENSE00001779244	chr2:198285857-198285753	105	SF3B1_HUMAN	66-100	35	0	-	-
2.4a	ENST00000335508	4a	ENSE00000784199	chr2:198285266-198285152	115	SF3B1_HUMAN	101-139	39	0	-	-
2.4h	ENST00000335508	4h	ENSE00000784198	chr2:198283312-198283233	80	SF3B1_HUMAN	139-165	27	0	-	-
2.5b	ENST00000335508	5b	ENSE00000784196	chr2:198281635-198281465	171	SF3B1_HUMAN	166-222	57	0	-	-
2.6b	ENST00000335508	6b	ENSE00000964860	chr2:198274731-198274494	238	SF3B1_HUMAN	223-302	80	0	-	-
2.7b	ENST00000335508	7b	ENSE00000964861	chr2:198273305-198273093	213	SF3B1_HUMAN	302-373	72	0	-	-
2.8a	ENST00000335508	8a	ENSE00000964862	chr2:198272843-198272722	122	SF3B1_HUMAN	373-413	41	2	P:377-413 Q:377-413	37 37
2.9	ENST00000335508	9	ENSE00000964863	chr2:198270196-198269999	198	SF3B1_HUMAN	414-479	66	2	P:414-415 Q:414-415	2 2
2.10	ENST00000335508	10	ENSE00000964864	chr2:198269901-198269800	102	SF3B1_HUMAN	480-513	34	0	-	-
2.11	ENST00000335508	11	ENSE00000964865	chr2:198268488-198268309	180	SF3B1_HUMAN	514-573	60	0	-	-
2.12	ENST00000335508	12	ENSE00000964866	chr2:198267759-198267673	87	SF3B1_HUMAN	574-602	29	0	-	-
2.13	ENST00000335508	13	ENSE00000964867	chr2:198267550-198267280	271	SF3B1_HUMAN	603-693	91	0	-	-
2.15b	ENST00000335508	15b	ENSE00000964868	chr2:198266854-198266709	146	SF3B1_HUMAN	693-741	49	0	-	-
2.16	ENST00000335508	16	ENSE00000964869	chr2:198266612-198266466	147	SF3B1_HUMAN	742-790	49	0	-	-
2.17	ENST00000335508	17	ENSE00000964870	chr2:198266249-198266124	126	SF3B1_HUMAN	791-832	42	0	-	-
2.18	ENST00000335508	18	ENSE00000964871	chr2:198265660-198265439	222	SF3B1_HUMAN	833-906	74	0	-	-
2.19	ENST00000335508	19	ENSE00000964872	chr2:198265158-198264976	183	SF3B1_HUMAN	907-967	61	0	-	-
2.20	ENST00000335508	20	ENSE00000964873	chr2:198264890-198264779	112	SF3B1_HUMAN	968-1005	38	0	-	-
2.22b	ENST00000335508	22b	ENSE00000964874	chr2:198263305-198263185	121	SF3B1_HUMAN	1005-1045	41	0	-	-
2.23a	ENST00000335508	23a	ENSE00000964875	chr2:198262840-198262709	132	SF3B1_HUMAN	1045-1089	45	0	-	-
2.24	ENST00000335508	24	ENSE00000784174	chr2:198261052-198260780	273	SF3B1_HUMAN	1089-1180	92	0	-	-
2.25c	ENST00000335508	25c	ENSE00000964876	chr2:198257912-198257696	217	SF3B1_HUMAN	1180-1252	73	0	-	-
2.26b	ENST00000335508	26b	ENSE00001337127	chr2:198257185-198256698	488	SF3B1_HUMAN	1253-1304	52	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:114
 aligned with SF3B6_HUMAN | Q9Y3B4 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:114
                                    21        31        41        51        61        71        81        91       101       111       121    
          SF3B6_HUMAN    12 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 125
               SCOP domains d2f9da1 A:12-125 Pre-mRNA branch site protein p14                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee......hhhhhhhhhhh...eeeeeee.......eeeeee.hhhhhhhhhhhhh..ee..ee.eeee.hhhhhh...hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------RRM  PDB: A:19-94 UniProt: 19-94                                            ------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:12-50 UniProt: 11-50 ----------------------------------------------Exon 1.4  PDB: A:97-125       Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.3  PDB: A:50-96 UniProt: 50-96          ----------------------------- Transcript 1 (2)
                 2f9d A  12 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 125
                                    21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with SF3B6_HUMAN | Q9Y3B4 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:114
                                    21        31        41        51        61        71        81        91       101       111       121    
          SF3B6_HUMAN    12 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 125
               SCOP domains d2f9db_ B: Pre-mRNA branch site protein p14                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee......hhhhhhhhhhhhh.eeeeeee.......eeeeee.hhhhhhhhhhhhh..ee..ee.eeee.hhhhhh...hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------RRM  PDB: B:19-94 UniProt: 19-94                                            ------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:12-50 UniProt: 11-50 ----------------------------------------------Exon 1.4  PDB: B:97-125       Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.3  PDB: B:50-96 UniProt: 50-96          ----------------------------- Transcript 1 (2)
                 2f9d B  12 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 125
                                    21        31        41        51        61        71        81        91       101       111       121

Chain P from PDB  Type:PROTEIN  Length:39
 aligned with SF3B1_HUMAN | O75533 from UniProtKB/Swiss-Prot  Length:1304

    Alignment length:39
                                   386       396       406         
          SF3B1_HUMAN   377 SMTPEQLQAWRWEREIDERNRPLSDEELDAMFPEGYKVL 415
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhh..hhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
               Transcript 2 Exon 2.8a  PDB: P:377-413            2. Transcript 2
                 2f9d P 377 SmTPEQLQAWRWEREIDERNRPLSDEELDAmFPEGYKVL 415
                             |     386       396       406|        
                             |                          407-MSE    
                           378-MSE

Chain Q from PDB  Type:PROTEIN  Length:39
 aligned with SF3B1_HUMAN | O75533 from UniProtKB/Swiss-Prot  Length:1304

    Alignment length:39
                                   386       396       406         
          SF3B1_HUMAN   377 SMTPEQLQAWRWEREIDERNRPLSDEELDAMFPEGYKVL 415
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhh..hhhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
               Transcript 2 Exon 2.8a  PDB: Q:377-413            2. Transcript 2
                 2f9d Q 377 SmTPEQLQAWRWEREIDERNRPLSDEELDAmFPEGYKVL 415
                             |     386       396       406|        
                           378-MSE                      407-MSE

Legend:		→ Mismatch	(orange background)
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		→ 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: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: Pre-mRNA branch site protein p14 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2f9da1	A:12-125
1b	d2f9db_	B:

(no "CATH Domain" information available for 2F9D)

(no "Pfam Domain" information available for 2F9D)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SF3B6_HUMAN | Q9Y3B4)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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:0001825	blastocyst formation	The initial formation of a blastocyst from a solid ball of cells known as a morula.
	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:0005689	U12-type spliceosomal complex	Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.
	GO:0005686	U2 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U2.
	GO:0005684	U2-type spliceosomal complex	Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron that has canonical consensus sequences near the 5' and 3' ends.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0071011	precatalytic spliceosome	A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.

Chain P,Q (SF3B1_HUMAN | O75533)

molecular function
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	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:0000375	RNA splicing, via transesterification reactions	Splicing of RNA via a series of two transesterification reactions.
	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.
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0000245	spliceosomal complex assembly	The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions.
cellular component
	GO:0034693	U11/U12 snRNP	A ribonucleoprotein complex formed by the association of the U11 and U12 small nuclear ribonucleoproteins.
	GO:0005689	U12-type spliceosomal complex	Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.
	GO:0005686	U2 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U2.
	GO:0071004	U2-type prespliceosome	A spliceosomal complex that is formed by association of the 5' splice site with the U1 snRNP, while the branch point sequence is recognized by the U2 snRNP. The prespliceosome includes many proteins in addition to those found in the U1 and U2 snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation.
	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:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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: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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	2f9d
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	SF3B1_HUMAN \| O75533	:	2f9j 2fho 2peh 3lqv 4oz1 5ife
	SF3B6_HUMAN \| Q9Y3B4	:	2f9j 2fho 3lqv

(no "Related Entries Specified in the PDB File" available for 2F9D)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (5, 10)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (23, 31)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File