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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE YEAST PML1 SPLICING FACTOR AND ITS INTEGRATION INTO THE RES COMPLEX

Authors :   M. A. Brooks, A. Dziembowski, S. Quevillon-Cheruel, V. Henriot, C. Fau H. Van Tilbeurgh, B. Seraphin

Date :   27 Aug 08 (Deposition) - 26 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Mrna Processing, Pml1/Snu17/Bud13, Pre-Mrna Splicing, Saccharomyces Cerevisiae, Phospho-Peptide Recognition, Res, Nucleus, Mrna Splicing, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Brooks, A. Dziembowski, S. Quevillon-Cheruel, V. Henriot, C. Faux, H. Van Tilbeurgh, B. Seraphin
Structure Of The Yeast Pml1 Splicing Factor And Its Integration Into The Res Complex
Nucleic Acids Res. V. 37 129 2009
PubMed-ID: 19033360 | Reference-DOI: 10.1093/NAR/GKN894

Molecule 1 - PRE-MRNA LEAKAGE PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Fragment	:	FHA DOMAIN, RESIDUES 25-204
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Strain	:	S288C
	Synonym	:	PML1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:182 , ASN A:203 , HIS A:205	BINDING SITE FOR RESIDUE GOL A 301
2	AC2	SOFTWARE	ALA A:58 , ILE A:59 , ASN A:147 , LEU B:68 , LEU B:70	BINDING SITE FOR RESIDUE GOL A 302
3	AC3	SOFTWARE	ARG A:108 , SER A:137 , LYS A:138	BINDING SITE FOR RESIDUE SO4 A 401
4	AC4	SOFTWARE	ILE A:151 , TYR B:78 , LEU B:152 , CYS B:154 , GLU B:179 , LEU B:180 , PHE B:201 , ASN B:203	BINDING SITE FOR RESIDUE GOL B 301
5	AC5	SOFTWARE	ARG B:108 , SER B:137 , LYS B:138	BINDING SITE FOR RESIDUE SO4 B 401

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FHA_DOMAIN	PS50006	Forkhead-associated (FHA) domain profile.	PML1_YEAST	104-172	2	A:104-172 B:104-172

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FHA_DOMAIN	PS50006	Forkhead-associated (FHA) domain profile.	PML1_YEAST	104-172	1	A:104-172 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FHA_DOMAIN	PS50006	Forkhead-associated (FHA) domain profile.	PML1_YEAST	104-172	1	- B:104-172

(no "Exon" information available for 2JKD)

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:150
 aligned with PML1_YEAST | Q07930 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:159
                                                                                                                                                                                     204   
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198     |   
           PML1_YEAST    49 ALKHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELGHSLDTDLDDRTEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNV---   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhh..hhhhh.eeeeeeee.........eeee.....eeeeee....---------.......eee.........eeeeeeee..eeeeeeee.......ee..ee......eee....eee...hhhhh.eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------FHA_DOMAIN  PDB: A:104-172 UniProt: 104-172                          ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jkd A  49 ALKHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELGH---------TEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNVHHH 207
                                    58        68        78        88        98       108   |     -   |   128       138       148       158       168       178       188       198         
                                                                                         112       122

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with PML1_YEAST | Q07930 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:157
                                                                                                                                                                                   204   
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   |   
           PML1_YEAST    51 KHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELGHSLDTDLDDRTEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNV---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------FHA-2jkd          B01 B:104-189                                                       ------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------FHA-2jkd          B02 B:104-189                                                       ------------------ Pfam domains (2)
         Sec.struct. author .........hhhhhhhhh..hhhhh.eeeeeeee..hhhhh..eeee.....eeeeee...----------.......eee.........eeeeeeee..eeeeeeee.......ee..ee......ee.....eee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------FHA_DOMAIN  PDB: B:104-172 UniProt: 104-172                          ----------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jkd B  51 KHVEPQDAISPDNYMDMLGLEARDRTMYELVIYRKNDKDKGPWKRYDLNGRSCYLVGRELG----------TEIVVADIGIPEETSSKQHCVIQFRNVRGILKCYVMDLDSSNGTCLNNVVIPGARYIELRSGDVLTLSEFEEDNDYELIFMNVHHH 207
                                    60        70        80        90       100       110|        - |     130       140       150       160       170       180       190       200       
                                                                                      111        122

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 '\|'

(no "SCOP Domain" information available for 2JKD)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SMAD-FHA (27)

Family: FHA (18)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (8)

1a	FHA-2jkdB01	B:104-189
1b	FHA-2jkdB02	B:104-189

Asymmetric Unit(hide GO term definitions)

Chain A,B (PML1_YEAST | Q07930)

molecular function
	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.
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:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	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:0051237	maintenance of RNA location	Any process in which RNA is maintained in a location and prevented from moving elsewhere.
cellular component
	GO:0070274	RES complex	A protein complex that is required for efficient splicing, and prevents leakage of unspliced pre-mRNAs from the nucleus (named for pre-mRNA REtention and Splicing). In Saccharomyces, the complex consists of Ist3p, Bud13p, and Pml1p.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

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(no "Cis Peptide Bonds" information available for 2jkd)

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	2jkd
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	PML1_YEAST \| Q07930	:	2mkc 2my3 3els 3elv 5gm6 5lqw

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Description

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Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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