3FWB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   SAC3:SUS1:CDC31 COMPLEX

Authors :   M. Stewart, D. Jani

Date :   17 Jan 09 (Deposition) - 14 Apr 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Gene Gating, Complex, Cell Cycle, Cell Division, Mitosis, Mrna Transport, Nuclear Pore Complex, Nucleus, Phosphoprotein, Protein Transport, Translocation, Transport, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Jani, S. Lutz, N. J. Marshall, T. Fischer, A. Kohler, A. M. Ellisdon, E. Hurt, M. Stewart
Sus1, Cdc31, And The Sac3 Cid Region Form A Conserved Interaction Platform That Promotes Nuclear Pore Association And Mrna Export.
Mol. Cell V. 33 727 2009
PubMed-ID: 19328066 | Reference-DOI: 10.1016/J.MOLCEL.2009.01.033

Molecule 1 - CELL DIVISION CONTROL PROTEIN 31
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CDC31, DSK1, YOR257W
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	NUCLEOPORIN CDC31, NUCLEAR PORE PROTEIN CDC31

Molecule 2 - NUCLEAR MRNA EXPORT PROTEIN SAC3
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 752-805
	Gene	:	LEP1, SAC3, YD8358.13, YDR159W
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	LEUCINE PERMEASE TRANSCRIPTIONAL REGULATOR

Molecule 3 - PROTEIN SUS1
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SUS1, YBR111W-A
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3FWB)

(no "Site" information available for 3FWB)

(no "SS Bond" information available for 3FWB)

(no "Cis Peptide Bond" information available for 3FWB)

(no "SAP(SNP)/Variant" information available for 3FWB)

Asymmetric/Biological Unit (2, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CDC31_YEAST	20-55 93-128 129-161	3	A:20-55 A:93-128 A:129-161
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CDC31_YEAST	33-45 142-154	2	A:33-45 A:142-154

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YOR257W	1	YOR257W.1	XV:811008-811493	486	CDC31_YEAST	1-161	161	1	A:9-161	153

Asymmetric/Biological 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:153
 aligned with CDC31_YEAST | P06704 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:153
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158   
          CDC31_YEAST     9 QSGPLNSELLEEQKQEIYEAFSLFDMNNDGFLDYHELKVAMKALGFELPKREILDLIDEYDSEGRHLMKYDDFYIVMGEKILKRDPLDEIKRAFQLFDDDHTGKISIKNLRRVAKELGETLTDEELRAMIEEFDLDGDGEINENEFIAICTDS 161
               SCOP domains d3fwba_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhh........eehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------EF_HAND_2  PDB: A:20-55             -------------------------------------EF_HAND_2  PDB: A:93-128            EF_HAND_2  PDB: A:129-161         PROSITE (1)
                PROSITE (2) ------------------------EF_HAND_1    ------------------------------------------------------------------------------------------------EF_HAND_1    ------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:9-161 UniProt: 1-161 [INCOMPLETE]                                                                                                        Transcript 1
                 3fwb A   9 QSGPLNSELLEEQKQEIYEAFSLFDMNNDGFLDYHELKVAMKALGFELPKREILDLIDEYDSEGRHLMKYDDFYIVMGEKILKRDPLDEIKRAFQLFDDDHTGKISIKNLRRVAKELGETLTDEELRAMIEEFDLDGDGEINENEFIAICTDS 161
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158

Chain B from PDB  Type:PROTEIN  Length:54
 aligned with SAC3_YEAST | P46674 from UniProtKB/Swiss-Prot  Length:1301

    Alignment length:54
                                   761       771       781       791       801    
           SAC3_YEAST   752 SEANYRKDFIDTMTRELYDAFLHERLYLIYMDSRAELKRNSTLKKKFFEKWQAS 805
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 3fwb B 752 SEANYRKDFIDTMTRELYDAFLHERLYLIYMDSRAELKRNSTLKKKFFEKWQAS 805
                                   761       771       781       791       801

Chain C from PDB  Type:PROTEIN  Length:90
 aligned with SUS1_YEAST | Q6WNK7 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:90
                                    15        25        35        45        55        65        75        85        95
           SUS1_YEAST     6 AQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDT  95
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 3fwb C   6 AQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDT  95
                                    15        25        35        45        55        65        75        85        95

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	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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: automated matches (54)

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

d3fwba_

(no "CATH Domain" information available for 3FWB)

(no "Pfam Domain" information available for 3FWB)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CDC31_YEAST | P06704)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
	GO:0005200	structural constituent of cytoskeleton	The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007020	microtubule nucleation	The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation).
	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0043549	regulation of kinase activity	Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0030474	spindle pole body duplication	Construction of a new spindle pole body.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005825	half bridge of spindle pole body	Structure adjacent to the plaques of the spindle pole body.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0000111	nucleotide-excision repair factor 2 complex	One of several protein complexes involved in nucleotide-excision repair; possesses damaged DNA binding activity. In S. cerevisiae, it is composed of Rad4p and Rad23p.
	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:0005816	spindle pole body	The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.
	GO:0070390	transcription export complex 2	A protein complex that couples SAGA-dependent gene expression to mRNA export at the inner side of the nuclear pore complex (NPC). The TREX-2 complex is tethered to the inner side of the NPC via the nucleoporins Nup1 and Nup60; in S. cerevisiae it contains Sac3p, Thp1p, Sus1p and Cdc31p.

Chain B (SAC3_YEAST | P46674)

molecular function
	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:0030029	actin filament-based process	Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins.
	GO:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0071033	nuclear retention of pre-mRNA at the site of transcription	The process involved in retention of aberrant or improperly formed mRNAs, e.g. those that are incorrectly or incompletely spliced or that have incorrectly formed 3'-ends, within the nucleus at the site of transcription.
	GO:0000973	posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery	The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed.
	GO:0006611	protein export from nucleus	The directed movement of a protein from the nucleus into the cytoplasm.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042274	ribosomal small subunit biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0006283	transcription-coupled nucleotide-excision repair	The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	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:0070390	transcription export complex 2	A protein complex that couples SAGA-dependent gene expression to mRNA export at the inner side of the nuclear pore complex (NPC). The TREX-2 complex is tethered to the inner side of the NPC via the nucleoporins Nup1 and Nup60; in S. cerevisiae it contains Sac3p, Thp1p, Sus1p and Cdc31p.

Chain C (SUS1_YEAST | Q6WNK7)

molecular function
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
	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).
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
	GO:0051568	histone H3-K4 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
	GO:0034729	histone H3-K79 methylation	The modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone.
	GO:0016578	histone deubiquitination	The modification of histones by removal of ubiquitin groups.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0071033	nuclear retention of pre-mRNA at the site of transcription	The process involved in retention of aberrant or improperly formed mRNAs, e.g. those that are incorrectly or incompletely spliced or that have incorrectly formed 3'-ends, within the nucleus at the site of transcription.
	GO:0016973	poly(A)+ mRNA export from nucleus	The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0000973	posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery	The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0032880	regulation of protein localization	Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0071819	DUBm complex	A protein complex that forms part of SAGA-type complexes SAGA and SLIK, and mediates deubiquitination of histone H2B. In S. cerevisiae, the DUBm consists of the proteins Ubp8p, Sgf11p, Sus1p, and Sgf73p.
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0000124	SAGA complex	A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	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:0070390	transcription export complex 2	A protein complex that couples SAGA-dependent gene expression to mRNA export at the inner side of the nuclear pore complex (NPC). The TREX-2 complex is tethered to the inner side of the NPC via the nucleoporins Nup1 and Nup60; in S. cerevisiae it contains Sac3p, Thp1p, Sus1p and Cdc31p.

Asymmetric/Biological Unit
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UniProtKB/Swiss-Prot
	CDC31_YEAST \| P06704	:	2doq 2gv5 3fwc 4mbe
	SAC3_YEAST \| P46674	:	3fwc 3t5v 4c31 4mbe 4trq 5g5p 5l3t
	SUS1_YEAST \| Q6WNK7	:	3fwc 3kik 3kjl 3m99 3mhh 3mhs 4c31 4fip 4fjc 4fk5 4mbe 4wa6 4zux

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