3KIK - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   SGF11:SUS1 COMPLEX

Authors :   M. Stewart, A. M. Ellisdon

Date :   02 Nov 09 (Deposition) - 08 Dec 09 (Release) - 23 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E  (1x)
Biol. Unit 2: B,F  (1x)
Biol. Unit 3: C,G  (1x)
Biol. Unit 4: D,H  (1x)

Keywords :   Articulated Hirpin Fold, Saga Complex, Activator, Chromatin Regulator, Metal-Binding, Nucleus, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Mrna Transport, Nuclear Pore Complex, Protein Transport, Translocation, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Ellisdon, D. Jani, A. Kohler, E. Hurt, M. Stewart
Structural Basis For The Interaction Between Yeast Spt-Ada-Gcn5 Acetyltransferase (Saga) Complex Components Sgf11 And Sus1
J. Biol. Chem. V. 285 3850 2010
PubMed-ID: 20007317 | Reference-DOI: 10.1074/JBC.M109.070839

Molecule 1 - PROTEIN SUS1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNMTK
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	POPR
	Gene	:	SUS1, YBR111W-A
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - SAGA-ASSOCIATED FACTOR 11
	Chains	:	E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T-1
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PGEX
	Fragment	:	SUS1 BINDING REGION OF SGF11
	Gene	:	SGF11, YPL047W
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	11 KDA SAGA-ASSOCIATED FACTOR

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A				E
Biological Unit 2 (1x)	:		B				F
Biological Unit 3 (1x)	:			C				G
Biological Unit 4 (1x)	:				D				H

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3KIK)

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

Asymmetric Unit

No.	Residues
1	Met C:3	-	Asp C:4

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

(no "PROSITE Motif" information available for 3KIK)

(no "Exon" information available for 3KIK)

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:94
 aligned with SUS1_YEAST | Q6WNK7 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:94
                                    12        22        32        42        52        62        72        82        92    
            SUS1_YEAST    3 MDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ 96
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3kik A  3 MDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ 96
                                    12        22        32        42        52        62        72        82        92

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with SUS1_YEAST | Q6WNK7 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:92
                                    13        23        33        43        53        63        73        83        93  
            SUS1_YEAST    4 DTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDT 95
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  3kik B  4 DTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDT 95
                                    13        23        33        43        53        63        73        83        93

Chain C from PDB  Type:PROTEIN  Length:93
 aligned with SUS1_YEAST | Q6WNK7 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:93
                                    12        22        32        42        52        62        72        82        92   
            SUS1_YEAST    3 MDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDT 95
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                  3kik C  3 MDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDT 95
                                    12        22        32        42        52        62        72        82        92

Chain D from PDB  Type:PROTEIN  Length:92
 aligned with SUS1_YEAST | Q6WNK7 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:92
                                    14        24        34        44        54        64        74        84        94  
            SUS1_YEAST    5 TAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ 96
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --EnY2-3kikD01 D:7-90                                                                 ------ Pfam domains (1)
           Pfam domains (2) --EnY2-3kikD02 D:7-90                                                                 ------ Pfam domains (2)
           Pfam domains (3) --EnY2-3kikD03 D:7-90                                                                 ------ Pfam domains (3)
           Pfam domains (4) --EnY2-3kikD04 D:7-90                                                                 ------ Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  3kik D  5 TAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ 96
                                    14        24        34        44        54        64        74        84        94

Chain E from PDB  Type:PROTEIN  Length:27
 aligned with SGF11_YEAST | Q03067 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:27
                                    15        25       
           SGF11_YEAST    6 ITIDSISNGILNNLLTTLIQDIVARET 32
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author ........................... Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3kik E  6 STIDSISNGILNNLLTTLIQDIVARET 32
                                    15        25

Chain F from PDB  Type:PROTEIN  Length:27
 aligned with SGF11_YEAST | Q03067 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:27
                                    15        25       
           SGF11_YEAST    6 ITIDSISNGILNNLLTTLIQDIVARET 32
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                  3kik F  6 STIDSISNGILNNLLTTLIQDIVARET 32
                                    15        25

Chain G from PDB  Type:PROTEIN  Length:28
 aligned with SGF11_YEAST | Q03067 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:28
                                    15        25        
           SGF11_YEAST    6 ITIDSISNGILNNLLTTLIQDIVARETT 33
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                  3kik G  6 STIDSISNGILNNLLTTLIQDIVARETT 33
                                    15        25

Chain H from PDB  Type:PROTEIN  Length:28
 aligned with SGF11_YEAST | Q03067 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:28
                                    14        24        
           SGF11_YEAST    5 TITIDSISNGILNNLLTTLIQDIVARET 32
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                  3kik H  5 GSTIDSISNGILNNLLTTLIQDIVARET 32
                                    14        24

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 3KIK)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: EnY2] (4)

Family: EnY2 (4)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (4)

1a	EnY2-3kikD01	D:7-90
1b	EnY2-3kikD02	D:7-90
1c	EnY2-3kikD03	D:7-90
1d	EnY2-3kikD04	D:7-90

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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.

Chain E,F,G,H (SGF11_YEAST | Q03067)

molecular function
	GO:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
	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: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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0016578	histone deubiquitination	The modification of histones by removal of ubiquitin groups.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	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:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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: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: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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		Met C:3 - Asp C:4	[ RasMol ]

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Description

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