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Title :   CRYSTAL STRUCTURE OF THE SPT6 TANDEM SH2 DOMAIN FROM SACCHAROMYCES CEREVISIAE, FORM SE-SPT6 (1247-1451)

Authors :   D. Close, C. P. Hill

Date :   01 Dec 10 (Deposition) - 30 Mar 11 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A

Keywords :   Tandem Sh2, Transcription Elongation, Nucleus, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Close, S. J. Johnson, M. A. Sdano, S. M. Mcdonald, H. Robinson, T. Formosa, C. P. Hill
Crystal Structures Of The S. Cerevisiae Spt6 Core And C-Terminal Tandem Sh2 Domain.
J. Mol. Biol. V. 408 697 2011
PubMed-ID: 21419780 | Reference-DOI: 10.1016/J.JMB.2011.03.002

Molecule 1 - TRANSCRIPTION ELONGATION FACTOR SPT6
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1247-1451
	Gene	:	CRE2, G6169, SPT6, SSN20, YGR116W
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Strain	:	S288C
	Synonym	:	CHROMATIN ELONGATION FACTOR SPT6

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:23 , ARG A:1282 , SER A:1284 , SER A:1285	BINDING SITE FOR RESIDUE SO4 A 1

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

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

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	SPT6_YEAST	1257-1354	1	A:1257-1354

(no "Exon" information available for 3PSJ)

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
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Chain A from PDB  Type:PROTEIN  Length:189
 aligned with SPT6_YEAST | P23615 from UniProtKB/Swiss-Prot  Length:1451

    Alignment length:189
                                  1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391      1401      1411      1421      1431         
          SPT6_YEAST   1252 RVINHPYYFPFNGRQAEDYLRSKERGEFVIRQSSRGDDHLVITWKLDKDLFQHIDIQELEKENPLALGKVLIVDNQKYNDLDQIIVEYLQNKVRLLNEMTSSEKFKSGTKKDVVKFIEDYSRVNPNKSVYYFSLNHDNPGWFYLMFKINANSKLYTWNVKLTNTGYFLVNYNYPSVIQLCNGFKTLLKS 1440
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------SH2-3psjA01 A:1258-1339                                                           ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee..hhhhhhhhhhh.....eeeee......eeeeeeeee..eeeeeeeeee..........eeee..eee.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh....eeeeee......eeeeeee.......eeeeeee....eee..eee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SH2  PDB: A:1257-1354 UniProt: 1257-1354                                                          -------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3psj A 1252 RVINHPYYFPFNGRQAEDYLRSKERGEFVIRQSSRGDDHLVITWKLDKDLFQHIDIQELEKENPLALGKVLIVDNQKYNDLDQIIVEYLQNKVRLLNEmTSSEKFKSGTKKDVVKFIEDYSRVNPNKSVYYFSLNHDNPGWFYLmFKINANSKLYTWNVKLTNTGYFLVNYNYPSVIQLCNGFKTLLKS 1440
                                  1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381      1391    | 1401      1411      1421      1431         
                                                                                                                           1350-MSE                                      1396-MSE

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 3PSJ)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SH2] (119)

Family: SH2 (119)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (3)

SH2-3psjA01

A:1258-1339

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SPT6_YEAST | P23615)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0031491	nucleosome binding	Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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:0001073	transcription antitermination factor activity, DNA binding	Binds to DNA, typically within region of the promoter and transcribed region, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind DNA include the lambda Q protein.
	GO:0000991	transcription factor activity, core RNA polymerase II binding	Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
	GO:0070827	chromatin maintenance	The chromatin organization process that preserves chromatin in a stable functional or structural state.
	GO:0006325	chromatin organization	Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0000433	negative regulation of transcription from RNA polymerase II promoter by glucose	Any process involving glucose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0034728	nucleosome organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of one or more nucleosomes.
	GO:0016973	poly(A)+ mRNA export from nucleus	The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
	GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	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:0071931	positive regulation of transcription involved in G1/S transition of mitotic cell cycle	Any process that activates or increases transcription as part of the G1/S transition of the mitotic cell cycle.
	GO:0032784	regulation of DNA-templated transcription, elongation	Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
	GO:0000414	regulation of histone H3-K36 methylation	Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3.
	GO:0031440	regulation of mRNA 3'-end processing	Any process that modulates the frequency, rate or extent of mRNA 3'-end processing, any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0060303	regulation of nucleosome density	Any process that modulates the number of nucleosomes in a given region of a chromosome.
	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:0043618	regulation of transcription from RNA polymerase II promoter in response to stress	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0001178	regulation of transcriptional start site selection at RNA polymerase II promoter	Any process that modulates the rate, frequency or extent of a process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
	GO:0031564	transcription antitermination	Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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:0035327	transcriptionally active chromatin	The ordered and organized complex of DNA and protein that forms regions of the chromosome that are being actively transcribed.

Asymmetric/Biological Unit
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	SPT6_YEAST \| P23615	:	2l3t 3oak 3psf 3psi 3psk

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