3H7H - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN TRANSCRIPTION ELONGATION FACTOR DSIF, HSPT4/HSPT5 (176-273)

Authors :   S. Wenzel, B. M. Wohrl, P. Rosch, B. M. Martins

Date :   27 Apr 09 (Deposition) - 08 Dec 09 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Helices Surrounding Beta Sheet, Transcription, Activator, Metal- Binding, Nucleus, Repressor, Transcription Regulation, Zinc-Finger, Methylation, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Wenzel, B. M. Martins, P. Rosch, B. M. Wohrl
Crystal Structure Of The Human Transcription Elongation Factor Dsif Hspt4 Subunit In Complex With The Hspt5 Dimerization Interface
Biochem. J. V. 425 373 2010
PubMed-ID: 19860741 | Reference-DOI: 10.1042/BJ20091422

Molecule 1 - TRANSCRIPTION ELONGATION FACTOR SPT4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETGB_1A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HSPT4, DRB SENSITIVITY-INDUCING FACTOR SMALL SUBUNIT, DSIF SMALL SUBUNIT, DSIF P14

Molecule 2 - TRANSCRIPTION ELONGATION FACTOR SPT5
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 176-273
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HSPT5, DRB SENSITIVITY-INDUCING FACTOR LARGE SUBUNIT, DSIF LARGE SUBUNIT, DSIF P160, TAT-COTRANSACTIVATOR 1 PROTEIN, TAT-CT1 PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:35 , CYS A:36 , TYR A:39 , VAL A:106 , HOH A:174 , HOH A:200	BINDING SITE FOR RESIDUE BME A 118
2	AC2	SOFTWARE	CYS A:16 , CYS A:19 , CYS A:33 , CYS A:36	BINDING SITE FOR RESIDUE ZN A 119

(no "SS Bond" information available for 3H7H)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:104	-	Gly A:105

(no "SAP(SNP)/Variant" information available for 3H7H)

(no "PROSITE Motif" information available for 3H7H)

(no "Exon" information available for 3H7H)

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:118
 aligned with SPT4H_HUMAN | P63272 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:118
                            1 2                                                                                                                   
                            | |      9        19        29        39        49        59        69        79        89        99       109        
          SPT4H_HUMAN     1 M-ALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRDTAIKT 117
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh......eeee.....eeehhhhhhhh...hhhhhh...hhhhhhhhee..eeeeeee.hhhhhhhhhhh.......eeeeeee....hhhhhhhhhhh..........ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3h7h A   0 MGALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRDTAIKT 117
                                     9        19        29        39        49        59        69        79        89        99       109

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with SPT5H_HUMAN | O00267 from UniProtKB/Swiss-Prot  Length:1087

    Alignment length:95
                                   184       194       204       214       224       234       244       254       264     
          SPT5H_HUMAN   175 KDPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGYWNQQMVPIKEMTDVLKVVKE 269
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhhh.........eeee......eeeeee.hhhhhhhhhh.hhhhhhhh...ee.hhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 3h7h B 175 MDPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYKQTHVKQAIEGVGNLRLGYWNQQMVPIKEMTDVLKVVKE 269
                                   184       194       204       214       224       234       244       254       264

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 3H7H)

(no "CATH Domain" information available for 3H7H)

(no "Pfam Domain" information available for 3H7H)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SPT4H_HUMAN | P63272)

molecular function
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0032785	negative regulation of DNA-templated transcription, elongation	Any process that stops, prevents, or reduces 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:0034244	negative regulation of transcription elongation from RNA polymerase II promoter	Any process that stops, prevents, or reduces 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: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:0032786	positive regulation of DNA-templated transcription, elongation	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 a DNA-dependent RNA polymerase.
	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:0050434	positive regulation of viral transcription	Any process that activates or increases the frequency, rate or extent of viral 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: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:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0032044	DSIF complex	A heterodimeric protein complex formed of Spt4 and Spt5 proteins which is expressed in eukaryotes from yeast to man. DSIF is an inhibitory elongation factor that promotes RNA polymerase II transcriptional pausing, but can also stimulate transcriptional elongation under certain conditions, and may play a role in RNA processing via its physical association with mRNA capping enzymes.
	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.

Chain B (SPT5H_HUMAN | O00267)

molecular function
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any 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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006370	7-methylguanosine mRNA capping	Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
	GO:0006354	DNA-templated transcription, elongation	The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
	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: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:0032785	negative regulation of DNA-templated transcription, elongation	Any process that stops, prevents, or reduces 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:1900364	negative regulation of mRNA polyadenylation	Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.
	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:0032786	positive regulation of DNA-templated transcription, elongation	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 a DNA-dependent RNA polymerase.
	GO:0016239	positive regulation of macroautophagy	Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.
	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:0050434	positive regulation of viral transcription	Any process that activates or increases the frequency, rate or extent of viral transcription.
	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: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:0010033	response to organic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
	GO:0039692	single stranded viral RNA replication via double stranded DNA intermediate	A viral genome replication where the template is single-stranded RNA (ssRNA), and which proceeds via a double stranded DNA (dsDNA) intermediate molecule. Viral genomic RNA is first reverse transcribed into dsDNA, which integrates into the host chromosomal DNA, where it is transcribed by host RNA polymerase II.
	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:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0032044	DSIF complex	A heterodimeric protein complex formed of Spt4 and Spt5 proteins which is expressed in eukaryotes from yeast to man. DSIF is an inhibitory elongation factor that promotes RNA polymerase II transcriptional pausing, but can also stimulate transcriptional elongation under certain conditions, and may play a role in RNA processing via its physical association with mRNA capping enzymes.
	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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BME	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:104 - Gly A:105	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3h7h
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SPT4H_HUMAN \| P63272
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	SPT5H_HUMAN \| O00267
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SPT4H_HUMAN \| P63272
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	SPT5H_HUMAN \| O00267
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SPT5H_HUMAN \| O00267	:	2do3 2e6z 2e70 4l1u

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (29, 45)

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