3NFQ - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CONSERVED CENTRAL DOMAIN OF YEAST SPN1/IWS1

Authors :   L. A. Stargell, K. Luger

Date :   10 Jun 10 (Deposition) - 13 Oct 10 (Release) - 17 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Spn1, Transcription, Rna Polymerase Ii (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Pujari, C. A. Radebaugh, J. V. Chodaparambil, U. M. Muthurajan, A. R. Almeida, J. A. Fischbeck, K. Luger, L. A. Stargell
The Transcription Factor Spn1 Regulates Gene Expression Via A Highly Conserved Novel Structural Motif.
J. Mol. Biol. V. 404 1 2010
PubMed-ID: 20875428 | Reference-DOI: 10.1016/J.JMB.2010.09.040

Molecule 1 - TRANSCRIPTION FACTOR IWS1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	ROSETTA PLYSS
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	MINI-SPN1 CONSERVED DOMAIN, RESIDUES 141-310
	Gene	:	IWS1, SPN1, YPR133C
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Strain	:	FT5
	Synonym	:	INTERACTS WITH SPT6 PROTEIN 1, SUPPRESSES POSTRECRUITMENT FUNCTIONS PROTEIN 1

		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 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3NFQ)

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIIS_N	PS51319	TFIIS N-terminal domain profile.	IWS1_YEAST	219-296	2	A:79-154 B:79-150

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIIS_N	PS51319	TFIIS N-terminal domain profile.	IWS1_YEAST	219-296	1	A:79-154 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIIS_N	PS51319	TFIIS N-terminal domain profile.	IWS1_YEAST	219-296	1	- B:79-150

(no "Exon" information available for 3NFQ)

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:147
 aligned with IWS1_YEAST | Q06505 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:147
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       
           IWS1_YEAST   148 DDLEQYLDEKILRLKDEMNIAAQLDIDTLNKRIETGDTSLIAMQKVKLLPKVVSVLSKANLADTILDNNLLQSVRIWLEPLPDGSLPSFEIQKSLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWTRPII 294
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------TFIIS_N  PDB: A:79-154 UniProt: 219-296                                      PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfq A   8 DDLEQYLDEKILRLKDEmNIAAQLDIDTLNKRIETGDTSLIAmQKVKLLPKVVSVLSKANLADTILDNNLLQSVRIWLEPLPDGSLPSFEIQKSLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWTRPII 154
                                    17       |27        37        47  |     57        67        77        87        97       107       117       127       137       147       
                                            25-MSE                   50-MSE

Chain B from PDB  Type:PROTEIN  Length:143
 aligned with IWS1_YEAST | Q06505 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:143
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287   
           IWS1_YEAST   148 DDLEQYLDEKILRLKDEMNIAAQLDIDTLNKRIETGDTSLIAMQKVKLLPKVVSVLSKANLADTILDNNLLQSVRIWLEPLPDGSLPSFEIQKSLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWT 290
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------Med26-3nfqB01 B:101-150                            Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------Med26-3nfqB02 B:101-150                            Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------TFIIS_N  PDB: B:79-150 UniProt: 219-296                                  PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nfq B   8 DDLEQYLDEKILRLKDEmNIAAQLDIDTLNKRIETGDTSLIAmQKVKLLPKVVSVLSKANLADTILDNNLLQSVRIWLEPLPDGSLPSFEIQKSLFAALNDLPVKTEHLKESGLGRVVIFYTKSKRVEAQLARLAEKLIAEWT 150
                                    17       |27        37        47  |     57        67        77        87        97       107       117       127       137       147   
                                            25-MSE                   50-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 3NFQ)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Med26] (7)

Family: Med26 (7)

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

1a	Med26-3nfqB01	B:101-150
1b	Med26-3nfqB02	B:101-150

Asymmetric Unit(hide GO term definitions)

Chain A,B (IWS1_YEAST | Q06505)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0001076	transcription factor activity, RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, 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.
	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:0016973	poly(A)+ mRNA export from nucleus	The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
	GO:0060303	regulation of nucleosome density	Any process that modulates the number of nucleosomes in a given region of a chromosome.
	GO:0034243	regulation of transcription elongation from RNA polymerase II promoter	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 RNA polymerase II.
	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: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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	3nfq
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