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Title :   STRUCTURE OF HUMAN TFIIS DOMAIN II

Authors :   X. P. Hu, G. Averell, X. Y. Ye, J. Hou, H. Luo

Date :   07 Jun 10 (Deposition) - 18 May 11 (Release) - 18 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

Chains :   Asym./Biol. Unit : A

Keywords :   Helix Bundle, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Ye, A. Gnatt, X. P. Hu
Structure Of Human Tfiis Domain Ii
To Be Published
PubMed: search

Molecule 1 - TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET151
	Expression System Strain	:	BL21 DE3 PLYS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	TFIIS DOMAIN II, RESIDUES 131-232
	Gene	:	GTF2S, TCEA1, TFIIS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1, TRANSCRIPTION ELONGATION FACTOR TFIIS.O

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:201 , HOH A:1261	BINDING SITE FOR RESIDUE NA A 1229
2	AC2	SOFTWARE	SER A:196 , ASN A:197	BINDING SITE FOR RESIDUE NA A 1230

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

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

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TFIIS_CENTRAL	PS51321	TFIIS central domain profile.	TCEA1_HUMAN	140-256	1	A:140-228

(no "Exon" information available for 3NDQ)

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:97
 aligned with TCEA1_HUMAN | P23193 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:97
                                   141       151       161       171       181       191       201       211       221       
          TCEA1_HUMAN   132 RAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEM 228
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----TFIIS_M-3ndqA01 A:136-228                                                                     Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------TFIIS_CENTRAL  PDB: A:140-228 UniProt: 140-256                                            PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3ndq A 132 RAPSTSDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEM 228
                                   141       151       161       171       181       191       201       211       221

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 3NDQ)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: TFIIS_M] (2)

Family: TFIIS_M (2)

Homo sapiens (Human) (1)

TFIIS_M-3ndqA01

A:136-228

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TCEA1_HUMAN | P23193)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic 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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:1901919	positive regulation of exoribonuclease activity	Any process that activates or increases the frequency, rate or extent of exoribonuclease activity.
	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: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.
	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.
cellular component
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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
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	TCEA1_HUMAN \| P23193	:	1tfi 5iy6 5iy7 5iy8 5iya 5iyb 5iyc

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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

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