2RNR - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE COMPLEX BETWEEN TFIIE ALPHA C-TERMINAL ACIDIC DOMAIN AND TFIIH P62 PH DOMAIN

Authors :   M. Okuda, Y. Nishimura

Date :   31 Jan 08 (Deposition) - 01 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   General Transcription Factor, Human Tfiie Alpha, Human Tfiih P62, Acidic Domain, Ph Domain, Dna Damage, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Okuda, A. Tanaka, M. Satoh, S. Mizuta, M. Takazawa, Y. Ohkuma, Y. Nishimura
Structural Insight Into The Tfiie-Tfiih Interaction: Tfiie And P53 Share The Binding Region On Tfiih
Embo J. V. 27 1161 2008
PubMed-ID: 18354501 | Reference-DOI: 10.1038/EMBOJ.2008.47
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET3A
	Expression System Vector Type	:	VECTOR
	Fragment	:	C-TERMINAL ACIDIC DOMAIN, UNP RESIDUES 378-439
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TFIIE-ALPHA, GENERAL TRANSCRIPTION FACTOR IIE SUBUNIT 1, GENERAL TRANSCRIPTION FACTOR IIE 56 KDA SUBUNIT

Molecule 2 - TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P62 SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PGEX4T-1
	Expression System Vector Type	:	VECTOR
	Fragment	:	PH DOMAIN, UNP RESIDUES 1-108
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BASIC TRANSCRIPTION FACTOR 2 62 KDA SUBUNIT, BTF2- P62, GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 1


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2RNR)

(no "Site" information available for 2RNR)

(no "SS Bond" information available for 2RNR)

(no "Cis Peptide Bond" information available for 2RNR)

(no "SAP(SNP)/Variant" information available for 2RNR)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BSD	PS50858	BSD domain profile.	TF2H1_HUMAN	99-154 180-232	1	B:99-108 -

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1g	ENST00000265963	1g	ENSE00002143325	chr11:18344143-18344287	145	TF2H1_HUMAN	-	0	0	-	-
1.4b	ENST00000265963	4b	ENSE00002171519	chr11:18354607-18354775	169	TF2H1_HUMAN	1-52	52	1	B:1-52	52
1.5c	ENST00000265963	5c	ENSE00000886580	chr11:18357301-18357493	193	TF2H1_HUMAN	52-116	65	1	B:52-108	57
1.7a	ENST00000265963	7a	ENSE00000886581	chr11:18359656-18359821	166	TF2H1_HUMAN	116-171	56	0	-	-
1.8	ENST00000265963	8	ENSE00001597724	chr11:18361111-18361204	94	TF2H1_HUMAN	172-203	32	0	-	-
1.9	ENST00000265963	9	ENSE00001742103	chr11:18362808-18362957	150	TF2H1_HUMAN	203-253	51	0	-	-
1.10	ENST00000265963	10	ENSE00001748719	chr11:18363075-18363154	80	TF2H1_HUMAN	253-279	27	0	-	-
1.11b	ENST00000265963	11b	ENSE00001692627	chr11:18369135-18369262	128	TF2H1_HUMAN	280-322	43	0	-	-
1.12a	ENST00000265963	12a	ENSE00001662355	chr11:18369379-18369466	88	TF2H1_HUMAN	322-351	30	0	-	-
1.13b	ENST00000265963	13b	ENSE00001609933	chr11:18373428-18373516	89	TF2H1_HUMAN	352-381	30	0	-	-
1.14c	ENST00000265963	14c	ENSE00001683216	chr11:18373876-18373993	118	TF2H1_HUMAN	381-420	40	0	-	-
1.15b	ENST00000265963	15b	ENSE00001765402	chr11:18379499-18379589	91	TF2H1_HUMAN	421-451	31	0	-	-
1.16a	ENST00000265963	16a	ENSE00001676092	chr11:18380072-18380187	116	TF2H1_HUMAN	451-489	39	0	-	-
1.17	ENST00000265963	17	ENSE00001763947	chr11:18382162-18382254	93	TF2H1_HUMAN	490-520	31	0	-	-
1.18d	ENST00000265963	18d	ENSE00001106704	chr11:18387330-18388577	1248	TF2H1_HUMAN	521-548	28	0	-	-

2.1b	ENST00000283875	1b	ENSE00001559931	chr3:120461579-120461641	63	T2EA_HUMAN	-	0	0	-	-
2.3c	ENST00000283875	3c	ENSE00001012283	chr3:120469370-120469847	478	T2EA_HUMAN	1-150	150	0	-	-
2.4	ENST00000283875	4	ENSE00001012285	chr3:120489575-120489776	202	T2EA_HUMAN	150-217	68	0	-	-
2.5b	ENST00000283875	5b	ENSE00001074548	chr3:120495270-120495511	242	T2EA_HUMAN	217-298	82	0	-	-
2.6	ENST00000283875	6	ENSE00001206456	chr3:120499890-120501916	2027	T2EA_HUMAN	298-439	142	1	A:378-439	62

NMR Structure

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:62
 aligned with T2EA_HUMAN | P29083 from UniProtKB/Swiss-Prot  Length:439

    Alignment length:62
                                   387       397       407       417       427       437  
           T2EA_HUMAN   378 EEDEEEDDEFEEVADDPIVMVAGRPFSYSEVSQRPELVAQMTPEEKEAYIAMGQRMFEDLFE 439
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains TFIIE-A_C-term-2rnrA01 A:378-439                               Pfam domains
         Sec.struct. author ..........eee....eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.6  PDB: A:378-439 UniProt: 298-439 [INCOMPLETE]         Transcript 2
                 2rnr A 378 EEDEEEDDEFEEVADDPIVMVAGRPFSYSEVSQRPELVAQMTPEEKEAYIAMGQRMFEDLFE 439
                                   387       397       407       417       427       437

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with TF2H1_HUMAN | P32780 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
          TF2H1_HUMAN     1 MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKAN 108
               SCOP domains d2rnrb_ B: TFIIH basal transcription factor complex p62 subunit (BTF2-p62), N-terminal domain                SCOP domains
               CATH domains 2rnrB00 B:1-108 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                  CATH domains
               Pfam domains --------TFIIH_BTF_p62_N-2rnrB02 B:9-81                                           -----------------BSD-2rnrB0 Pfam domains
         Sec.struct. author .........eeeeeeee...eeeeee...eeeeee.......eeee...eeeeee.......eeeeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------BSD        PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: B:1-52 UniProt: 1-52                -------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.5c  PDB: B:52-108 UniProt: 52-116 [INCOMPLETE]     Transcript 1 (2)
                 2rnr B   1 MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKAN 108
                                    10        20        30        40        50        60        70        80        90       100

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PH domain-like barrel (258)

Superfamily: PH domain-like (257)

Family: TFIIH domain (9)

Protein domain: TFIIH basal transcription factor complex p62 subunit (BTF2-p62), N-terminal domain (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d2rnrb_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: PH-domain like (150)

Homologous Superfamily: Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) (147)

Human (Homo sapiens) (85)

2rnrB00

B:1-108

NMR Structure(hide GO term definitions)

Chain A (T2EA_HUMAN | P29083)

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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042795	snRNA transcription from RNA polymerase II promoter	The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
	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:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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 (TF2H1_HUMAN | P32780)

molecular function
	GO:0008094	DNA-dependent ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
	GO:0008353	RNA polymerase II carboxy-terminal domain kinase activity	Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats.
	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: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:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
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:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0070911	global genome nucleotide-excision repair	The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
	GO:0006289	nucleotide-excision repair	A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
	GO:0000717	nucleotide-excision repair, DNA duplex unwinding	The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.
	GO:0033683	nucleotide-excision repair, DNA incision	A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
	GO:0006295	nucleotide-excision repair, DNA incision, 3'-to lesion	The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
	GO:0006296	nucleotide-excision repair, DNA incision, 5'-to lesion	The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
	GO:0006294	nucleotide-excision repair, preincision complex assembly	The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
	GO:0006293	nucleotide-excision repair, preincision complex stabilization	The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
	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:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006363	termination of RNA polymerase I transcription	The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit.
	GO:0006362	transcription elongation from RNA polymerase I promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.
	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:0006361	transcription initiation from RNA polymerase I promoter	Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	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:0000439	core TFIIH complex	The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD.
	GO:0005675	holo TFIIH complex	A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex.
	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.

NMR Structure
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	2rnr
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1d8j	SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA NMR 20 STRUCTURES
1d8k	SOLUTION STRUCTURE OF THE CENTRAL CORE DOMAIN OF TFIIE BETA NMR MINIMIZED AVERAGE STRUCTURE
1vd4	SOLUTION STRUCTURE OF THE ZINC FINGER DOMAIN OF TFIIE ALPHA
2rnq

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Ligands, Modified Residues, Ions (0, 0)

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Exons (3, 3)

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