3U1U - JenaLib

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Title :   CRYSTAL STRUCTURE OF RNA POLYMERASE-ASSOCIATED PROTEIN RTF1 HOMOLOG PLUS-3 DOMAIN

Authors :   Y. Guo, W. Tempel, C. Bian, A. K. Wernimont, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, J. Min, Structural Genomics Consor (Sgc)

Date :   30 Sep 11 (Deposition) - 04 Apr 12 (Release) - 04 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Plus-3, Transcription Elongation, Structural Genomics, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Guo, W. Tempel, C. Bian, A. K. Wernimont, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, J. Min
Crystal Structure Of Rna Polymerase-Associated Protein Rtf1 Homolog Plus-3 Domain
To Be Published
PubMed: search

Molecule 1 - RNA POLYMERASE-ASSOCIATED PROTEIN RTF1 HOMOLOG
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28-MHL
	Expression System Strain	:	BL21(DE3)-V2R-PRARE2
	Expression System Taxid	:	469008
	Fragment	:	UNP RESIDUES 347-482
	Gene	:	RTF1, KIAA0252
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 36)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	4	Ligand/Ion	SULFATE ION
4	UNX	23	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (4, 36)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	4	Ligand/Ion	SULFATE ION
4	UNX	23	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (3, 15)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION
4	UNX	9	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:374 , THR A:420 , HOH A:620 , THR B:411 , ALA B:412 , LYS B:413 , ARG B:438	BINDING SITE FOR RESIDUE SO4 A 500
2	AC2	SOFTWARE	HIS A:374 , THR A:422 , ASN A:423	BINDING SITE FOR RESIDUE SO4 A 501
3	AC3	SOFTWARE	PHE A:460 , GLY A:463 , MSE A:464 , GLN A:465 , HOH A:621 , HOH A:630	BINDING SITE FOR RESIDUE GOL A 502
4	AC4	SOFTWARE	SER B:350 , TYR B:415 , GLN B:416 , ARG B:421 , HOH B:612	BINDING SITE FOR RESIDUE SO4 B 500
5	AC5	SOFTWARE	ARG A:366 , ILE B:391 , ARG B:401 , ARG B:435 , HOH B:621	BINDING SITE FOR RESIDUE SO4 B 501

(no "SS Bond" information available for 3U1U)

(no "Cis Peptide Bond" information available for 3U1U)

(no "SAP(SNP)/Variant" information available for 3U1U)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLUS3	PS51360	Plus3 domain profile.	RTF1_HUMAN	353-484	2	A:353-482 B:353-482

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLUS3	PS51360	Plus3 domain profile.	RTF1_HUMAN	353-484	2	A:353-482 B:353-482

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PLUS3	PS51360	Plus3 domain profile.	RTF1_HUMAN	353-484	2	A:353-482 B:353-482

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000389629	1a	ENSE00002188164	chr15:41709302-41709511	210	RTF1_HUMAN	1-66	66	0	-	-
1.2	ENST00000389629	2	ENSE00001685099	chr15:41730519-41730629	111	RTF1_HUMAN	67-103	37	0	-	-
1.4b	ENST00000389629	4b	ENSE00001644351	chr15:41745099-41745246	148	RTF1_HUMAN	104-153	50	0	-	-
1.5	ENST00000389629	5	ENSE00000931009	chr15:41749870-41750074	205	RTF1_HUMAN	153-221	69	0	-	-
1.6	ENST00000389629	6	ENSE00001029847	chr15:41756969-41757083	115	RTF1_HUMAN	221-259	39	0	-	-
1.7	ENST00000389629	7	ENSE00000931011	chr15:41758339-41758450	112	RTF1_HUMAN	260-297	38	0	-	-
1.8	ENST00000389629	8	ENSE00000931012	chr15:41762455-41762590	136	RTF1_HUMAN	297-342	46	0	-	-
1.9	ENST00000389629	9	ENSE00000931013	chr15:41763370-41763547	178	RTF1_HUMAN	342-401	60	2	A:348-401 (gaps) B:350-401 (gaps)	54 52
1.10b	ENST00000389629	10b	ENSE00000931014	chr15:41766818-41766900	83	RTF1_HUMAN	402-429	28	2	A:402-429 B:402-429	28 28
1.11	ENST00000389629	11	ENSE00001152999	chr15:41767723-41767810	88	RTF1_HUMAN	429-458	30	2	A:429-458 B:429-458	30 30
1.12	ENST00000389629	12	ENSE00001152995	chr15:41767910-41768017	108	RTF1_HUMAN	459-494	36	2	A:459-482 B:459-482	24 24
1.13	ENST00000389629	13	ENSE00001152991	chr15:41768644-41768721	78	RTF1_HUMAN	495-520	26	0	-	-
1.14b	ENST00000389629	14b	ENSE00001152986	chr15:41769363-41769484	122	RTF1_HUMAN	521-561	41	0	-	-
1.15	ENST00000389629	15	ENSE00001152980	chr15:41769656-41769713	58	RTF1_HUMAN	561-580	20	0	-	-
1.16	ENST00000389629	16	ENSE00000931020	chr15:41770746-41770823	78	RTF1_HUMAN	581-606	26	0	-	-
1.17	ENST00000389629	17	ENSE00001506418	chr15:41771301-41771396	96	RTF1_HUMAN	607-638	32	0	-	-
1.18	ENST00000389629	18	ENSE00000931022	chr15:41772412-41772523	112	RTF1_HUMAN	639-676	38	0	-	-
1.19b	ENST00000389629	19b	ENSE00001944328	chr15:41772779-41775761	2983	RTF1_HUMAN	676-710	35	0	-	-

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:131
 aligned with RTF1_HUMAN | Q92541 from UniProtKB/Swiss-Prot  Length:710

    Alignment length:135
                                   357       367       377       387       397       407       417       427       437       447       457       467       477     
           RTF1_HUMAN   348 PKSQPVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEA 482
               SCOP domains d3u1ua_ A: RNA polymerase-associated protein R    TF1 homolog                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhh...hhhhhhhhh...hhhhhhh..eeeeeee.----.eeeeeeeeeeeeeeeeeee..eeeeeeeeeee..eeeeee.hhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PLUS3  PDB: A:353-482 UniProt: 353-484                                                                                             PROSITE
           Transcript 1 (1) Exon 1.9  PDB: A:348-401 (gaps) UniProt: 342-401      Exon 1.10b  PDB: A:402-429  -----------------------------Exon 1.12  PDB: A:459-48 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------Exon 1.11  PDB: A:429-458     ------------------------ Transcript 1 (2)
                 3u1u A 348 PKSQPVSLPEELNRVRLSRHKLERWCHmPFFAKTVTGCFVRIGIGN----PVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFmKWKEAmFSAGmQLPTLDEINKKELSIKEA 482
                                   357       367       377       387     |   -|      407       417       427       437       447     | 457 |    |467       477     
                                                     375-MSE           393  398                                                    453-MSE |    |                  
                                                                                                                                         459-MSE|                  
                                                                                                                                              464-MSE

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with RTF1_HUMAN | Q92541 from UniProtKB/Swiss-Prot  Length:710

    Alignment length:133
                                   359       369       379       389       399       409       419       429       439       449       459       469       479   
           RTF1_HUMAN   350 SQPVSLPEELNRVRLSRHKLERWCHMPFFAKTVTGCFVRIGIGNHNSKPVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAMFSAGMQLPTLDEINKKELSIKEA 482
               SCOP domains d3u1ub_ B: RNA polymerase-associated protein     RTF1 homolog                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh.hhhhhhhhh...hhhhhhh..eeeeeee.----.eeeeeeeeeeeeeeeeeee..eeeeeeeeeee..eeeeee.hhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PLUS3  PDB: B:353-482 UniProt: 353-484                                                                                             PROSITE
           Transcript 1 (1) Exon 1.9  PDB: B:350-401 (gaps) UniProt: 342-401    Exon 1.10b  PDB: B:402-429  -----------------------------Exon 1.12  PDB: B:459-48 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------Exon 1.11  PDB: B:429-458     ------------------------ Transcript 1 (2)
                 3u1u B 350 SQPVSLPEELNRVRLSRHKLERWCHmPFFAKTVTGCFVRIGIGN----PVYRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFmKWKEAmFSAGmQLPTLDEINKKELSIKEA 482
                                   359       369     | 379       389   |   399       409       419       429       439       449   |   459    |  469       479   
                                                   375-MSE           393  398                                                    453-MSE |    |                  
                                                                                                                                       459-MSE|                  
                                                                                                                                            464-MSE

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Plus3-like (4)

Family: Plus3 (4)

Protein domain: RNA polymerase-associated protein RTF1 homolog (3)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d3u1ua_	A:
1b	d3u1ub_	B:

(no "CATH Domain" information available for 3U1U)

(no "Pfam Domain" information available for 3U1U)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RTF1_HUMAN | Q92541)

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:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0016055	Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
	GO:0001832	blastocyst growth	An increase in size of a blastocyst due to expansion of the blastocoelic cavity cell shape changes and cell proliferation.
	GO:0001711	endodermal cell fate commitment	The cell differentiation process that results in commitment of a cell to become part of the endoderm.
	GO:0080182	histone H3-K4 trimethylation	The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone.
	GO:0016570	histone modification	The covalent alteration of one or more amino acid residues within a histone protein.
	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:0051571	positive regulation of histone H3-K4 methylation	Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0019827	stem cell population maintenance	The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
	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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0016593	Cdc73/Paf1 complex	A multiprotein complex that associates with RNA polymerase II and general RNA polymerase II transcription factor complexes and may be involved in both transcriptional initiation and elongation. In Saccharomyces the complex contains Paf1p, Cdc73p, Ctr9p, Rtf1p, and Leo1p.
	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.

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	RTF1_HUMAN \| Q92541	:	2bze 2db9 4l1p 4l1u

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