2NPI - JenaLib

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Title :   CLP1-ATP-PCF11 COMPLEX

Authors :   C. G. Noble, B. Beuth, I. A. Taylor

Date :   27 Oct 06 (Deposition) - 19 Dec 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

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

Keywords :   Clp1-Pcf11 Complex, Atp Binding, Ternary Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. G. Noble, B. Beuth, I. A. Taylor
Structure Of A Nucleotide-Bound Clp1-Pcf11 Polyadenylation Factor
Nucleic Acids Res. V. 35 87 2007
PubMed-ID: 17151076 | Reference-DOI: 10.1093/NAR/GKL1010

Molecule 1 - PROTEIN CLP1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PACYCDUET-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CLP1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - PROTEIN PCF11
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PACYCDUET-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 454-563
	Gene	:	PCF11
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	CO-EXPRESSED, RECOMBINANT MATERIAL
	Synonym	:	PROTEIN 1 OF CF I

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:137 , ASP B:251 , ATP B:1600 , HOH B:2506	BINDING SITE FOR RESIDUE MG B 2500
2	AC2	SOFTWARE	THR A:137 , ATP A:600	BINDING SITE FOR RESIDUE MG A 1500
3	AC3	SOFTWARE	ASP A:33 , GLN A:35 , PHE A:56 , LYS A:72 , PRO A:74 , GLN A:133 , THR A:134 , GLY A:135 , LYS A:136 , THR A:137 , SER A:138 , ASP A:311 , GLY A:312 , VAL A:313 , SER A:314 , VAL A:316 , MG A:1500	BINDING SITE FOR RESIDUE ATP A 600
4	AC4	SOFTWARE	ASP B:33 , GLN B:35 , PHE B:56 , LYS B:72 , PRO B:74 , GLN B:133 , THR B:134 , GLY B:135 , LYS B:136 , THR B:137 , SER B:138 , SER B:254 , ASP B:311 , GLY B:312 , SER B:314 , LYS B:321 , MG B:2500 , HOH B:2506	BINDING SITE FOR RESIDUE ATP B 1600

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

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

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

(no "PROSITE Motif" information available for 2NPI)

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR228C	1	YDR228C.1	IV:923803-921923	1881	PCF11_YEAST	1-626	626	2	C:477-498 D:475-499	22 25

2.1	YOR250C	1	YOR250C.1	XV:802308-800971	1338	CLP1_YEAST	1-445	445	2	A:18-445 B:18-445	428 428

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:428
 aligned with CLP1_YEAST | Q08685 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:428
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437        
           CLP1_YEAST    18 TGDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTFQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIRMSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAMILTSYRYLE 445
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....ee..ee.....eeeeeeee..eee..ee.....eeeee..ee..ee....eeeee...........ee..hhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhh...eeee..............eeee............................ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhh...hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhh........eeeeee.....eeee............eee...hhhhhh.eeeeee......hhhhhh...eeeeeeeeeee....eeeeee..........eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:18-445 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                          Transcript 2
                 2npi A  18 TGDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTFQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTmKYIYNLHFmLEKIRmSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPmVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKLNVNImLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAmILTSYRYLE 445
                                    27        37        47        57        67        77        87        97     | 107    |  117|      127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437        
                                                                                                               103-MSE  112-MSE |                                                                                     206-MSE                                                                277-MSE                                                                                                                                                        436-MSE     
                                                                                                                              118-MSE

Chain B from PDB  Type:PROTEIN  Length:428
 aligned with CLP1_YEAST | Q08685 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:428
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437        
           CLP1_YEAST    18 TGDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTFQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIRMSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAMILTSYRYLE 445
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------MobB-2npiB01 B:124-252                                                                                                           ------Clp1-2npiB03 B:259-445                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------MobB-2npiB02 B:124-252                                                                                                           ------Clp1-2npiB04 B:259-445                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ......eeeee...eeeeee......eeeeeee..eee..ee.....eeee...eeeeee...eeeeee.........eeee..hhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh.....eeee..............eeee............................ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhh...hhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhh........eeeeee.hhheeeee.hhhhhh.....eee...hhhhhh.eeeeee......hhhhhh...eeeeeeeeeee....eeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:18-445 UniProt: 1-445 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                          Transcript 2
                 2npi B  18 TGDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTFQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTmKYIYNLHFmLEKIRmSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPmVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKLNVNImLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAmILTSYRYLE 445
                                    27        37        47        57        67        77        87        97     | 107    |  117|      127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437        
                                                                                                               103-MSE  112-MSE |                                                                                     206-MSE                                                                277-MSE                                                                                                                                                        436-MSE     
                                                                                                                              118-MSE

Chain C from PDB  Type:PROTEIN  Length:22
 aligned with PCF11_YEAST | P39081 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:22
                                   486       496  
          PCF11_YEAST   477 IQSRNWYLSDSQWAAFKDDEIT 498
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
               Transcript 1 Exon 1.1 [INCOMPLETE]  Transcript 1
                 2npi C 477 IQSRNWYLSDSQWAAFKDDEIT 498
                                   486       496

Chain D from PDB  Type:PROTEIN  Length:25
 aligned with PCF11_YEAST | P39081 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:25
                                   484       494     
          PCF11_YEAST   475 KNIQSRNWYLSDSQWAAFKDDEITS 499
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
           Pfam domains (1) CFIA_Pcf11-2npiD01        Pfam domains (1)
           Pfam domains (2) CFIA_Pcf11-2npiD02        Pfam domains (2)
         Sec.struct. author ..........hhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:475-499  Transcript 1
                 2npi D 475 KNIQSRNWYLSDSQWAAFKDDEITS 499
                                   484       494

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 2NPI)

(no "CATH Domain" information available for 2NPI)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CLP1_YEAST | Q08685)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0051731	polynucleotide 5'-hydroxyl-kinase activity	Catalysis of the reaction: NTP + 5'-dephosphopolynucleotide = NDP + 5'-phosphopolynucleotide. The polynucleotide may be DNA or RNA.
	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).
biological process
	GO:0090202	gene looping	The formation and maintenance of DNA loops that juxtapose sequentially separated regions of RNA polymerase II-transcribed genes.
	GO:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0006378	mRNA polyadenylation	The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0098789	pre-mRNA cleavage required for polyadenylation	The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
	GO:0006388	tRNA splicing, via endonucleolytic cleavage and ligation	Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
cellular component
	GO:0005849	mRNA cleavage factor complex	Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
	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 C,D (PCF11_YEAST | P39081)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000993	RNA polymerase II core binding	Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	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).
biological process
	GO:0006353	DNA-templated transcription, termination	The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
	GO:0006379	mRNA cleavage	Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
	GO:0006378	mRNA polyadenylation	The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0098789	pre-mRNA cleavage required for polyadenylation	The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006369	termination of RNA polymerase II transcription	The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005849	mRNA cleavage factor complex	Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
	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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	2npi
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	PCF11_YEAST \| P39081
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	CLP1_YEAST \| Q08685	:	4c0b 4c0h 4oi4
	PCF11_YEAST \| P39081	:	1sz9 1sza 2bf0 2nax 4c0b 4c0h 4oi4

(no "Related Entries Specified in the PDB File" available for 2NPI)

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (2, 4)

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