4OI4 - JenaLib

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Title :   PROTEIN COMPLEX OF CLP1 BOUND TO ATP AND MG2+ WITH PCF11DELTAN454DELTAC563 OF S. CEREVISIAE

Authors :   A. Dikfidan, B. Loll, C. Zeymer, T. Clausen, A. Meinhart

Date :   18 Jan 14 (Deposition) - 14 May 14 (Release) - 14 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D,U
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: U  (1x)

Keywords :   Polynucleotide Kinase, Clp1, Pcf11, Cleavage Factor Ia, 3'-End Mrna Processing, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Dikfidan, B. Loll, C. Zeymer, I. Magler, T. Clausen, A. Meinhart
Rna Specificity And Regulation Of Catalysis In The Eukaryotic Polynucleotide Kinase Clp1.
Mol. Cell V. 54 975 2014
PubMed-ID: 24813946 | Reference-DOI: 10.1016/J.MOLCEL.2014.04.005

Molecule 1 - MRNA CLEAVAGE AND POLYADENYLATION FACTOR CLP1
	Chains	:	A, C
	EC Number	:	2.7.1.78
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEM
	Expression System Strain	:	BL21(DE3)-RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CLP1, YOR250C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C

Molecule 2 - PROTEIN PCF11
	Chains	:	B, D, U
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX
	Expression System Strain	:	BL21(DE3)-RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CLP1 INTERACTION DOMAIN (UNP RESIDUES 454-563, SEE REMARK 999)
	Gene	:	PCF11, YDR228C, YD9934.13C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	PROTEIN 1 OF CF I

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	U
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					U

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GOL	3	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ATP	-1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:33 , GLN A:35 , PHE A:56 , LYS A:72 , PRO A:74 , SER A:132 , GLN A:133 , THR A:134 , GLY A:135 , LYS A:136 , THR A:137 , SER A:138 , SER A:254 , ASP A:311 , GLY A:312 , VAL A:313 , SER A:314 , LYS A:321 , MG A:502 , GOL A:503 , HOH A:675 , HOH A:687 , HOH A:698 , HOH A:712	BINDING SITE FOR RESIDUE ATP A 501
2	AC2	SOFTWARE	THR A:137 , ATP A:501 , HOH A:613 , HOH A:687 , HOH A:698	BINDING SITE FOR RESIDUE MG A 502
3	AC3	SOFTWARE	TRP A:71 , SER A:138 , ARG A:141 , PRO A:187 , TRP A:189 , ATP A:501 , HOH A:675	BINDING SITE FOR RESIDUE GOL A 503
4	AC4	SOFTWARE	ASP C:33 , GLN C:35 , PHE C:56 , LYS C:72 , PRO C:74 , SER C:132 , GLN C:133 , THR C:134 , GLY C:135 , LYS C:136 , THR C:137 , SER C:138 , SER C:254 , ASP C:311 , GLY C:312 , VAL C:313 , SER C:314 , LYS C:321 , MG C:502 , GOL C:503 , HOH C:668	BINDING SITE FOR RESIDUE ATP C 501
5	AC5	SOFTWARE	THR C:137 , ATP C:501 , HOH C:651 , HOH C:667 , HOH C:668	BINDING SITE FOR RESIDUE MG C 502
6	AC6	SOFTWARE	PHE C:56 , TRP C:71 , THR C:137 , ARG C:141 , PRO C:187 , TRP C:189 , ATP C:501	BINDING SITE FOR RESIDUE GOL C 503
7	AC7	SOFTWARE	THR C:67 , GLN C:185 , LEU C:186 , SER C:336 , LEU C:337 , ASP C:338 , HOH C:631 , HOH C:652	BINDING SITE FOR RESIDUE GOL C 504

(no "SS Bond" information available for 4OI4)

(no "Cis Peptide Bond" information available for 4OI4)

(no "SAP(SNP)/Variant" information available for 4OI4)

(no "PROSITE Motif" information available for 4OI4)

(no "Exon" information available for 4OI4)

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:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...eeeeee.....eeeeeeee..eee..ee.....eeeee..eeeeee...eeeeee.........eeee..hhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhh.......eeee............eeeeee............................eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..hhhhh...hhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhee..ee...eeeeee.hhh.eeee.hhhhhh.....eee...hhhhhh.eeeeeeeee...hhhhhhhh.eeeeeeeeeee....eeeeee........eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oi4 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

Chain B from PDB  Type:PROTEIN  Length:25
                                                         
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 4oi4 B 475 KNIQSRNWYLSDSQWAAFKDDEITS 499
                                   484       494

Chain C from PDB  Type:PROTEIN  Length:427
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeeeee.....eeeeeeeeeeeee..ee.....eeeee..eeeeeeeeeeeeeee....hhhhh.eee..hhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh.....eeee............eeeeee............................eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..hhhhh...hhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhee..ee...eeeeee.hhh.eeee.hhhhhh.....eee...hhhhhh.eeeeee......hhhhhhh..eeeeeeeeeee....eeeeee..........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oi4 C  19 GDNEWHKLVIPKGSDWQIDLKAEGKLIVKVNSGIVEIFGTELAVDDEYTFQNWKFPIYAVEETELLWKCPDLTTNTITVKPNHTMKYIYNLHFMLEKIRMSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLYINLDPQQPIFTVPGCISATPISDILDAQLPTWGQSLTSGATLLHNKQPMVKNFGLERINENKDLYLECISQLGQVVGQRLHLDPQVRRSGCIVDTPSISQLDENLAELHHIIEKLNVNIMLVLCSETDPLWEKVKKTFGPELGNNNIFFIPKLDGVSAVDDVYKRSLQRTSIREYFYGSLDTALSPYAIGVDYEDLTIWKPSNVFDNEVGRVELFPVTITPSNLQHAIIAITFAERRADQATVIKSPILGFALITEVNEKRRKLRVLLPVPGRLPSKAMILTSYRYLE 445
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438

Chain D from PDB  Type:PROTEIN  Length:24
                                                        
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author .........hhhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                 4oi4 D 476 NIQSRNWYLSDSQWAAFKDDEITS 499
                                   485       495

Chain U from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4oi4 U 451 PEFGSQNT 458

Legend:		→ Mismatch	(orange background)
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	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 4OI4)

(no "CATH Domain" information available for 4OI4)

(no "Pfam Domain" information available for 4OI4)

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Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4oi4)

Biological Units
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	4oi4
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	CLP1_YEAST \| Q08685
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	PCF11_YEAST \| P39081
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	2.7.1.78
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UniProtKB/Swiss-Prot
	CLP1_YEAST \| Q08685	:	2npi 4c0b 4c0h
	PCF11_YEAST \| P39081	:	1sz9 1sza 2bf0 2nax 2npi 4c0b 4c0h

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (22, 29)

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