4B8A - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF YEAST NOT1 MIF4G DOMAIN CO-CRYSTALLIZED WITH CAF1

Authors :   J. Basquin, E. Conti

Date :   26 Aug 12 (Deposition) - 21 Nov 12 (Release) - 20 Apr 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Transcription-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Basquin, V. V. Roudko, M. Rode, C. Basquin, B. Seraphin, E. Conti
Architecture Of The Nuclease Module Of The Yeast Ccr4-Not Complex: The Not1-Caf1-Ccr4 Interaction.
Mol. Cell V. 48 207 2012
PubMed-ID: 22959269 | Reference-DOI: 10.1016/J.MOLCEL.2012.08.014

Molecule 1 - GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS STAR
	Expression System Vector	:	PEC_SUMO_HT_A
	Expression System Vector Type	:	PLASMID
	Fragment	:	MIF4G, RESIDUES 755-1000
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE S288C
	Organism Taxid	:	559292
	Synonym	:	CELL DIVISION CYCLE PROTEIN 39, NOT1

Molecule 2 - POLY(A) RIBONUCLEASE POP2
	Chains	:	B
	EC Number	:	3.1.13.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYS STAR
	Expression System Vector	:	PEC_SUMO_HT_A
	Expression System Vector Type	:	PLASMID
	Fragment	:	NUCLEASE DOMAIN, RESIDUES 151-433
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE S288C
	Organism Taxid	:	559292
	Synonym	:	CCR4-ASSOCIATED FACTOR 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4B8A)

(no "Site" information available for 4B8A)

(no "SS Bond" information available for 4B8A)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:950	-	Pro A:951

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_POP2_YEAST_002 *	L	278	S	POP2_YEAST	---	---	B	L	134	S
2	UniProt	VAR_POP2_YEAST_003 *	K	412	M	POP2_YEAST	---	---	B	K	268	M
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 4B8A)

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNR052C	1	YNR052C.1	XIV:720650-719349	1302	POP2_YEAST	1-433	433	1	B:6-283 (gaps)	278

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
	(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:232
 aligned with NOT1_YEAST | P25655 from UniProtKB/Swiss-Prot  Length:2108

    Alignment length:232
                                   768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988  
          NOT1_YEAST    759 QEMIPLKFFAVDEVSCQINQEGAPKDVVEKVLFVLNNVTLANLNNKVDELKKSLTPNYFSWFSTYLVTQRAKTEPNYHDLYSKVIVAMGSGLLHQFMVNVTLRQLFVLLSTKDEQAIDKKHLKNLASWLGCITLALNKPIKHKNIAFREMLIEAYKENRLEIVVPFVTKILQRASESKIFKPPNPWTVGILKLLIELNEKANWKLSLTFEVEVLLKSFNLTTKSLKPSNFIN  990
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4b8a A  769 QEMIPLKFFAVDEVSCQINQEGAPKDVVEKVLFVLNNVTLANLNNKVDELKKSLTPNYFSWFSTYLVTQRAKTEPNYHDLYSKVIVAMGSGLLHQFMVNVTLRQLFVLLSTKDEQAIDKKHLKNLASWLGCITLALNKPIKHKNIAFREMLIEAYKENRLEIVVPFVTKILQRASESKIFKPPNPWTVGILKLLIELNEKANWKLSLTFEVEVLLKSFNLTTKSLKPSNFIN 1000
                                   778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with POP2_YEAST | P39008 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:278
                                   159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419        
          POP2_YEAST    150 IFLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDFLNPIQLGLSLSDANGNKPDNGPSTWQFNFEFDPKKEIMSTESLELLRKSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSIFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIY  427
               SCOP domains d4b8ab_ B: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..eeehhhhhhhhhhhhhhhh....eeeeeeee......-------.hhhhhhhhhhhhhhh.eeeeeeeee............eeeee...............------..hhhhhhhhh.hhhhhhhhhhh.........eeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhh..eeehhhhhhhhhhhhh-------------..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------------------------------------------------------------------------------M--------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:6-283 (gaps) UniProt: 1-433 [INCOMPLETE]                                                                                                                                                                                                                              Transcript 1
                4b8a B    6 MFLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLAR-------KVDYHYQTMRANVDFLNPIQLGLSLSDANGNKPDNGPSTWQFNFEFDPKKEIMSTESL------GINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNKEDFEWWVHQYMPNFYDLNLVYKIIQEFKN-------------QYSLTTLADELGLPRFSIFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIY  283
                                    15        25        35        45       | -     |  65        75        85        95       105       115  |    125       135       145       155       165       175       185       195       205      |  -         -|      235       245       255       265       275        
                                                                          53      61                                                      118    125                                                                                    212           226

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: CAF1-like ribonuclease (3)

Protein domain: automated matches (1)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 559292] (1)

d4b8ab_

(no "CATH Domain" information available for 4B8A)

(no "Pfam Domain" information available for 4B8A)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NOT1_YEAST | P25655)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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:0032947	protein complex scaffold activity	A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
biological process
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
	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:0007124	pseudohyphal growth	A pattern of cell growth that occurs in conditions of nitrogen limitation and abundant fermentable carbon source. Cells become elongated, switch to a unipolar budding pattern, remain physically attached to each other, and invade the growth substrate.
	GO:0051726	regulation of cell cycle	Any process that modulates the rate or extent of progression through the cell cycle.
	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:0000749	response to pheromone involved in conjugation with cellular fusion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus that contributes to the process of conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae.
	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:0030015	CCR4-NOT core complex	The core of the CCR4-NOT complex. In Saccharomyces the CCR4-NOT core complex comprises Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p.
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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 (POP2_YEAST | P39008)

molecular function
	GO:0000175	3'-5'-exoribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	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).
biological process
	GO:0090503	RNA phosphodiester bond hydrolysis, exonucleolytic	The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	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: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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0030015	CCR4-NOT core complex	The core of the CCR4-NOT complex. In Saccharomyces the CCR4-NOT core complex comprises Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p.
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4b8a)

	Sites
(no "Sites" information available for 4b8a)

	Cis Peptide Bonds
		Pro A:950 - Pro A:951	[ RasMol ]

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	4b8a
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Access by UniProt ID/Accession number
	NOT1_YEAST \| P25655
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	POP2_YEAST \| P39008
		Comparative Protein Structure Models	:	ModBase
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	3.1.13.4
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	NOT1_YEAST \| P25655
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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NOT1_YEAST \| P25655	:	4b89 4b8b 4b8c 4cv5
	POP2_YEAST \| P39008	:	1uoc 4b8c

1uoc	X-RAY STRUCTURE OF THE YEAST POP2 PROTEIN
4b89	MIF4G DOMAIN OF THE YEAST NOT1
4b8b	N-TERMINAL DOMAIN OF THE YEAST NOT1
4b8c	NUCLEASE MODULE OF THE YEAST CCR4-NOT COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (27, 38)

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