3GVT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE AND RNA BINDING OF THE MOUSE PUMILIO-2 PUF DOMAIN

Authors :   H. T. Jenkins, T. A. Edwards

Date :   31 Mar 09 (Deposition) - 30 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Rna-Binding, Pumilio, Puf Domain, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. T. Jenkins, R. Baker-Wilding, T. A. Edwards
Structure And Rna Binding Of The Mouse Pumilio-2 Puf Domain
J. Struct. Biol. V. 167 271 2009
PubMed-ID: 19540345 | Reference-DOI: 10.1016/J.JSB.2009.06.007

Molecule 1 - PUMILIO HOMOLOG 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-19B
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PUF DOMAIN, UNP RESIDUES 706-1056
	Gene	:	PUM2
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	PUMILIO 2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	DTT	-1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:25 , HOH A:81 , THR A:752 , GLY A:801 , HIS A:802 , PRO A:805	BINDING SITE FOR RESIDUE DTT A 1
2	AC2	SOFTWARE	GLY A:839 , HIS A:840 , VAL A:841 , LEU A:842 , LYS A:843	BINDING SITE FOR RESIDUE GOL A 1057
3	AC3	SOFTWARE	ARG A:1017	BINDING SITE FOR RESIDUE GOL A 1058

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

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

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

Asymmetric Unit (2, 18)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUM_HD	PS50303	Pumilio homology domain (PUM-HD) profile.	PUM2_MOUSE	706-1048	2	A:706-1048 B:706-1048
2	PUM	PS50302	Pumilio RNA-binding repeat profile.	PUM2_MOUSE	726-761 762-797 798-835 836-871 872-907 908-943 944-979 980-1022	16	A:726-761 B:726-761 A:762-797 B:762-797 A:798-835 B:798-835 A:836-871 B:836-871 A:872-907 B:872-907 A:908-943 B:908-943 A:944-979 B:944-979 A:980-1022 B:980-1022

Biological Unit 1 (2, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUM_HD	PS50303	Pumilio homology domain (PUM-HD) profile.	PUM2_MOUSE	706-1048	1	A:706-1048 -
2	PUM	PS50302	Pumilio RNA-binding repeat profile.	PUM2_MOUSE	726-761 762-797 798-835 836-871 872-907 908-943 944-979 980-1022	8	A:726-761 - A:762-797 - A:798-835 - A:836-871 - A:872-907 - A:908-943 - A:944-979 - A:980-1022 -

Biological Unit 2 (2, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUM_HD	PS50303	Pumilio homology domain (PUM-HD) profile.	PUM2_MOUSE	706-1048	1	- B:706-1048
2	PUM	PS50302	Pumilio RNA-binding repeat profile.	PUM2_MOUSE	726-761 762-797 798-835 836-871 872-907 908-943 944-979 980-1022	8	- B:726-761 - B:762-797 - B:798-835 - B:836-871 - B:872-907 - B:908-943 - B:944-979 - B:980-1022

(no "Exon" information available for 3GVT)

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:342
 aligned with PUM2_MOUSE | Q80U58 from UniProtKB/Swiss-Prot  Length:1066

    Alignment length:344
                                   715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045    
          PUM2_MOUSE    706 GRSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYYL 1049
               SCOP domains d3gvta_ A: automated matches                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3gvtA00 A:706-1049 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhh..hhhhh--hhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..eehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PUM_HD  PDB: A:706-1048 UniProt: 706-1048                                                                                                                                                                                                                                                                                                              - PROSITE (1)
                PROSITE (2) --------------------PUM  PDB: A:726-761 UniProt: 726-761PUM  PDB: A:762-797 UniProt: 762-797PUM  PDB: A:798-835 UniProt: 798-835  PUM  PDB: A:836-871 UniProt: 836-871PUM  PDB: A:872-907 UniProt: 872-907PUM  PDB: A:908-943 UniProt: 908-943PUM  PDB: A:944-979 UniProt: 944-979PUM  PDB: A:980-1022 UniProt: 980-1022     --------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gvt A  706 GRSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQ--SEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYYL 1049
                                   715       725       735       745       755       765       775       785       795       805       815       825  |  | 835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045    
                                                                                                                                                    828  |                                                                                                                                                                                                                          
                                                                                                                                                       831

Chain B from PDB  Type:PROTEIN  Length:342
 aligned with PUM2_MOUSE | Q80U58 from UniProtKB/Swiss-Prot  Length:1066

    Alignment length:344
                                   715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045    
          PUM2_MOUSE    706 GRSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYYL 1049
               SCOP domains d3gvtb_ B: automated matches                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3gvtB00 B:706-1049 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhh--hhhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhee..eehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PUM_HD  PDB: B:706-1048 UniProt: 706-1048                                                                                                                                                                                                                                                                                                              - PROSITE (1)
                PROSITE (2) --------------------PUM  PDB: B:726-761 UniProt: 726-761PUM  PDB: B:762-797 UniProt: 762-797PUM  PDB: B:798-835 UniProt: 798-835  PUM  PDB: B:836-871 UniProt: 836-871PUM  PDB: B:872-907 UniProt: 872-907PUM  PDB: B:908-943 UniProt: 908-943PUM  PDB: B:944-979 UniProt: 944-979PUM  PDB: B:980-1022 UniProt: 980-1022     --------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3gvt B  706 GRSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQIVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQ--SEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYYL 1049
                                   715       725       735       745       755       765       775       785       795       805       815       825  |  | 835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045    
                                                                                                                                                    828  |                                                                                                                                                                                                                          
                                                                                                                                                       831

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: ARM repeat (317)

Family: Pumilio repeat (19)

Protein domain: automated matches (7)

Mouse (Mus musculus) [TaxId: 10090] (2)

1a	d3gvta_	A:
1b	d3gvtb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Alpha Horseshoe (399)

Topology: Leucine-rich Repeat Variant (77)

Homologous Superfamily: Leucine-rich Repeat Variant (75)

Mouse (Mus musculus) (10)

1a	3gvtA00	A:706-1049
1b	3gvtB00	B:706-1049

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PUM2_MOUSE | Q80U58)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003730	mRNA 3'-UTR binding	Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
	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:1900246	positive regulation of RIG-I signaling pathway	Any process that activates or increases the frequency, rate or extent of RIG-I signaling pathway.
	GO:2000637	positive regulation of gene silencing by miRNA	Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA.
	GO:0010608	posttranscriptional regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript.
	GO:0051983	regulation of chromosome segregation	Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
	GO:0043488	regulation of mRNA stability	Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
	GO:0006417	regulation of translation	Any process that modulates 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:0034063	stress granule assembly	The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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	3gvt
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Description

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