3Q0S - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO2 IN COMPLEX WITH ERK2 NRE

Authors :   G. Lu, T. M. T. Hall

Date :   15 Dec 10 (Deposition) - 16 Mar 11 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   G. Lu, T. M. Hall
Alternate Modes Of Cognate Rna Recognition By Human Pumilio Proteins.
Structure V. 19 361 2011
PubMed-ID: 21397187 | Reference-DOI: 10.1016/J.STR.2010.12.019

Molecule 1 - PUMILIO HOMOLOG 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST527
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 706-1056
	Gene	:	PUM2, KIAA0235, PUMH2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PUMILIO-2

*Molecule 2 - 5'-R(UPGPUPAPCPAPUPC)-3'**
	Chains	:	B
	Engineered	:	YES
	Other Details	:	THIS RNA SEQUENCE OCCURS NATURALLY IN HUMANS.
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3Q0S)

(no "Site" information available for 3Q0S)

Asymmetric/Biological Unit

No.	Residues
1	A:982	-	A:983

(no "Cis Peptide Bond" information available for 3Q0S)

(no "SAP(SNP)/Variant" information available for 3Q0S)

Asymmetric/Biological Unit (2, 9)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUM_HD	PS50303	Pumilio homology domain (PUM-HD) profile.	PUM2_HUMAN	706-1048	1	A:706-1048
2	PUM	PS50302	Pumilio RNA-binding repeat profile.	PUM2_HUMAN	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

(no "Exon" information available for 3Q0S)

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:343
 aligned with PUM2_HUMAN | Q8TB72 from UniProtKB/Swiss-Prot  Length:1066

    Alignment length:343
                                   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_HUMAN    706 GRSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYY 1048
               SCOP domains d3q0sa_ A: automated matches                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0sA01 A:990-1021          --------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0sA02 A:990-1021          --------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0sA03 A:990-1021          --------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0sA04 A:990-1021          --------------------------- Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0sA05 A:990-1021          --------------------------- Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0sA06 A:990-1021          --------------------------- Pfam domains (6)
           Pfam domains (7) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0sA07 A:990-1021          --------------------------- Pfam domains (7)
           Pfam domains (8) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUF-3q0sA08 A:990-1021          --------------------------- Pfam domains (8)
         Sec.struct. author ..hhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh.. 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
                3q0s A  706 GRSRLLEDFRNNRFPNLQLRDLIGHIVEFSQDQHGSRFIQQKLERATPAERQMVFNEILQAAYQLMTDVFGNYVIQKFFEFGSLDQKLALATRIRGHVLPLALQMYGCRVIQKALESISSDQQVISEMVKELDGHVLKCVKDQNGNHVVQKCIECVQPQSLQFIIDAFKGQVFVLSTHPYGCRVIQRILEHCTAEQTLPILEELHQHTEQLVQDQYGNYVIQHVLEHGRPEDKSKIVSEIRGKVLALSQHKFASNVVEKCVTHASRAERALLIDEVCCQNDGPHSALYTMMKDQYANYVVQKMIDMAEPAQRKIIMHKIRPHITTLRKYTYGKHILAKLEKYY 1048
                                   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

Chain B from PDB  Type:RNA  Length:8
                                         
                3q0s B    1 UGUACAUC    8

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: All alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: ARM repeat (317)

Family: Pumilio repeat (19)

Protein domain: automated matches (7)

Human (Homo sapiens) [TaxId: 9606] (4)

d3q0sa_

(no "CATH Domain" information available for 3Q0S)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TPR (230)

Family: PUF (24)

Homo sapiens (Human) (13)

1a	PUF-3q0sA01	A:990-1021
1b	PUF-3q0sA02	A:990-1021
1c	PUF-3q0sA03	A:990-1021
1d	PUF-3q0sA04	A:990-1021
1e	PUF-3q0sA05	A:990-1021
1f	PUF-3q0sA06	A:990-1021
1g	PUF-3q0sA07	A:990-1021
1h	PUF-3q0sA08	A:990-1021

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PUM2_HUMAN | Q8TB72)

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:0060964	regulation of gene silencing by miRNA	Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3q0s)

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	3q0s
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	PUM2_HUMAN \| Q8TB72
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UniProtKB/Swiss-Prot
	PUM2_HUMAN \| Q8TB72	:	3q0q 3q0r

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 9)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 8)

Gene Ontology (15, 15)

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