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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURAL BASIS OF ATAXIN-2 RECOGNITION BY POLY(A)-BINDING PROTEIN

Authors :   G. Kozlov, K. Gehring

Date :   25 Nov 09 (Deposition) - 23 Feb 10 (Release) - 12 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Protein-Protein Complex, Acetylation, Alternative Splicing, Cytoplasm, Methylation, Mrna Processing, Mrna Splicing, Nucleus, Phosphoprotein, Rna-Binding, Spliceosome, Neurodegeneration, Parkinsonism, Polymorphism, Spinocerebellar Ataxia, Triplet Repeat Expansion, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Kozlov, N. Safaee, A. Rosenauer, K. Gehring
Structural Basis Of Binding Of P-Body-Associated Proteins Gw182 And Ataxin-2 By The Mlle Domain Of Poly(A)-Binding Protein.
J. Biol. Chem. V. 285 13599 2010
PubMed-ID: 20181956 | Reference-DOI: 10.1074/JBC.M109.089540

Molecule 1 - POLYADENYLATE-BINDING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN
	Gene	:	PABPC1, PAB1, PABP1, PABPC2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	POLY(A)-BINDING PROTEIN 1, PABP 1

Molecule 2 - ATAXIN-2
	Chains	:	B
	Engineered	:	YES
	Fragment	:	PABPC1-BINDING FRAGMENT
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CHEMICALLY SYNTHESIZED
	Synonym	:	SPINOCEREBELLAR ATAXIA TYPE 2 PROTEIN, TRINUCLEOTIDE REPEAT- CONTAINING GENE 13 PROTEIN
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CD	1	Ligand/Ion	CADMIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:598 , HIS A:617 , GLU A:621 , HOH B:30 , ASN B:917	BINDING SITE FOR RESIDUE CD A 1
2	AC2	SOFTWARE	GLU A:557 , HIS A:617 , LYS A:620 , SER B:925 , PHE B:926 , SER B:927	BINDING SITE FOR RESIDUE SO4 A 627
3	AC3	SOFTWARE	HIS A:574 , PRO A:575 , THR A:576 , LEU A:577 , GLU A:601 , ARG A:604 , LYS B:919	BINDING SITE FOR RESIDUE SO4 A 2

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

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

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

(no "PROSITE Motif" information available for 3KTR)

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1e	ENST00000318607	1e	ENSE00002107718	chr8:101734940-101733619	1322	PABP1_HUMAN	1-65	65	0	-	-
1.2e	ENST00000318607	2e	ENSE00002179154	chr8:101730508-101730315	194	PABP1_HUMAN	65-129	65	0	-	-
1.2i	ENST00000318607	2i	ENSE00001088711	chr8:101730116-101730001	116	PABP1_HUMAN	130-168	39	0	-	-
1.3b	ENST00000318607	3b	ENSE00001676241	chr8:101727829-101727690	140	PABP1_HUMAN	168-215	48	0	-	-
1.4c	ENST00000318607	4c	ENSE00001088702	chr8:101725409-101725315	95	PABP1_HUMAN	215-246	32	0	-	-
1.5a	ENST00000318607	5a	ENSE00001088717	chr8:101725017-101724880	138	PABP1_HUMAN	247-292	46	0	-	-
1.6a	ENST00000318607	6a	ENSE00001088710	chr8:101724685-101724590	96	PABP1_HUMAN	293-324	32	0	-	-
1.7b	ENST00000318607	7b	ENSE00002184139	chr8:101721959-101721687	273	PABP1_HUMAN	325-415	91	0	-	-
1.8c	ENST00000318607	8c	ENSE00001088708	chr8:101721451-101721361	91	PABP1_HUMAN	416-446	31	0	-	-
1.9b	ENST00000318607	9b	ENSE00001088705	chr8:101719225-101719115	111	PABP1_HUMAN	446-483	38	0	-	-
1.10b	ENST00000318607	10b	ENSE00002199412	chr8:101719033-101718879	155	PABP1_HUMAN	483-534	52	0	-	-
1.11	ENST00000318607	11	ENSE00001088703	chr8:101717901-101717817	85	PABP1_HUMAN	535-563	29	1	A:543-563	21
1.12a	ENST00000318607	12a	ENSE00001088713	chr8:101717284-101717154	131	PABP1_HUMAN	563-606	44	1	A:563-606	44
1.13a	ENST00000318607	13a	ENSE00001088716	chr8:101716618-101716525	94	PABP1_HUMAN	607-636	30	1	A:607-623	17
1.14e	ENST00000318607	14e	ENSE00001378950	chr8:101715587-101715144	444	PABP1_HUMAN	-	0	0	-	-

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:81
 aligned with PABP1_HUMAN | P11940 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:81
                                   552       562       572       582       592       602       612       622 
          PABP1_HUMAN   543 EPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAA 623
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains -PABP-3ktrA01 A:544-614                                                 --------- Pfam domains
         Sec.struct. author ...hhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11            -------------------------------------------Exon 1.13a        Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.12a  PDB: A:563-606 UniProt: 563-606 ----------------- Transcript 1 (2)
                 3ktr A 543 SPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAA 623
                                   552       562       572       582       592       602       612       622

Chain B from PDB  Type:PROTEIN  Length:16
 aligned with ATX2_HUMAN | Q99700 from UniProtKB/Swiss-Prot  Length:1313

    Alignment length:16
                                   922      
           ATX2_HUMAN   913 TLNPNAKEFNPRSFSQ 928
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains PAM2-3ktrB01  -- Pfam domains
         Sec.struct. author ................ Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 3ktr B 913 TLNPNAKEFNPRSFSQ 928
                                   922

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 3KTR)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PABP] (14)

Family: PABP (14)

Homo sapiens (Human) (13)

PABP-3ktrA01

A:544-614

Clan: no clan defined [family: PAM2] (7)

Family: PAM2 (7)

Homo sapiens (Human) (7)

PAM2-3ktrB01

B:913-926

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PABP1_HUMAN | P11940)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0008143	poly(A) binding	Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
	GO:0008266	poly(U) RNA binding	Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0008494	translation activator activity	Any of a group of soluble proteins functioning in the activation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	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:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0048255	mRNA stabilization	Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.
	GO:2000623	negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Any process that stops, prevents or reduces the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	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:1900153	positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
	GO:0060213	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening	Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
	GO:0045727	positive regulation of translation	Any process that activates or increases 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:0045070	positive regulation of viral genome replication	Any process that activates or increases the frequency, rate or extent of viral genome replication.
	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:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
	GO:0071013	catalytic step 2 spliceosome	A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0036464	cytoplasmic ribonucleoprotein granule	A ribonucleoprotein granule located in the cytoplasm.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

Chain B (ATX2_HUMAN | Q99700)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0005154	epidermal growth factor receptor binding	Interacting selectively and non-covalently with the epidermal growth factor receptor.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0016070	RNA metabolic process	The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0050658	RNA transport	The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0033962	cytoplasmic mRNA processing body assembly	The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
	GO:0002091	negative regulation of receptor internalization	Any process that stops, prevents, or reduces the frequency, rate or extent of receptor internalization.
	GO:0010603	regulation of cytoplasmic mRNA processing body assembly	Any process that modulates the rate, frequency, or extent of the aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
	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:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	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:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005844	polysome	A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.
	GO:0005802	trans-Golgi network	The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

Asymmetric/Biological Unit
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