3ZZZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A RAVER1 PRI4 PEPTIDE IN COMPLEX WITH POLYPYRIMIDINE TRACT BINDING PROTEIN RRM2

Authors :   A. Joshi, O. Kotik-Kogan, S. Curry

Date :   06 Sep 11 (Deposition) - 28 Dec 11 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Protein Binding, Peptide Binding, Rna Recognition Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Joshi, M. B. Coelho, O. Kotik-Kogan, P. J. Simpson, S. J. Matthews, C. W. Smith, S. Curry
Crystallographic Analysis Of Polypyrimidine Tract-Binding Protein-Raver1 Interactions Involved In Regulation Of Alternative Splicing.
Structure V. 19 1816 2011
PubMed-ID: 22153504 | Reference-DOI: 10.1016/J.STR.2011.09.020

Molecule 1 - POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RNA RECOGNITION MOTIF 2, RESIDUES 156-285
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PTB, 57 KDA RNA-BINDING PROTEIN PPTB-1, HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN I, HNRNP I

Molecule 2 - RIBONUCLEOPROTEIN PTB-BINDING 1
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	MOTIF PRI4, RESIDUES 680-692
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	THIS FRAGMENT IS ACTUALLY FUSED TO THE N-TERMINUS OF MOLECULE 1, SEE REMARK 999
	Synonym	:	RAVER1, PROTEIN RAVER-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	IOD	5	Ligand/Ion	IODIDE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	IOD	4	Ligand/Ion	IODIDE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	IOD	1	Ligand/Ion	IODIDE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:259 , IOD A:1286	BINDING SITE FOR RESIDUE IOD A1285
2	AC2	SOFTWARE	SER A:258 , IOD A:1285 , IOD A:1288	BINDING SITE FOR RESIDUE IOD A1286
3	AC3	SOFTWARE	LYS A:266 , SER A:272 , SER C:682	BINDING SITE FOR RESIDUE IOD A1287
4	AC4	SOFTWARE	IOD A:1286	BINDING SITE FOR RESIDUE IOD A1288
5	AC5	SOFTWARE	SER B:258 , LEU D:688	BINDING SITE FOR RESIDUE IOD D1689

Asymmetric Unit

No.	Residues
1	A:250	-	A:251
2	B:250	-	B:251

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PTBP1_HUMAN	59-143 184-260 337-411 454-529	2	- A:184-260 B:184-260 - -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PTBP1_HUMAN	59-143 184-260 337-411 454-529	1	- A:184-260 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	PTBP1_HUMAN	59-143 184-260 337-411 454-529	1	- - B:184-260 - -

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000349038	1	ENSE00001155026	chr19:797392-797505	114	PTBP1_HUMAN	1-3	3	0	-	-
1.2	ENST00000349038	2	ENSE00001113327	chr19:799413-799443	31	PTBP1_HUMAN	3-13	11	0	-	-
1.3	ENST00000349038	3	ENSE00000892209	chr19:803561-803636	76	PTBP1_HUMAN	14-39	26	0	-	-
1.4	ENST00000349038	4	ENSE00000768682	chr19:804036-804208	173	PTBP1_HUMAN	39-96	58	0	-	-
1.5	ENST00000349038	5	ENSE00000892212	chr19:804292-804438	147	PTBP1_HUMAN	97-145	49	0	-	-
1.6	ENST00000349038	6	ENSE00000892214	chr19:804532-804702	171	PTBP1_HUMAN	146-202	57	2	A:180-202 B:180-202	23 23
1.7	ENST00000349038	7	ENSE00000892216	chr19:804829-804939	111	PTBP1_HUMAN	203-239	37	2	A:203-239 B:203-239	37 37
1.8	ENST00000349038	8	ENSE00000892217	chr19:805013-805187	175	PTBP1_HUMAN	240-298	59	2	A:240-284 B:240-284	45 45
1.10	ENST00000349038	10	ENSE00000464365	chr19:806408-806556	149	PTBP1_HUMAN	298-347	50	0	-	-
1.11	ENST00000349038	11	ENSE00000892219	chr19:807869-807902	34	PTBP1_HUMAN	348-359	12	0	-	-
1.12	ENST00000349038	12	ENSE00000768789	chr19:808360-808452	93	PTBP1_HUMAN	359-390	32	0	-	-
1.13	ENST00000349038	13	ENSE00000768790	chr19:808546-808762	217	PTBP1_HUMAN	390-462	73	0	-	-
1.14	ENST00000349038	14	ENSE00000768792	chr19:810543-810620	78	PTBP1_HUMAN	462-488	27	0	-	-
1.15	ENST00000349038	15	ENSE00001155037	chr19:810694-812327	1634	PTBP1_HUMAN	488-531	44	0	-	-

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:105
 aligned with PTBP1_HUMAN | P26599 from UniProtKB/Swiss-Prot  Length:531

    Alignment length:105
                                   189       199       209       219       229       239       249       259       269       279     
          PTBP1_HUMAN   180 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGD 284
               SCOP domains d3zzza_ A: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhh.eeeeeeeee..eeeeeeee.hhhhhhhhhhhhh..eee..eeeeeeee..............eee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RRM  PDB: A:184-260 UniProt: 184-260                                         ------------------------ PROSITE
               Transcript 1 Exon 1.6  PDB: A:180-20Exon 1.7  PDB: A:203-239             Exon 1.8  PDB: A:240-284 UniProt: 240-298     Transcript 1
                 3zzz A 180 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGD 284
                                   189       199       209       219       229       239       249       259       269       279

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with PTBP1_HUMAN | P26599 from UniProtKB/Swiss-Prot  Length:531

    Alignment length:105
                                   189       199       209       219       229       239       249       259       269       279     
          PTBP1_HUMAN   180 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGD 284
               SCOP domains d3zzzb_ B: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhh.eeeeeeee....eeeeeee.hhhhhhhhhhhhh..eee..eeeeeeee..............eee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RRM  PDB: B:184-260 UniProt: 184-260                                         ------------------------ PROSITE
               Transcript 1 Exon 1.6  PDB: B:180-20Exon 1.7  PDB: B:203-239             Exon 1.8  PDB: B:240-284 UniProt: 240-298     Transcript 1
                 3zzz B 180 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGD 284
                                   189       199       209       219       229       239       249       259       269       279

Chain C from PDB  Type:PROTEIN  Length:7
 aligned with RAVR1_MOUSE | Q9CW46 from UniProtKB/Swiss-Prot  Length:748

    Alignment length:7
          RAVR1_MOUSE   682 SEGLLGL 688
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ..eee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 3zzz C 682 SEGLLGL 688

Chain D from PDB  Type:PROTEIN  Length:7
 aligned with RAVR1_MOUSE | Q9CW46 from UniProtKB/Swiss-Prot  Length:748

    Alignment length:7
          RAVR1_MOUSE   682 SEGLLGL 688
               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
                 3zzz D 682 SEGLLGL 688

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: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Canonical RBD (214)

Protein domain: automated matches (24)

Human (Homo sapiens) [TaxId: 9606] (21)

1a	d3zzza_	A:
1b	d3zzzb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTBP1_HUMAN | P26599)

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:0008187	poly-pyrimidine tract binding	Interacting selectively and non-covalently with any stretch of pyrimidines (cytosine or uracil) in an RNA molecule.
	GO:0036002	pre-mRNA binding	Interacting selectively and non-covalently with pre-messenger RNA (pre-mRNA), an intermediate molecule between DNA and protein that may contain introns and, at least in part, encodes one or more proteins. Introns are removed from pre-mRNA to form a 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:0075522	IRES-dependent viral translational initiation	Process by which viral mRNA translation is initiated, where a domain in the 5' untranslated region (UTR) of the viral mRNA called an internal ribosome entry site (IRES) binds the host 43S preinitiation complex, circumventing regular cap-dependent translation initiation.
	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:0008543	fibroblast growth factor receptor signaling pathway	The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
	GO:0010467	gene expression	The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	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:0033119	negative regulation of RNA splicing	Any process that stops, prevents, or reduces the frequency, rate or extent of RNA splicing.
	GO:0048025	negative regulation of mRNA splicing, via spliceosome	Any process that stops, prevents or reduces the rate or extent of mRNA splicing via a spliceosomal mechanism.
	GO:0051148	negative regulation of muscle cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of muscle cell differentiation.
	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
cellular component
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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 C,D (RAVR1_MOUSE | Q9CW46)

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.
biological process
	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.
cellular component
	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.

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	Cis Peptide Bonds
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	3zzz
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	PTBP1_HUMAN \| P26599
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	RAVR1_MOUSE \| Q9CW46
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UniProtKB/Swiss-Prot
	PTBP1_HUMAN \| P26599	:	1qm9 1sjq 1sjr 2ad9 2adb 2adc 2evz 2n3o 3zzy
	RAVR1_MOUSE \| Q9CW46	:	1wi6 3zzy

1qm9	NMR, REPRESENTATIVE STRUCTURE
1sjq	NMR STRUCTURE OF RRM1 FROM HUMAN POLYPYRIMIDINE TRACTBINDING PROTEIN ISOFORM 1 (PTB1)
1sjr	NMR STRUCTURE OF RRM2 FROM HUMAN POLYPYRIMIDINE TRACTBINDING PROTEIN ISOFORM 1 (PTB1)
1wi6	SOLUTION STRUCTURE OF THE RNA BINDING DOMAIN FROM MOUSEHYPOTHETICAL PROTEIN BAB23670
2ad9	SOLUTION STRUCTURE OF POLYPYRIMIDINE TRACT BINDING PROTEINRBD1 COMPLEXED WITH CUCUCU RNA
2adb	SOLUTION STRUCTURE OF POLYPYRIMIDINE TRACT BINDING PROTEINRBD2 COMPLEXED WITH CUCUCU RNA
2adc	SOLUTION STRUCTURE OF POLYPYRIMIDINE TRACT BINDING PROTEINRBD34 COMPLEXED WITH CUCUCU RNA
2evz	STRUCTURE OF RNA BINDING DOMAINS 3 AND 4 OF POLYPYRIMIDINETRACT BINDING PROTEIN
3zzy	CRYSTAL STRUCTURE OF A RAVER1 PRI3 PEPTIDE IN COMPLEX WITH POLYPYRIMIDINE TRACT BINDING PROTEIN RRM2

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (3, 6)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (22, 27)

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