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Asym./Biol. Unit (Jmol Viewer)

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

Title :   X-RAY STRUCTURE OF A CORE U2AF65/U2AF35 HETERODIMER

Authors :   C. L. Kielkopf, N. A. Rodionova, M. R. Green, S. K. Burley

Date :   19 Jul 01 (Deposition) - 19 Sep 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Rrm, Rna Splicing, Proline, Ppii Helix, Peptide Recognition, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Kielkopf, N. A. Rodionova, M. R. Green, S. K. Burley
A Novel Peptide Recognition Mode Revealed By The X-Ray Structure Of A Core U2Af35/U2Af65 Heterodimer.
Cell(Cambridge, Mass. ) V. 106 595 2001
PubMed-ID: 11551507 | Reference-DOI: 10.1016/S0092-8674(01)00480-9
(for further references see the PDB file header)

Molecule 1 - SPLICING FACTOR U2AF 35 KDA SUBUNIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-4T2
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	U2 SNRNP AUXILIARY FACTOR SMALL SUBUNIT

Molecule 2 - SPLICING FACTOR U2AF 65 KDA SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-4T2
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	U2 SNRNP AUXILIARY FACTOR LARGE SUBUNIT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	HEZ	2	Ligand/Ion	HEXANE-1,6-DIOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:106 , MET B:110 , HOH B:214	BINDING SITE FOR RESIDUE HEZ B 201
2	AC2	SOFTWARE	LYS A:92 , ASP A:129 , ARG A:133 , ASP B:93	BINDING SITE FOR RESIDUE HEZ A 202

(no "SS Bond" information available for 1JMT)

(no "Cis Peptide Bond" information available for 1JMT)

(no "SAP(SNP)/Variant" information available for 1JMT)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	U2AF1_HUMAN	65-147	1	A:65-146

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000291552	1a	ENSE00001856022	chr21:44527697-44527561	137	U2AF1_HUMAN	1-15	15	0	-	-
1.2c	ENST00000291552	2c	ENSE00001719187	chr21:44524512-44524425	88	U2AF1_HUMAN	15-44	30	1	A:43-44	2
1.2i	ENST00000291552	2i	ENSE00001798362	chr21:44520629-44520563	67	U2AF1_HUMAN	45-67	23	1	A:45-67 (gaps)	23
1.3d	ENST00000291552	3d	ENSE00001717447	chr21:44515853-44515804	50	U2AF1_HUMAN	67-83	17	1	A:67-83	17
1.3e	ENST00000291552	3e	ENSE00001783248	chr21:44515646-44515548	99	U2AF1_HUMAN	84-116	33	1	A:84-116	33
1.3f	ENST00000291552	3f	ENSE00001050518	chr21:44514898-44514765	134	U2AF1_HUMAN	117-161	45	1	A:117-146	30
1.4a	ENST00000291552	4a	ENSE00001268168	chr21:44514673-44514581	93	U2AF1_HUMAN	161-192	32	0	-	-
1.4e	ENST00000291552	4e	ENSE00001905286	chr21:44513359-44513066	294	U2AF1_HUMAN	192-240	49	0	-	-

2.1	ENST00000308924	1	ENSE00001247615	chr19:56165416-56166519	1104	U2AF2_HUMAN	1-17	17	0	-	-
2.2	ENST00000308924	2	ENSE00001172989	chr19:56170576-56170711	136	U2AF2_HUMAN	17-62	46	0	-	-
2.3	ENST00000308924	3	ENSE00000953888	chr19:56171543-56171587	45	U2AF2_HUMAN	62-77	16	0	-	-
2.4	ENST00000308924	4	ENSE00001172973	chr19:56171882-56171985	104	U2AF2_HUMAN	77-112	36	1	B:90-112	23
2.5	ENST00000308924	5	ENSE00001178740	chr19:56172404-56172555	152	U2AF2_HUMAN	112-162	51	1	B:112-112	1
2.6	ENST00000308924	6	ENSE00001172954	chr19:56173868-56173984	117	U2AF2_HUMAN	163-201	39	0	-	-
2.7	ENST00000308924	7	ENSE00001172945	chr19:56174972-56175110	139	U2AF2_HUMAN	202-248	47	0	-	-
2.8	ENST00000308924	8	ENSE00000876731	chr19:56179873-56179952	80	U2AF2_HUMAN	248-274	27	0	-	-
2.9	ENST00000308924	9	ENSE00001178763	chr19:56180036-56180158	123	U2AF2_HUMAN	275-315	41	0	-	-
2.10b	ENST00000308924	10b	ENSE00001172923	chr19:56180449-56180547	99	U2AF2_HUMAN	316-348	33	0	-	-
2.11	ENST00000308924	11	ENSE00001178717	chr19:56180810-56181058	249	U2AF2_HUMAN	349-431	83	0	-	-
2.12	ENST00000308924	12	ENSE00001320361	chr19:56185300-56186081	782	U2AF2_HUMAN	432-475	44	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:98
 aligned with U2AF1_HUMAN | Q01081 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:104
                                    52        62        72        82        92       102       112       122       132       142    
          U2AF1_HUMAN    43 SQTIALLNIYRNPQNSSQSADGLRCAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 146
               SCOP domains d1jmta_ A: U2A      F35 (35 KDa subunit)                                                                 SCOP domains
               CATH domains 1jmtA00 A:43-1      46  [code=3.30.70.330, no name defined]                                              CATH domains
               Pfam domains ------------------------------------------------RRM_5-1jmtA01 A:91-145                                 - Pfam domains
         Sec.struct. author ..eeeeeeeee...------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee........eeeeeeee.hhhhhhhhhhhhh..ee..ee..eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------RRM  PDB: A:65-146 UniProt: 65-147                                                 PROSITE
           Transcript 1 (1) 1.Exon 1.2i              ----------------Exon 1.3e  PDB: A:84-116         Exon 1.3f  PDB: A:117-146      Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.3d        --------------------------------------------------------------- Transcript 1 (2)
                 1jmt A  43 SQTIALLNIYRNPQ------DGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 146
                                    52   |     -|       72        82        92       102       112       122       132       142    
                                        56     63

Chain B from PDB  Type:PROTEIN  Length:23
 aligned with U2AF2_HUMAN | P26368 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:23
                                    99       109   
          U2AF2_HUMAN    90 KYWDVPPPGFEHITPMQYKAMQA 112
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author .............hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
           Transcript 2 (1) Exon 2.4  PDB: B:90-112 Transcript 2 (1)
           Transcript 2 (2) ----------------------2 Transcript 2 (2)
                 1jmt B  90 KYWDVPPPGFEHITPMQYKAMQA 112
                                    99       109

Legend:		→ Mismatch	(orange background)
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	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) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: RNA-binding domain, RBD (289)

Family: Splicing factor U2AF subunits (1)

Protein domain: U2AF35 (35 KDa subunit) (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1jmta_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.330, no name defined] (307)

Human (Homo sapiens) (81)

1jmtA00

A:43-146

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RRM (206)

Family: RRM_5 (7)

Homo sapiens (Human) (3)

RRM_5-1jmtA01

A:91-145

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (U2AF1_HUMAN | Q01081)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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:0006405	RNA export from nucleus	The directed movement of RNA from the nucleus to the cytoplasm.
	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:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	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:1903955	positive regulation of protein targeting to mitochondrion	Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
	GO:1903146	regulation of mitophagy	Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
	GO:0006369	termination of RNA polymerase II transcription	The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
cellular component
	GO:0015030	Cajal body	A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
	GO:0089701	U2AF	A heterodimeric protein complex consisting of conserved large and small U2AF subunits that contributes to spliceosomal RNA splicing by binding to consensus sequences at the 3' splice site. U2AF is required to stabilize the association of the U2 snRNP with the branch point.
	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:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	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.
	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 (U2AF2_HUMAN | P26368)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0030628	pre-mRNA 3'-splice site binding	Interacting selectively and non-covalently with the pre-mRNA 3' splice site sequence.
	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:0006405	RNA export from nucleus	The directed movement of RNA from the nucleus to the cytoplasm.
	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:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	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: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:0033120	positive regulation of RNA splicing	Any process that activates or increases the frequency, rate or extent of RNA splicing.
	GO:1903955	positive regulation of protein targeting to mitochondrion	Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
	GO:1903146	regulation of mitophagy	Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
	GO:0006369	termination of RNA polymerase II transcription	The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
cellular component
	GO:0000974	Prp19 complex	A protein complex consisting of Prp19 and associated proteins that is involved in the transition from the precatalytic spliceosome to the activated form that catalyzes step 1 of splicing, and which remains associated with the spliceosome through the second catalytic step. It is widely conserved, found in both yeast and mammals, though the exact composition varies. In S. cerevisiae, it contains Prp19p, Ntc20p, Snt309p, Isy1p, Syf2p, Cwc2p, Prp46p, Clf1p, Cef1p, and Syf1p.
	GO:0071004	U2-type prespliceosome	A spliceosomal complex that is formed by association of the 5' splice site with the U1 snRNP, while the branch point sequence is recognized by the U2 snRNP. The prespliceosome includes many proteins in addition to those found in the U1 and U2 snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation.
	GO:0089701	U2AF	A heterodimeric protein complex consisting of conserved large and small U2AF subunits that contributes to spliceosomal RNA splicing by binding to consensus sequences at the 3' splice site. U2AF is required to stabilize the association of the U2 snRNP with the branch point.
	GO:0000243	commitment complex	A spliceosomal complex that is formed by association of the U1 snRNP with the 5' splice site of an unspliced intron in an RNA transcript.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	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.
	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.

Asymmetric/Biological Unit
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	1jmt
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