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Title :   CRYSTAL STRUCTURE OF THE 25KDA SUBUNIT OF HUMAN CLEAVAGE FACTOR IM IN COMPLEX WITH RNA UUGUAU

Authors :   Q. Yang, G. M. Gilmartin, S. Doublie

Date :   30 Mar 10 (Deposition) - 02 Jun 10 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.22

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

Keywords :   Cpsf5, Cf Im, Mrna Processing, Cleavage Factor, Nudix Protein, Protein-Rna Complex, Rna Binding Protein, Rna Binding-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Yang, G. M. Gilmartin, S. Doublie
Structural Basis Of Ugua Recognition By The Nudix Protein Cfi(M)25 And Implications For A Regulatory Role In Mrna 3' Processing.
Proc. Natl. Acad. Sci. Usa V. 107 10062 2010
PubMed-ID: 20479262 | Reference-DOI: 10.1073/PNAS.1000848107

Molecule 1 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 5
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	HIS6-MBP FUSION VECTOR
	Expression System Strain	:	ROSETTA (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CFIM25, CPSF25, CPSF5, NUDT21
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 25 KDA SUBUNIT, CPSF 25 KDA SUBUNIT, PRE-MRNA CLEAVAGE FACTOR IM 25 KDA SUBUNIT, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 21, NUDIX MOTIF 21

*Molecule 2 - RNA (5'-R(UPUPGPUPAPU)-3')*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:81 , LYS A:105 , LEU A:106 , LYS A:172 , ILE A:211 , U C:2	BINDING SITE FOR RESIDUE GOL A 228
2	AC2	SOFTWARE	ARG A:68 , PHE A:71 , ASP A:72 , ARG B:78 , GLY B:114	BINDING SITE FOR RESIDUE GOL A 229
3	AC3	SOFTWARE	GLU B:81 , LYS B:105 , LEU B:106 , LYS B:172 , ILE B:211 , U C:6	BINDING SITE FOR RESIDUE GOL B 228

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	CPSF5_HUMAN	76-201	2	A:76-201 B:76-201

Asymmetric/Biological Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000300291	1	ENSE00001482691	chr16:56485287-56484999	289	CPSF5_HUMAN	1-39	39	2	A:28-39 B:18-39	12 22
1.2	ENST00000300291	2	ENSE00001108683	chr16:56481901-56481701	201	CPSF5_HUMAN	39-106	68	2	A:39-106 B:39-106	68 68
1.3	ENST00000300291	3	ENSE00001108681	chr16:56480601-56480538	64	CPSF5_HUMAN	106-127	22	2	A:106-127 B:106-127	22 22
1.4	ENST00000300291	4	ENSE00001108678	chr16:56473658-56473569	90	CPSF5_HUMAN	128-157	30	2	A:128-157 B:128-157	30 30
1.5	ENST00000300291	5	ENSE00001108686	chr16:56468741-56468666	76	CPSF5_HUMAN	158-183	26	2	A:158-183 B:158-183	26 26
1.6	ENST00000300291	6	ENSE00001108677	chr16:56468357-56468243	115	CPSF5_HUMAN	183-221	39	2	A:183-221 B:183-221	39 39
1.7	ENST00000300291	7	ENSE00001108679	chr16:56466645-56463045	3601	CPSF5_HUMAN	221-227	7	2	A:221-227 B:221-227	7 7

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:200
 aligned with CPSF5_HUMAN | O43809 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:200
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227
          CPSF5_HUMAN    28 TKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.hhh.eeeeee........hhhhhhhhhhhhhhhhh.eeeeeeeeeee....eeeeeee.....ee..eee.....hhhhhhhhhhhhhhh.........eeeeeeeeeee...................eeeeeeeee....eeeeee...eeeeeehhhhh.hhhhhhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------NUDIX  PDB: A:76-201 UniProt: 76-201                                                                                          -------------------------- PROSITE
           Transcript 1 (1) Exon 1.1    ------------------------------------------------------------------Exon 1.3              Exon 1.4  PDB: A:128-157      Exon 1.5  PDB: A:158-183  -------------------------------------1.7     Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.2  PDB: A:39-106 UniProt: 39-106                             ----------------------------------------------------------------------------Exon 1.6  PDB: A:183-221               ------ Transcript 1 (2)
                 3mdg A  28 TKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with CPSF5_HUMAN | O43809 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:210
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227
          CPSF5_HUMAN    18 TQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------NUDIX_2-3mdgB01 B:35-222                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) -----------------NUDIX_2-3mdgB02 B:35-222                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author ..................eeee.hhh.eeeeee........hhhhhhhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeee.....ee..eee.....hhhhhhhhhhhhhhh.........eeeeeeeeeee...................eeeeeeeee....eeeeee...eeeeeehhhhh.hhhhhhhhhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------NUDIX  PDB: B:76-201 UniProt: 76-201                                                                                          -------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:18-39------------------------------------------------------------------Exon 1.3              Exon 1.4  PDB: B:128-157      Exon 1.5  PDB: B:158-183  -------------------------------------1.7     Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.2  PDB: B:39-106 UniProt: 39-106                             ----------------------------------------------------------------------------Exon 1.6  PDB: B:183-221               ------ Transcript 1 (2)
                 3mdg B  18 TQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227

Chain C from PDB  Type:RNA  Length:6
                                      
                 3mdg C   1 UUGUAU   6

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 3MDG)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX_2 (7)

Homo sapiens (Human) (7)

1a	NUDIX_2-3mdgB01	B:35-222
1b	NUDIX_2-3mdgB02	B:35-222

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CPSF5_HUMAN | O43809)

molecular function
	GO:0017091	AU-rich element binding	Interacting selectively and non-covalently with a region of RNA containing frequent adenine and uridine bases.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	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:0051262	protein tetramerization	The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
	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:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005849	mRNA cleavage factor complex	Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	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:0042382	paraspeckles	Discrete subnuclear bodies in the interchromatin nucleoplasmic space, often located adjacent to nuclear specks. 10-20 paraspeckles are typically found in human cell nuclei.

Asymmetric/Biological Unit
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	CPSF5_HUMAN \| O43809	:	2cl3 2j8q 3bap 3bho 3mdi 3n9u 3p5t 3p6y 3q2s 3q2t

2cl3	CF IM 25KDA STRUCTURE
2j8q	CF IM 25KDA STRUCTURE WITH SULFATE BOUND
3bap	CF IM 25KDA STRUCTURE
3bho	CF IM 25KDA STRUCTURE WITH AP4A
3mdi	CF IM 25KDA STRUCTURE WITH UGUAAA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (7, 14)

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