3Q2T - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CFIM68 RRM/CFIM25/RNA COMPLEX

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

Date :   20 Dec 10 (Deposition) - 16 Feb 11 (Release) - 06 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.06

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Cfim, Cfim25, Cfim68, Cpsf5, Cpsf6, Cpsf, 3' End Processing, Rna Processing, Cleavage Factor, Nudix Protein, Protein-Protein Complex, Protein-Rna Complex, Rrm, Nudix Fold, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Yang, M. Coseno, G. M. Gilmartin, S. Doublie
Crystal Structure Of A Human Cleavage Factor Cfi(M)25/Cfi(M)68/Rna Complex Provides An Insight Into Poly(A) Site Recognition And Rna Looping.
Structure V. 19 368 2011
PubMed-ID: 21295486 | Reference-DOI: 10.1016/J.STR.2010.12.021

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
	Fragment	:	RESIDUES 21-227
	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, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 21, NUDIX MOTIF 21, PRE-MRNA CLEAVAGE FACTOR IM 25 KDA SUBUNIT

Molecule 2 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22 C-TERMINAL HIS6 TAG
	Expression System Strain	:	ROSETTA (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RRM DOMAIN, RESIDUES 13-235
	Gene	:	CFIM68, CPSF6
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 68 KDA SUBUNIT, CPSF 68 KDA SUBUNIT, PRE-MRNA CLEAVAGE FACTOR IM 68 KDA SUBUNIT, PROTEIN HPBRII-4/7

Molecule 3 - RNA
	Chains	:	E, F
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESIZED BY DHARMACON
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3Q2T)

(no "Site" information available for 3Q2T)

(no "SS Bond" information available for 3Q2T)

(no "Cis Peptide Bond" information available for 3Q2T)

(no "SAP(SNP)/Variant" information available for 3Q2T)

Asymmetric/Biological Unit (2, 4)

	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
2	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	CPSF6_HUMAN	81-161	2	C:81-161 D:81-161

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:21-39 B:21-39	19 19
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 (gaps) B:128-157 (gaps)	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:205
 aligned with CPSF5_HUMAN | O43809 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:207
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
          CPSF5_HUMAN    21 GNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee.hhh.eeeeee........hhhhhhhhhhhhhhhh..eeeeeeeeeee....eeeeeeee...eee..eee.....hhhhhhhhhhhhhhh...--....eeeeeeeeeee...................eeeeeeeee....eeeeee...eeeeeehhhhh.hhhhhhhhhhhhhhhhhh.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 (gapsExon 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)
                 3q2t A  21 GNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD--LQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
                                    30        40        50        60        70        80        90       100       110       120       130  |  | 140       150       160       170       180       190       200       210       220       
                                                                                                                                          133  |                                                                                           
                                                                                                                                             136

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with CPSF5_HUMAN | O43809 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:207
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
          CPSF5_HUMAN    21 GNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------NUDIX_2-3q2tB01 B:35-222                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) --------------NUDIX_2-3q2tB02 B:35-222                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author ...............eeee.hhh.eeeeee........hhhhhhhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeee.....ee..eee.....hhhhhhhhhhhhhh....----..eeeeeeeeeee...................eeeeeeeee....eeeeee...eeeeeehhhhh.hhhhhhhhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------NUDIX  PDB: B:76-201 UniProt: 76-201                                                                                          -------------------------- PROSITE
           Transcript 1 (1) Exon 1.1           ------------------------------------------------------------------Exon 1.3              Exon 1.4  PDB: B:128-157 (gapsExon 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)
                 3q2t B  21 GNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQD----DWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
                                    30        40        50        60        70        80        90       100       110       120       130  |    140       150       160       170       180       190       200       210       220       
                                                                                                                                          133  138

Chain C from PDB  Type:PROTEIN  Length:93
 aligned with CPSF6_HUMAN | Q16630 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:93
                                    90       100       110       120       130       140       150       160       170   
          CPSF6_HUMAN    81 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPCNKQFLSQFEMQSRK 173
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh...ee...eee......eeeeeeeee...hhhhhhhhhh..........eeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) RRM  PDB: C:81-161 UniProt: 81-161                                               ------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 3q2t C  81 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRK 173
                                    90       100       110       120       130       140       150       160       170

Chain D from PDB  Type:PROTEIN  Length:92
 aligned with CPSF6_HUMAN | Q16630 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:92
                                    90       100       110       120       130       140       150       160       170  
          CPSF6_HUMAN    81 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPCNKQFLSQFEMQSR 172
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --RRM_6-3q2tD01 D:83-153                                                 ------------------- Pfam domains (1)
           Pfam domains (2) --RRM_6-3q2tD02 D:83-153                                                 ------------------- Pfam domains (2)
         Sec.struct. author .eeeee......hhhhhhhhhhhhh.....eeeeee......eeeeeeee...hhhhhhhhhhhhhh.........ee....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) RRM  PDB: D:81-161 UniProt: 81-161                                               ----------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3q2t D  81 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSR 172
                                    90       100       110       120       130       140       150       160       170

Chain E from PDB  Type:RNA  Length:5
                                     
                 3q2t E   1 UUGUA   5

Chain F from PDB  Type:RNA  Length:5
                                     
                 3q2t F   1 UUGUA   5

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 3Q2T)

(no "CATH Domain" information available for 3Q2T)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX_2 (7)

Homo sapiens (Human) (7)

1a	NUDIX_2-3q2tB01	B:35-222
1b	NUDIX_2-3q2tB02	B:35-222

Clan: RRM (206)

Family: RRM_6 (14)

Homo sapiens (Human) (12)

2a	RRM_6-3q2tD01	D:83-153
2b	RRM_6-3q2tD02	D:83-153

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.

Chain C,D (CPSF6_HUMAN | Q16630)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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: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:0051262	protein tetramerization	The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005849	mRNA cleavage factor complex	Any macromolecular complex involved in cleavage or polyadenylation of mRNA 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: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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3q2s	CRYSTAL STRUCTURE OF CFIM68 RRM/CFIM25 COMPLEX

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

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Exons (7, 14)

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