3N9U - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE 25 KDA SUBUNIT AND THE 59 KDA SUBUNIT (RRM DOMAIN) OF HUMAN CLEAVAGE FACTOR IM

Authors :   L. Tresaugues, M. Welin, C. H. Arrowsmith, H. Berglund, C. Bountra, R. C A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Jo T. Karlberg, S. Kol, T. Kotenyova, M. Moche, T. N. Nielsen, T. Nyman, C. H. Schuler, P. Schutz, M. I. Siponen, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, M. Wisniewska, P. Nordlund, Structural Gen Consortium (Sgc)

Date :   31 May 10 (Deposition) - 21 Jul 10 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.92

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

Keywords :   Protein-Protein Complex, Coexpression, Heterotetramer, Mrna Maturation, Polyadenylation, Mrna Cleavage, Cleavage And Polyadenylation Specificity Factor Subunit 5, Cleavage And Polyadenylation Specificity Factor Subunit 7, Pre-Mrna Cleavage Factor Im 25 Kda Subunit, Pre-Mrna Cleavage Factor Im 59 Kda Subunit, Nudix, Hydrolase, Rrm Domain, Nudt21, Cpsf5, Cpsf7, Structural Genomics, Structural Genomics Consortium, Sgc, Sgc Stockholm, Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Tresaugues, M. Welin, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, M. Moche, T. K. Nielsen, T. Nyman, C. Persson, H. Schuler, P. Schutz, M. I. Siponen, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, M. Wisniewska, P. Nordlund
Crystal Structure Of The Complex Between The 25 Kda Subunit And The 59 Kda Subunit (Rrm Domain) Of Human Cleavage Facto Im
To Be Published
PubMed: search

Molecule 1 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 5
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21 (DE3) R3 PRARE
	Expression System Taxid	:	469008
	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, PRE-MRNA CLEAVAGE FACTOR IM 25 KDA SUBUNIT, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 21, NUDIX MOTIF 21

Molecule 2 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 7
	Chains	:	C, I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21 (DE3) R3 PRARE
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RRM DOMAIN, RESIDUES 50-182
	Gene	:	CPSF7
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 59 KDA SUBUNIT, CPSF 59 KDA SUBUNIT, PRE-MRNA CLEAVAGE FACTOR IM 59 KDA SUBUNIT

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	I

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	BINDING SITE FOR RESIDUE GOL A 228
2	AC2	SOFTWARE	GLU B:81 , LYS B:105 , LEU B:106 , LYS B:172 , ILE B:211 , HOH B:267 , HOH B:313 , HOH B:317 , HOH B:326	BINDING SITE FOR RESIDUE GOL B 228
3	AC3	SOFTWARE	TYR A:202 , PRO B:156 , GLN B:157 , HOH B:391	BINDING SITE FOR RESIDUE GOL B 229

(no "SS Bond" information available for 3N9U)

Asymmetric/Biological Unit

No.	Residues
1	Gly C:87	-	Ser C:88
2	Gly I:87	-	Ser I:88

(no "SAP(SNP)/Variant" information available for 3N9U)

Asymmetric/Biological Unit (2, 3)

	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.	CPSF7_HUMAN	82-162	1	C:82-162

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:22-39 B:27-39	18 13
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:206
 aligned with CPSF5_HUMAN | O43809 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:206
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      
          CPSF5_HUMAN    22 NKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeee.hhh.eeeeee........hhhhhhhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeee..eee..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)
                 3n9u A  22 NKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with CPSF5_HUMAN | O43809 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:201
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226 
          CPSF5_HUMAN    27 QTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------NUDIX_2-3n9uB01 B:35-222                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) --------NUDIX_2-3n9uB02 B:35-222                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author ........eeeee.hhh.eeeeee........hhhhhhhhhhhhhhhh..eeeeeeeeeeee..eeeeeeeee...eee..eee.....hhhhhhhhhhhhhhh.........eeeeeeeeeee...................eeeeeeeee....eeeeee...eeeeeehhhhh.hhhhhhhhhhhhhhhhh.eeeee. 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      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)
                 3n9u B  27 QTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN 227
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226

Chain C from PDB  Type:PROTEIN  Length:96
 aligned with CPSF7_HUMAN | Q8N684 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:96
                                    91       101       111       121       131       141       151       161       171      
          CPSF7_HUMAN    82 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKREC 177
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh....eeeeeeee......eeeeeeeee.hhhhhhhhhhhh...ee..ee.eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) RRM  PDB: C:82-162 UniProt: 82-162                                               --------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3n9u C  82 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKREC 177
                                    91       101       111       121       131       141       151       161       171

Chain I from PDB  Type:PROTEIN  Length:87
 aligned with CPSF7_HUMAN | Q8N684 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:92
                                    93       103       113       123       133       143       153       163       173  
          CPSF7_HUMAN    84 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKR 175
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) RRM_1-3n9uI01 I:84-156                                                   ------------------- Pfam domains (1)
           Pfam domains (2) RRM_1-3n9uI02 I:84-156                                                   ------------------- Pfam domains (2)
         Sec.struct. author .eee......hhhhhhhhhhh.......eeeeee......eeeeeeee.-----hhhhhhhh...ee..ee.eee..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) RRM  PDB: - UniProt: 82-162                                                    ------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 3n9u I  84 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVV-----VHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKR 175
                                    93       103       113       123        |-    |  143       153       163       173  
                                                                          132   138

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 3N9U)

(no "CATH Domain" information available for 3N9U)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX_2 (7)

Homo sapiens (Human) (7)

1a	NUDIX_2-3n9uB01	B:35-222
1b	NUDIX_2-3n9uB02	B:35-222

Clan: RRM (206)

Family: RRM_1 (131)

Homo sapiens (Human) (94)

2a	RRM_1-3n9uI01	I:84-156
2b	RRM_1-3n9uI02	I:84-156

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,I (CPSF7_HUMAN | Q8N684)

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: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:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	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: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.

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

(no "Related Entries Specified in the PDB File" available for 3N9U)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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Exons (7, 14)

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