3UL0 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   MOUSE IMPORTIN ALPHA: MOUSE CBP80Y8D CNLS COMPLEX

Authors :   M. Marfori, J. K. Forwood, T. G. Lonhienne, B. Kobe

Date :   10 Nov 11 (Deposition) - 03 Oct 12 (Release) - 03 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Arm Repeat, Armadillo Repeat, Nuclear Transport, Nuclear Localisation Signal Binding, Importin Beta Binding, Protein Transport-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Marfori, T. G. Lonhienne, J. K. Forwood, B. Kobe
Structural Basis Of High-Affinity Nuclear Localization Signal Interactions With Importin-Alpha
Traffic V. 13 532 2012
PubMed-ID: 22248489 | Reference-DOI: 10.1111/J.1600-0854.2012.01329.X

Molecule 1 - IMPORTIN SUBUNIT ALPHA-2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 70-529
	Gene	:	KPNA2
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	IMPORTIN ALPHA P1, KARYOPHERIN SUBUNIT ALPHA-2, PENDULIN, PORE TARGETING COMPLEX 58 KDA SUBUNIT, PTAC58, RAG COHORT PROTEIN 1, SRP1-ALPHA

Molecule 2 - NUCLEAR CAP-BINDING PROTEIN SUBUNIT 1
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	MCBP80 CNLS PEPTIDE, RESIDUES 1-23
	Gene	:	CBP80
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	CAP-BINDING PROTEIN 80, CBP80

		1	2
Asymmetric/Biological Unit	:	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3UL0)

(no "Site" information available for 3UL0)

(no "SS Bond" information available for 3UL0)

Asymmetric/Biological Unit

No.	Residues
1	Asn B:241	-	Pro B:242

(no "SAP(SNP)/Variant" information available for 3UL0)

Asymmetric/Biological Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARM_REPEAT	PS50176	Armadillo/plakoglobin ARM repeat profile.	IMA1_MOUSE	162-204 119-162 204-230 251-293 293-335 335-377	6	B:162-204 B:119-162 B:204-230 B:251-293 B:293-335 B:335-377

Asymmetric/Biological Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSMUST00000030014	1	ENSMUSE00000632760	chr4:46151485-46151758	274	NCBP1_MOUSE	1-12	12	1	C:1-12	12
1.2	ENSMUST00000030014	2	ENSMUSE00000369929	chr4:46157657-46157745	89	NCBP1_MOUSE	12-41	30	1	C:12-23	12
1.3	ENSMUST00000030014	3	ENSMUSE00000332768	chr4:46158246-46158346	101	NCBP1_MOUSE	42-75	34	0	-	-
1.4	ENSMUST00000030014	4	ENSMUSE00000370423	chr4:46160251-46160407	157	NCBP1_MOUSE	75-127	53	0	-	-
1.5	ENSMUST00000030014	5	ENSMUSE00000409329	chr4:46162734-46162841	108	NCBP1_MOUSE	128-163	36	0	-	-
1.6	ENSMUST00000030014	6	ENSMUSE00000363396	chr4:46163511-46163632	122	NCBP1_MOUSE	164-204	41	0	-	-
1.7	ENSMUST00000030014	7	ENSMUSE00000178206	chr4:46164888-46164957	70	NCBP1_MOUSE	204-227	24	0	-	-
1.8	ENSMUST00000030014	8	ENSMUSE00000178215	chr4:46165782-46165997	216	NCBP1_MOUSE	228-299	72	0	-	-
1.9	ENSMUST00000030014	9	ENSMUSE00000178211	chr4:46168622-46168719	98	NCBP1_MOUSE	300-332	33	0	-	-
1.10	ENSMUST00000030014	10	ENSMUSE00000178214	chr4:46169632-46169695	64	NCBP1_MOUSE	332-353	22	0	-	-
1.11a	ENSMUST00000030014	11a	ENSMUSE00000344201	chr4:46170695-46170805	111	NCBP1_MOUSE	354-390	37	0	-	-
1.12a	ENSMUST00000030014	12a	ENSMUSE00000178218	chr4:46172531-46172595	65	NCBP1_MOUSE	391-412	22	0	-	-
1.13	ENSMUST00000030014	13	ENSMUSE00000335449	chr4:46174133-46174195	63	NCBP1_MOUSE	412-433	22	0	-	-
1.14	ENSMUST00000030014	14	ENSMUSE00000178217	chr4:46174964-46175038	75	NCBP1_MOUSE	433-458	26	0	-	-
1.15	ENSMUST00000030014	15	ENSMUSE00000178221	chr4:46175833-46175936	104	NCBP1_MOUSE	458-493	36	0	-	-
1.16a	ENSMUST00000030014	16a	ENSMUSE00000382957	chr4:46178038-46178160	123	NCBP1_MOUSE	493-534	42	0	-	-
1.17	ENSMUST00000030014	17	ENSMUSE00000351046	chr4:46179610-46179712	103	NCBP1_MOUSE	534-568	35	0	-	-
1.18	ENSMUST00000030014	18	ENSMUSE00000385725	chr4:46180174-46180267	94	NCBP1_MOUSE	568-599	32	0	-	-
1.19a	ENSMUST00000030014	19a	ENSMUSE00000178212	chr4:46181323-46181426	104	NCBP1_MOUSE	600-634	35	0	-	-
1.20	ENSMUST00000030014	20	ENSMUSE00000178203	chr4:46182001-46182115	115	NCBP1_MOUSE	634-672	39	0	-	-
1.21	ENSMUST00000030014	21	ENSMUSE00000178210	chr4:46182817-46182945	129	NCBP1_MOUSE	673-715	43	0	-	-
1.22	ENSMUST00000030014	22	ENSMUSE00000178202	chr4:46183344-46183457	114	NCBP1_MOUSE	716-753	38	0	-	-
1.23b	ENSMUST00000030014	23b	ENSMUSE00000389281	chr4:46184765-46185275	511	NCBP1_MOUSE	754-790	37	0	-	-

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 B from PDB  Type:PROTEIN  Length:426
 aligned with IMA1_MOUSE | P52293 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:426
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490      
           IMA1_MOUSE    71 QGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYF 496
               SCOP domains d3ul0b_ B: Importin alpha                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------ARM_REPEAT  PDB: B:162-204 UniProt: 162-204----------------------------------------------ARM_REPEAT  PDB: B:251-293 UniProt: 251-293-----------------------------------------ARM_REPEAT  PDB: B:335-377 UniProt: 335-377----------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------ARM_REPEAT  PDB: B:119-162 UniProt: 119-162 -----------------------------------------ARM_REPEAT  PDB: B:204-230 --------------------------------------------------------------ARM_REPEAT  PDB: B:293-335 UniProt: 293-335----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ul0 B  71 QGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYF 496
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490

Chain C from PDB  Type:PROTEIN  Length:23
 aligned with NCBP1_MOUSE | Q3UYV9 from UniProtKB/Swiss-Prot  Length:790

    Alignment length:23
                                    10        20   
          NCBP1_MOUSE     1 MSRRRHSYENDGGQPHKRRKTSD  23
               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 1 (1) Exon 1.1    ----------- Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.2     Transcript 1 (2)
                 3ul0 C   1 MSRRRHSDENDGGQPHKRRKTSD  23
                                    10        20

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: ARM repeat (317)

Family: Armadillo repeat (77)

Protein domain: Importin alpha (17)

Mouse (Mus musculus) [TaxId: 10090] (17)

d3ul0b_

(no "CATH Domain" information available for 3UL0)

(no "Pfam Domain" information available for 3UL0)

Asymmetric/Biological Unit(hide GO term definitions)

Chain B (IMA1_MOUSE | P52293)

molecular function
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	GO:0008139	nuclear localization sequence binding	Interacting selectively and non-covalently with a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus.
	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:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
	GO:0006607	NLS-bearing protein import into nucleus	The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
	GO:0006606	protein import into nucleus	The directed movement of a protein from the cytoplasm to the nucleus.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	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 (NCBP1_MOUSE | Q3UYV9)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000339	RNA cap binding	Interacting selectively and non-covalently with a 7-methylguanosine (m7G) group or derivative located at the 5' end of an RNA 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:0006370	7-methylguanosine mRNA capping	Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
	GO:0016070	RNA metabolic process	The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	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:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0045292	mRNA cis splicing, via spliceosome	The joining together, after removal of an intervening sequence composed of one or more introns, of two segments of the same RNA molecule via spliceosomal catalysis to produce an mRNA composed only of exon sequences that all came from the same primary transcript.
	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:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0031442	positive regulation of mRNA 3'-end processing	Any process that activates or increases the frequency, rate or extent of mRNA 3'-end processing.
	GO:0098789	pre-mRNA cleavage required for polyadenylation	The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
	GO:1900363	regulation of mRNA polyadenylation	Any process that modulates the frequency, rate or extent of mRNA polyadenylation.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0006446	regulation of translational initiation	Any process that modulates the frequency, rate or extent of translational initiation.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005845	mRNA cap binding complex	Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005846	nuclear cap binding complex	A conserved heterodimeric protein complex that binds to the 5' terminal cap structure m7G(5')ppp(5')N of nascent eukaryotic RNA polymerase II transcripts such as pre-mRNA and U snRNA. The consists of proteins known as CBP20 and CBP80, binds to cap structures in the nucleus, and is involved in pre-mRNA splicing, 3'-end formation, and RNA nuclear export.
	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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(no "Sites" information available for 3ul0)

	Cis Peptide Bonds
		Asn B:241 - Pro B:242	[ RasMol ]

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1ial	IMPORTIN ALPHA, MOUSE
3fex	CRYSTAL STRUCTURE OF THE CBC-IMPORTIN ALPHA COMPLEX
3fey	CRYSTAL STRUCTURE OF THE CBC-IMPORTIN ALPHA COMPLEX
3ukw
3ukx
3uky
3ukz
3ul1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (2, 2)

Sequences/Alignments

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SCOP Domains (1, 1)

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Gene Ontology (35, 40)

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