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Asym./Biol. Unit (Jmol Viewer)

Title :   MOUSE IMPORTIN ALPHA- PHOSPHORYLATED SV40 CN PEPTIDE COMPLEX

Authors :   M. R. M. Fontes, T. Teh, G. Toth, A. John, I. Pavo, D. A. Jans, B. Kobe

Date :   22 Jul 03 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Importin Alpha/Karyopherin Alpha, Nuclear Localisation Sequence (Nls) Recognition, Phosphorylation, Simian Virus (Sv40) Large Tumor-Antigen (T-Antigen) Nls, X-Ray Crystal Structure, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. R. M. Fontes, T. Teh, G. Toth, A. John, I. Pavo, D. A. Jans, B. Kobe
Role Of Flanking Sequences And Phosphorylation In The Recognition Of The Simian-Virus-40 Large T-Antigen Nuclear Localization Sequences By Importin-Alpha
Biochem. J. V. 375 339 2003
PubMed-ID: 12852786 | Reference-DOI: 10.1042/BJ20030510
(for further references see the PDB file header)

Molecule 1 - LARGE T ANTIGEN
	Chains	:	A, B
	Engineered	:	YES
	Fragment	:	CN PEPTIDE - SER112 CHEMICALLY PHOSPHORYLATED
	Mutation	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN SIMIAN VIRUS 40 (SV40) LARGE TUMOR-ANTIGEN. SER112 WAS CHEMICALLY PHOSPHORYLATED
	Synthetic	:	YES

Molecule 2 - IMPORTIN ALPHA-2 SUBUNIT
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30A
	Expression System Taxid	:	562
	Fragment	:	NLS BINDING DOMAIN (70-529)
	Gene	:	KPNA2 OR RCH1
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	KARYOPHERIN ALPHA-2 SUBUNIT, SRP1-ALPHA, RAG COHORT PROTEIN 1, PENDULIN, PORE TARGETING COMPLEX 58 KDA SUBUNIT, PTAC58, IMPORTIN ALPHA P1

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1Q1S)

(no "Site" information available for 1Q1S)

(no "SS Bond" information available for 1Q1S)

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 1Q1S)

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	C:162-204 C:119-162 C:204-230 C:251-293 C:293-335 C:335-377

(no "Exon" information available for 1Q1S)

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:5
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:5
              LT_SV40   128 KKRKV 132
               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 ----- Transcript
                 1q1s A 128 KKRKV 132

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:15
                                   128     
              LT_SV40   119 DSQHSTPPKKKRKVE 133
               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 --------------- Transcript
                 1q1s B 119 DAQHAAPPKKKRKVE 133
                                   128

Chain C from PDB  Type:PROTEIN  Length:434
 aligned with IMA1_MOUSE | P52293 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:434
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493    
           IMA1_MOUSE    64 LQENRNNQGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFS 497
               SCOP domains d1q1sc_ C: Importin alpha                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1q1sC00 C:64-497 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------ARM_REPEAT  PDB: C:162-204 UniProt: 162-204----------------------------------------------ARM_REPEAT  PDB: C:251-293 UniProt: 251-293-----------------------------------------ARM_REPEAT  PDB: C:335-377 UniProt: 335-377------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------ARM_REPEAT  PDB: C:119-162 UniProt: 119-162 -----------------------------------------ARM_REPEAT  PDB: C:204-230 --------------------------------------------------------------ARM_REPEAT  PDB: C:293-335 UniProt: 293-335------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q1s C  64 MADIGSNQGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFS 497
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493

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(

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Folds(

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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)

d1q1sc_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Alpha Horseshoe (399)

Topology: Leucine-rich Repeat Variant (77)

Homologous Superfamily: Leucine-rich Repeat Variant (75)

[unclassified] (11)

1q1sC00

C:64-497

(no "Pfam Domain" information available for 1Q1S)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LT_SV40 | P03070)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003688	DNA replication origin binding	Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006268	DNA unwinding involved in DNA replication	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
	GO:0039686	bidirectional double-stranded viral DNA replication	A viral DNA replication process where replication occurs in both directions from the starting point. This creates two replication forks, moving in opposite directions.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039645	modulation by virus of host G1/S transition checkpoint	Any viral process that modulates the frequency, rate or extent of the host cell G1/S transition checkpoint.
	GO:0060153	modulation by virus of host cell cycle	Any viral process that modulates the rate or extent of progression through the cell cycle.
	GO:0039648	modulation by virus of host protein ubiquitination	Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
	GO:0039649	modulation by virus of host ubiquitin-protein ligase activity	The process in which a virus effects a change in host ubiquitin-protein ligase activity. Ubiquitin-protein ligase activity catalyzes the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0039576	suppression by virus of host JAK1 activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host JAK1 (Janus Kinase 1) activity. In the host, binding of a ligand to a receptor triggers activation of JAK proteins, which phosphorylate tyrosine residues on the receptor creating sites for STAT proteins to bind, which are in turn phosphorylated and activated by JAK proteins. By blocking JAK1 activity, many viruses block the host signal transduction pathway.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039502	suppression by virus of host type I interferon-mediated signaling pathway	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0039693	viral DNA genome replication	The replication of a viral DNA genome.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Chain C (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.

Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 1q1s)

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

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	LT_SV40 \| P03070
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1ejl	MOUSE IMPORTIN ALPHA - SV40 NLS PEPTIDE COMPLEX
1ejy	MOUSE IMPORTIN ALPHA - NUCLEOPLASMIN NLS PEPTIDE COMPLEX
1ial	MOUSE IMPORTIN ALPHA
1pjm	MOUSE IMPORTIN ALPHA - RB NLS PEPTIDE COMPLEX
1pjn	MOUSE IMPORTIN ALPHA - N1N2 NLS PEPTIDE COMPLEX

Description

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Ligands, Modified Residues, Ions (0, 0)

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