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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF IMPORTIN-ALPHA BOUND TO A CLIC4 NLS PEPTIDE

Authors :   A. V. Mynott, L. J. Brown, S. J. Harrop, P. M. G. Curmi

Date :   03 Sep 10 (Deposition) - 27 Jul 11 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Importin Alpha, Karyopherin Alpha, Nuclear Localisation Signal (Nls) Recognition, Chloride Intracellular Channel 4, Clic4 Nls, Armadillo Repeat, Nuclear Import, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. V. Mynott, S. J. Harrop, L. J. Brown, S. N. Breit, B. Kobe, P. M. G. Curm
Crystal Structure Of Importin-Alpha Bound To A Peptide Bearing The Nuclear Localisation Signal From Chloride Intracellular Channel Protein 4
Febs J. V. 278 1662 2011
PubMed-ID: 21388519 | Reference-DOI: 10.1111/J.1742-4658.2011.08086.X

Molecule 1 - PEPTIDE OF CHLORIDE INTRACELLULAR CHANNEL PROTEIN 4
	Chains	:	B
	Engineered	:	YES
	Fragment	:	NLS (NUCLEAR LOCALISATION SIGNAL) UNP RESIDUES 198-207
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
	Synonym	:	INTRACELLULAR CHLORIDE ION CHANNEL PROTEIN P64H1
	Synthetic	:	YES

Molecule 2 - IMPORTIN SUBUNIT ALPHA-2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-30A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NLS BINDING DOMAIN (UNP RESIDUES 70-529)
	Gene	:	KPNA2, RCH1
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	KARYOPHERIN SUBUNIT ALPHA-2, SRP1-ALPHA, RAG COHORT PROTEIN 1, PENDULIN, PORE TARGETING COMPLEX 58 KDA SUBUNIT, PTAC58, IMPORTIN ALPHA P1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3OQS)

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

Asymmetric/Biological Unit

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

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

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

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000374379	1a	ENSE00001463371	chr1:25071848-25072116	269	CLIC4_HUMAN	1-24	24	0	-	-
1.3a	ENST00000374379	3a	ENSE00001303385	chr1:25124233-25124342	110	CLIC4_HUMAN	25-61	37	0	-	-
1.4	ENST00000374379	4	ENSE00001129592	chr1:25140585-25140710	126	CLIC4_HUMAN	61-103	43	0	-	-
1.5	ENST00000374379	5	ENSE00001129588	chr1:25153501-25153607	107	CLIC4_HUMAN	103-139	37	0	-	-
1.6b	ENST00000374379	6b	ENSE00001129581	chr1:25166351-25166532	182	CLIC4_HUMAN	139-199	61	0	-	-
1.7b	ENST00000374379	7b	ENSE00001324395	chr1:25167264-25170815	3552	CLIC4_HUMAN	200-253	54	1	B:201-207	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:425
 aligned with IMA1_MOUSE | P52293 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:425
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491     
           IMA1_MOUSE    72 GTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYF 496
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------ARM_REPEAT  PDB: A:162-204 UniProt: 162-204----------------------------------------------ARM_REPEAT  PDB: A:251-293 UniProt: 251-293-----------------------------------------ARM_REPEAT  PDB: A:335-377 UniProt: 335-377----------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------ARM_REPEAT  PDB: A:119-162 UniProt: 119-162 -----------------------------------------ARM_REPEAT  PDB: A:204-230 --------------------------------------------------------------ARM_REPEAT  PDB: A:293-335 UniProt: 293-335----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oqs A  72 GTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYF 496
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491

Chain B from PDB  Type:PROTEIN  Length:7
 aligned with CLIC4_HUMAN | Q9Y696 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:7
          CLIC4_HUMAN   201 VAKKYRN 207
               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 1.7b    Transcript 1
                 3oqs B 201 VAKKYRN 207

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 3OQS)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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 B (CLIC4_HUMAN | Q9Y696)

molecular function
	GO:0005254	chloride channel activity	Enables the facilitated diffusion of a chloride (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0004364	glutathione transferase activity	Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
	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:0005244	voltage-gated ion channel activity	Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0048754	branching morphogenesis of an epithelial tube	The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0071277	cellular response to calcium ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
	GO:1902476	chloride transmembrane transport	The directed movement of chloride across a membrane.
	GO:0006821	chloride transport	The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0001886	endothelial cell morphogenesis	The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell.
	GO:0035088	establishment or maintenance of apical/basal cell polarity	Any cellular process that results in the specification, formation or maintenance polarization of a cell's architecture along its apical/basal axis so that the apical and basal regions of the cell have different membrane, extracellular matrix and sub-membrane cellular components.
	GO:0009566	fertilization	The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy).
	GO:0006749	glutathione metabolic process	The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0030216	keratinocyte differentiation	The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
	GO:0035264	multicellular organism growth	The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
	GO:0030336	negative regulation of cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
	GO:0051493	regulation of cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	GO:0034765	regulation of ion transmembrane transport	Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
	GO:0061299	retina vasculature morphogenesis in camera-type eye	The process in which the vasculature of the retina is generated and organized.
	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.
	GO:0007035	vacuolar acidification	Any process that reduces the pH of the vacuole, measured by the concentration of the hydrogen ion.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0045177	apical part of cell	The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	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:0034707	chloride channel complex	An ion channel complex through which chloride ions pass.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0030659	cytoplasmic vesicle membrane	The lipid bilayer surrounding a cytoplasmic vesicle.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0015630	microtubule cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
	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:0005902	microvillus	Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
	GO:0030496	midbody	A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
	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:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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		Asn A:241 - Pro A:242	[ RasMol ]

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