3Q5U - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   A MINIMAL NLS FROM HUMAN SCRAMBLASE 4 COMPLEXED WITH IMPORTIN ALPHA

Authors :   A. Bhardwaj, G. Cingolani

Date :   29 Dec 10 (Deposition) - 29 Jun 11 (Release) - 24 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Armadillo Repeat, Protein Transport, Protein Transport-Membrane Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Lott, A. Bhardwaj, P. J. Sims, G. Cingolani
A Minimal Nuclear Localization Signal (Nls) In Human Phospholipid Scramblase 4 That Binds Only The Minor Nls-Binding Site Of Importin {Alpha}1.
J. Biol. Chem. V. 286 28160 2011
PubMed-ID: 21690087 | Reference-DOI: 10.1074/JBC.M111.228007

Molecule 1 - 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	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 70-529
	Gene	:	KPNA2, RCH1
	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 - PHOSPHOLIPID SCRAMBLASE 4
	Chains	:	B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 271-283
	Other Details	:	HUMAN PLSCR4-NLS WAS SYNTHESIZED BY SOLID-PHASE METHODS AND PURIFIED BY REVERSE-PHASE HPLC (M.W. 1483.78 DALTONS)
	Synonym	:	PL SCRAMBLASE 4, CA(2+)-DEPENDENT PHOSPHOLIPID SCRAMBLASE 4, CELL GROWTH-INHIBITING GENE 43 PROTEIN, TRA1
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3Q5U)

(no "Site" information available for 3Q5U)

(no "SS Bond" information available for 3Q5U)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:241	-	Pro A:242
2	Gly B:273	-	Ser B:274

(no "SAP(SNP)/Variant" information available for 3Q5U)

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

(no "Exon" information available for 3Q5U)

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:423
 aligned with IMA1_MOUSE | P52293 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:423
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494   
           IMA1_MOUSE    75 NWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFS 497
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.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
                 3q5u A  75 NWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFS 497
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494

Chain B from PDB  Type:PROTEIN  Length:8
 aligned with PLS4_HUMAN | Q9NRQ2 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:8
           PLS4_HUMAN   273 GSIIRKWN 280
               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
                 3q5u B 273 GSIIRKWN 280

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 3Q5U)

(no "CATH Domain" information available for 3Q5U)

(no "Pfam Domain" information available for 3Q5U)

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 (PLS4_HUMAN | Q9NRQ2)

molecular function
	GO:0042609	CD4 receptor binding	Interacting selectively and non-covalently with a CD4, a receptor found on the surface of T cells, monocytes and macrophages.
	GO:0017124	SH3 domain binding	Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0017128	phospholipid scramblase activity	Catalysis of the movement of phospholipids from one membrane bilayer leaflet to the other, by an ATP-independent mechanism.
	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:0071222	cellular response to lipopolysaccharide	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 lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0017121	phospholipid scrambling	The movement of a population of phospholipid molecules from one leaflet of the plasma membrane bilayer to the opposite leaflet, resulting in loss of lipid asymmetry and surface exposure of phosphatidylserine (PS) and phosphatidylethanolamine (PE).
cellular component
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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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	Sites
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	Cis Peptide Bonds
		Asn A:241 - Pro A:242	[ RasMol ]
		Gly B:273 - Ser B:274	[ RasMol ]

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1y2a	STRUCTURE OF MAMMALIAN IMPORTIN BOUND TO THE NON-CLASSICAL PLSCR1-NLS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

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Gene Ontology (24, 26)

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