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Title :   STRUCTURE OF THE HUMAN SELENOPROTEIN S (VCP-INTERACTING MEMBRANE PROTEIN)

Authors :   J. R. Walker, R. Paramanathan, C. Butler-Cole, J. Weigelt, M. Sundstro C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Struct Genomics Consortium (Sgc)

Date :   28 May 07 (Deposition) - 05 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Anti-Parallel Coiled-Coil, Endoplasmic Reticulum, Membrane, Selenium, Selenocysteine, Transmembrane, Structural Genomics, Structural Genomics Consortium, Sgc, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Walker, R. Paramanathan, C. Butler-Cole, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Human Selenoprotein S (Vcp-Interacting Membrane Protein).
To Be Published
PubMed: search

Molecule 1 - SELENOPROTEIN S
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28-LIC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	COILED-COIL DOMAIN, RESIDUES 52-122
	Gene	:	SELS, VIMP, AD-015, SBBI8
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	VCP-INTERACTING MEMBRANE PROTEIN

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:99	BINDING SITE FOR RESIDUE CL A 1
2	AC2	SOFTWARE	ARG A:59 , HOH A:135	BINDING SITE FOR RESIDUE CL A 2
3	AC3	SOFTWARE	ARG A:65 , PRO A:72 , GLU A:80 , ALA A:81 , ALA A:84 , HOH A:128 , HOH A:142 , HOH A:158 , HOH A:162	BINDING SITE FOR RESIDUE GOL A 3

(no "SS Bond" information available for 2Q2F)

(no "Cis Peptide Bond" information available for 2Q2F)

(no "SAP(SNP)/Variant" information available for 2Q2F)

(no "PROSITE Motif" information available for 2Q2F)

Asymmetric Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000398226	1d	ENSE00002186657	chr15:101817655-101817547	109	SELS_HUMAN	1-26	26	0	-	-
1.1j	ENST00000398226	1j	ENSE00000703039	chr15:101816880-101816746	135	SELS_HUMAN	26-71	46	1	A:51-71 (gaps)	45
1.2a	ENST00000398226	2a	ENSE00002199543	chr15:101815566-101815460	107	SELS_HUMAN	71-106	36	1	A:71-106	36
1.2d	ENST00000398226	2d	ENSE00000703045	chr15:101814886-101814797	90	SELS_HUMAN	107-136	30	1	A:107-122	16
1.2f	ENST00000398226	2f	ENSE00000703049	chr15:101814700-101814625	76	SELS_HUMAN	137-162	26	0	-	-
1.3b	ENST00000398226	3b	ENSE00001532206	chr15:101813061-101812969	93	SELS_HUMAN	162-189	28	0	-	-
1.4b	ENST00000398226	4b	ENSE00002072396	chr15:101811850-101811022	829	SELS_HUMAN	-	0	0	-	-

Asymmetric 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:72
 aligned with SELS_HUMAN | Q9BQE4 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:96
                                    36        46        56        66        76        86        96       106       116      
           SELS_HUMAN    27 GSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSM 122
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------Selenoprotein_S-2q2fA01 A:52-122                                        Pfam domains
         Sec.struct. author .------------------------hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1j  PDB: A:51-71 (gaps) UniProt: 26-71-----------------------------------Exon 1.2d        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.2a  PDB: A:71-106            ---------------- Transcript 1 (2)
                 2q2f A  51 G------------------------SARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKmQEELNAQVEKHKEKLKQLEEEKRRQKIEmWDSm 122
                            |        -         -     |  56        66        76        86  |     96       106       116 |   |
                            |                       52                                   89-MSE                      118-MSE
                           51                                                                                            122-MSE

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 2Q2F)

(no "CATH Domain" information available for 2Q2F)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Selenoprotein_S] (1)

Family: Selenoprotein_S (1)

Homo sapiens (Human) (1)

Selenoprotein_S-2q2fA01

A:52-122

Asymmetric Unit(hide GO term definitions)

Chain A (SELS_HUMAN | Q9BQE4)

molecular function
	GO:0051117	ATPase binding	Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:1990381	ubiquitin-specific protease binding	Interacting selectively and non-covalently with a ubiquitin-specific protease.
biological process
	GO:0006983	ER overload response	The series of molecular signals generated by the accumulation of normal or misfolded proteins in the endoplasmic reticulum and leading to activation of transcription by NF-kappaB.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0032869	cellular response to insulin stimulus	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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	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:0034599	cellular response to oxidative stress	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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0030968	endoplasmic reticulum unfolded protein response	The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
	GO:0045184	establishment of protein localization	The directed movement of a protein to a specific location.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0002865	negative regulation of acute inflammatory response to antigenic stimulus	Any process that stops, prevents, or reduces the frequency, rate, or extent of an acute inflammatory response to an antigenic stimulus.
	GO:1902236	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
	GO:0046325	negative regulation of glucose import	Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.
	GO:0045719	negative regulation of glycogen biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
	GO:0050728	negative regulation of inflammatory response	Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
	GO:0032715	negative regulation of interleukin-6 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
	GO:2000110	negative regulation of macrophage apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage apoptotic process.
	GO:0051771	negative regulation of nitric-oxide synthase biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric-oxide synthase enzyme.
	GO:0032720	negative regulation of tumor necrosis factor production	Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
	GO:0006111	regulation of gluconeogenesis	Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0080164	regulation of nitric oxide metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
	GO:0009749	response to glucose	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
	GO:0051775	response to redox state	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.
	GO:0030970	retrograde protein transport, ER to cytosol	The directed movement of unfolded or misfolded proteins from the endoplasmic reticulum to the cytosol through the translocon.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
	GO:0036513	Derlin-1 retrotranslocation complex	A protein complex that functions in the retrotranslocation step of ERAD (ER-associated protein degradation), and includes at its core Derlin-1 oligomers forming a retrotranslocation channel.
	GO:0036502	Derlin-1-VIMP complex	A protein complex containing, in mammals, Derlin-1 and VCP-interacting membrane protein (VIMP). The complex links the p97/VCP-containing ATPase complex with Derlin-1 during translocation of protein substrates from the endoplasmic reticulum to the cytosol for degradation by the cytosolic proteasome.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005881	cytoplasmic microtubule	Any microtubule in the cytoplasm of a cell.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0030176	integral component of endoplasmic reticulum membrane	The component of the endoplasmic reticulum 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: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:0034362	low-density lipoprotein particle	A lipoprotein particle, rich in cholesterol esters and low in triglycerides that is typically composed of APOB100 and APOE and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm. LDL particles are formed from VLDL particles (via IDL) by the loss of triglyceride and gain of cholesterol ester. They transport endogenous cholesterol (and to some extent triglycerides) from peripheral tissues back to the liver.
	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.
	GO:0034361	very-low-density lipoprotein particle	A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver.

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Description

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Ligands, Modified Residues, Ions (3, 6)

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