4B2Z - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF OSH6 IN COMPLEX WITH PHOSPHATIDYLSERINE

Authors :   K. Maeda, K. Anand, A. Chiapparino, A. Kumar, M. Poletto, M. Kaksonen, A

Date :   19 Jul 12 (Deposition) - 26 Jun 13 (Release) - 18 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Transport Protein, Lipid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Maeda, K. Anand, A. Chiapparino, A. Kumar, M. Poletto, M. Kaksonen, A. C. Gavin
Interactome Map Uncovers Phosphatidylserine Transport By Oxysterol-Binding Proteins
Nature V. 501 257 2013
PubMed-ID: 23934110 | Reference-DOI: 10.1038/NATURE12430

Molecule 1 - OXYSTEROL-BINDING PROTEIN HOMOLOG 6
	Chains	:	A, B
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	OSH6 PROTEIN
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	DTU	1	Ligand/Ion	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3	P5S	2	Ligand/Ion	O-[(R)-{[(2R)-2,3-BIS(OCTADECANOYLOXY)PROPYL]OXY}(HYDROXY)PHOSPHORYL]-L-SERINE
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	DTT	-1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	DTU	1	Ligand/Ion	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3	P5S	1	Ligand/Ion	O-[(R)-{[(2R)-2,3-BIS(OCTADECANOYLOXY)PROPYL]OXY}(HYDROXY)PHOSPHORYL]-L-SERINE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
2	DTU	-1	Ligand/Ion	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3	P5S	1	Ligand/Ion	O-[(R)-{[(2R)-2,3-BIS(OCTADECANOYLOXY)PROPYL]OXY}(HYDROXY)PHOSPHORYL]-L-SERINE
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:132 , GLY A:133 , PHE A:372 , LYS A:375 , HOH A:2059 , HOH A:2145 , HOH A:2167	BINDING SITE FOR RESIDUE SO4 A1435
2	AC2	SOFTWARE	MET B:79 , PRO B:130 , GLN B:154 , PRO B:160 , GLU B:161 , CYS B:162 , VAL B:179 , PRO B:181 , HOH B:2061	BINDING SITE FOR RESIDUE SO4 B1435
3	AC3	SOFTWARE	LEU A:64 , ILE A:67 , LEU A:69 , ILE A:73 , MET A:79 , ARG A:82 , GLN A:86 , TRP A:112 , LYS A:125 , LYS A:126 , PRO A:127 , ASN A:129 , PRO A:160 , SER A:183 , SER A:190 , ALA A:191 , ALA A:192 , MET A:194 , THR A:198 , VAL A:222 , MET A:232 , ILE A:234 , HOH A:2049 , HOH A:2054 , HOH A:2055 , HOH A:2087	BINDING SITE FOR RESIDUE P5S A1436
4	AC4	SOFTWARE	LEU B:64 , ILE B:67 , THR B:68 , LEU B:69 , MET B:79 , GLN B:86 , TRP B:112 , TYR B:113 , VAL B:124 , LYS B:126 , PRO B:127 , ASN B:129 , PRO B:160 , TYR B:164 , SER B:183 , SER B:190 , ALA B:191 , ALA B:192 , THR B:198 , VAL B:222 , MET B:232 , HOH B:2055 , HOH B:2061 , HOH B:2062 , HOH B:2063 , HOH B:2096	BINDING SITE FOR RESIDUE P5S B1436
5	AC5	SOFTWARE	LEU A:408 , GLN A:409 , PRO A:412 , GLN A:417 , GLN A:418 , PHE A:419 , THR A:420 , LYS A:422 , PHE A:423 , HOH A:2158	BINDING SITE FOR RESIDUE DTU A1437
6	AC6	SOFTWARE	LYS A:243 , SER A:244 , PRO A:245 , TYR A:273 , GLY B:61 , ARG B:184 , LEU B:186 , MET B:193	BINDING SITE FOR RESIDUE DTT B1437

(no "SS Bond" information available for 4B2Z)

Asymmetric Unit

No.	Residues
1	His A:158	-	Pro A:159
2	His B:158	-	Pro B:159

(no "SAP(SNP)/Variant" information available for 4B2Z)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OSBP	PS01013	Oxysterol-binding protein family signature.	OSH6_YEAST	153-164	2	A:153-164 B:153-164

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OSBP	PS01013	Oxysterol-binding protein family signature.	OSH6_YEAST	153-164	1	A:153-164 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OSBP	PS01013	Oxysterol-binding protein family signature.	OSH6_YEAST	153-164	1	- B:153-164

(no "Exon" information available for 4B2Z)

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:399
 aligned with OSH6_YEAST | Q02201 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:399
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425         
           OSH6_YEAST    36 DTDDIDEDDESGHNIILNIISQLRPGCDLTRITLPTFILEKKSMLERVTNQLQFPEFLLQAHSEKDPLKRFLYVMKWYLAGWHIAPKAVKKPLNPVLGEYFTAYWDLPNKQQAYYISEQTSHHPPECAYFYMIPESSIRVDGVVIPKSRFLGNSSAAMMDGSTVLQFLDIKDGNGKPEKYVLTQPNVYVRGILFGKMRIELGDHMIIKSPNFQADIEFKTKGYVFGTYDAIEGTVKDYDGNAYYEISGKWNDVMYLKDLKQPRSSPKVFLDTHKESPLRPKVRPLSEQGEYESRKLWKKVTDALAVRNHPVATEEKFQIEDHQRQLAKKRIEDGVEFHPKLFRRSKPGEDLDYCIYKNIPVDEDPEKQIRSILQIAPILPGQQFTDKFFIPAFEKIKSQ 434
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...hhhhhhhhhhhhh.............hhh.eeeeehhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhh.........eee......eeeeeee.....eeeeeeeeee....eeeeeeeehhh.eeeeeee.eeeee...eeeeee..eeeeeeeeee.....eeeeeee...eeee.......eeee..eeeee....eeeeee............eeeeee.....eeeeeee....eeeeee........eeeee............hhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........eee........eee........hhhhhhhhhhhhh........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------OSBP        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b2z A  36 DTDDIDEDDESGHNIILNIISQLRPGCDLTRITLPTFILEKKSMLERVTNQLQFPEFLLQAHSEKDPLKRFLYVMKWYLAGWHIAPKAVKKPLNPVLGEYFTAYWDLPNKQQAYYISEQTSHHPPECAYFYMIPESSIRVDGVVIPKSRFLGNSSAAMMDGSTVLQFLDIKDGNGKPEKYVLTQPNVYVRGILFGKMRIELGDHMIIKSPNFQADIEFKTKGYVFGTYDAIEGTVKDYDGNAYYEISGKWNDVMYLKDLKQPRSSPKVFLDTHKESPLRPKVRPLSEQGEYESRKLWKKVTDALAVRNHPVATEEKFQIEDHQRQLAKKRIEDGVEFHPKLFRRSKPGEDLDYCIYKNIPVDEDPEKQIRSILQIAPILPGQQFTDKFFIPAFEKIKSQ 434
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425

Chain B from PDB  Type:PROTEIN  Length:400
 aligned with OSH6_YEAST | Q02201 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:400
                                    44        54        64        74        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
           OSH6_YEAST    35 IDTDDIDEDDESGHNIILNIISQLRPGCDLTRITLPTFILEKKSMLERVTNQLQFPEFLLQAHSEKDPLKRFLYVMKWYLAGWHIAPKAVKKPLNPVLGEYFTAYWDLPNKQQAYYISEQTSHHPPECAYFYMIPESSIRVDGVVIPKSRFLGNSSAAMMDGSTVLQFLDIKDGNGKPEKYVLTQPNVYVRGILFGKMRIELGDHMIIKSPNFQADIEFKTKGYVFGTYDAIEGTVKDYDGNAYYEISGKWNDVMYLKDLKQPRSSPKVFLDTHKESPLRPKVRPLSEQGEYESRKLWKKVTDALAVRNHPVATEEKFQIEDHQRQLAKKRIEDGVEFHPKLFRRSKPGEDLDYCIYKNIPVDEDPEKQIRSILQIAPILPGQQFTDKFFIPAFEKIKSQ 434
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...hhhhhhhhhhhhh.............hhh.eeeeehhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhh.........eee......eeeeeee.....eeeeeeeeee....eeeeeeeehhh.eeeeeee.eeeee...eeeeee..eeeeeeeeee.....eeeeeee...eeee.......eeee..eeeee....eeeeee............eeeeee.....eeeeeee....eeeeee........eeeee............hhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........eee........eee........hhhhhhhhhhh................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------OSBP        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b2z B  35 IDTDDIDEDDESGHNIILNIISQLRPGCDLTRITLPTFILEKKSMLERVTNQLQFPEFLLQAHSEKDPLKRFLYVMKWYLAGWHIAPKAVKKPLNPVLGEYFTAYWDLPNKQQAYYISEQTSHHPPECAYFYMIPESSIRVDGVVIPKSRFLGNSSAAMMDGSTVLQFLDIKDGNGKPEKYVLTQPNVYVRGILFGKMRIELGDHMIIKSPNFQADIEFKTKGYVFGTYDAIEGTVKDYDGNAYYEISGKWNDVMYLKDLKQPRSSPKVFLDTHKESPLRPKVRPLSEQGEYESRKLWKKVTDALAVRNHPVATEEKFQIEDHQRQLAKKRIEDGVEFHPKLFRRSKPGEDLDYCIYKNIPVDEDPEKQIRSILQIAPILPGQQFTDKFFIPAFEKIKSQ 434
                                    44        54        64        74        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

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 4B2Z)

(no "CATH Domain" information available for 4B2Z)

(no "Pfam Domain" information available for 4B2Z)

Asymmetric Unit(hide GO term definitions)

Chain A,B (OSH6_YEAST | Q02201)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0008142	oxysterol binding	Interacting selectively and non-covalently with oxysterol, an oxidized form of cholesterol.
	GO:0070300	phosphatidic acid binding	Interacting selectively and non-covalently with phosphatidic acid, any of a class of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
	GO:0043325	phosphatidylinositol-3,4-bisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
	GO:0080025	phosphatidylinositol-3,5-bisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions.
	GO:0070273	phosphatidylinositol-4-phosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
	GO:0010314	phosphatidylinositol-5-phosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-5-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 5' position.
	GO:0001786	phosphatidylserine binding	Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine.
	GO:0005548	phospholipid transporter activity	Enables the directed movement of phospholipids into, out of or within a cell, or between cells. Phospholipids are a class of lipids containing phosphoric acid as a mono- or diester.
biological process
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0006887	exocytosis	A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
	GO:0006869	lipid transport	The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0030011	maintenance of cell polarity	The maintenance of established anisotropic intracellular organization or cell growth patterns.
	GO:0015914	phospholipid transport	The directed movement of phospholipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Phospholipids are any lipids containing phosphoric acid as a mono- or diester.
	GO:0034727	piecemeal microautophagy of nucleus	Degradation of a cell nucleus by lysosomal microautophagy.
	GO:0055092	sterol homeostasis	Any process involved in the maintenance of an internal steady state of sterol within an organism or cell.
	GO:0016125	sterol metabolic process	The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
	GO:0015918	sterol transport	The directed movement of sterols into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
	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:0032541	cortical endoplasmic reticulum	A cortical network of highly dynamic tubules that are juxtaposed to the plasma membrane and undergo ring closure and tubule-branching movements.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	Cis Peptide Bonds
		His A:158 - Pro A:159	[ RasMol ]
		His B:158 - Pro B:159	[ RasMol ]

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	4b2z
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(no "Related Entries Specified in the PDB File" available for 4B2Z)

Description

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Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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