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Title :   CRYSTAL STRUCTURE OF THE YEAST PX-DOMAIN PROTEIN GRD19P (SORTING NEXIN 3) COMPLEXED TO PHOSPHATIDYLINOSYTOL-3-PHOSPAHTE.

Authors :   C. Z. Zhou, I. Li De La Sierra-Gallay, S. Cheruel, B. Collinet, P. Minard, K. Blondeau, G. Henkes, R. Aufrere, N. Leulliot, M. Graille, I. Sorel, P. Savarin, F. De La Torre, A. Poupon, J. Janin, H. Van Tilbeurgh

Date :   10 Feb 03 (Deposition) - 12 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Sorting Protein, Yeast Protein, Crystal Structure, Sorting Nexin, Complex With Phosphatidylinositol Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Z. Zhou, I. Li De La Sierra-Gallay, S. Cheruel, B. Collinet, P. Minard, K. Blondeau, G. Henkes, R. Aufrere, N. Leulliot, M. Graille, I. Sorel, P. Savarin, F. De La Torre, A. Poupon, J. Janin, H. Van Tilbeurgh
Crystal Structure Of The Yeast Phox Homology (Px) Protein Grd19P (Sorting Nexin 3) Complexed To Phosphatidylinositol-3-Phosphate
J. Biol. Chem. V. 278 50371 2003
PubMed-ID: 14514667 | Reference-DOI: 10.1074/JBC.M304392200

Molecule 1 - SORTING NEXIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	PX-DOMAIN
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Other Details	:	CHEMICALLY MODIFIED CYSTEINE. D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATE
	Other Details - Source	:	CLONED GENE
	Strain	:	S288C

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	PIB	2	Ligand/Ion	2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CME	1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	PIB	1	Ligand/Ion	2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CME	1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	PIB	1	Ligand/Ion	2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:81 , TYR A:82 , SER A:83 , GLU A:86 , LYS A:112 , ILE A:113 , ARG A:118 , ARG A:127 , HOH A:2012 , HOH A:2014 , HOH A:2047	BINDING SITE FOR RESIDUE PIB A1163
2	AC2	SOFTWARE	ARG B:81 , TYR B:82 , SER B:83 , GLU B:86 , LYS B:112 , ILE B:113 , ARG B:118 , ARG B:127 , HOH B:2030 , HOH B:2031	BINDING SITE FOR RESIDUE PIB B1164

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

(no "Cis Peptide Bond" information available for 1OCU)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PX	PS50195	PX domain profile.	SNX3_YEAST	38-161	2	A:38-161 B:38-161

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PX	PS50195	PX domain profile.	SNX3_YEAST	38-161	1	A:38-161 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PX	PS50195	PX domain profile.	SNX3_YEAST	38-161	1	- B:38-161

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YOR357C	1	YOR357C.1	XV:1009710-1009222	489	SNX3_YEAST	1-162	162	2	A:28-161 B:31-162	134 132

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:134
 aligned with SNX3_YEAST | Q08826 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:134
                                    37        47        57        67        77        87        97       107       117       127       137       147       157    
           SNX3_YEAST    28 IYAEPENFLEIEVHNPKTHIPNGMDSKGMFTDYEIICRTNLPSFHKRVSKVRRRYSDFEFFRKCLIKEISMLNHPKVMVPHLPGKILLSNRFSNEVIEERRQGLNTWMQSVAGHPLLQSGSKVLVRFIEAEKFV 161
               SCOP domains d1ocua_ A: Sorting nexin grd19                                                                                                         SCOP domains
               CATH domains 1ocuA00 A:28-161 PX Domain                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..........eeeeeeeeee........eeeeeeehhhhhhhhh.hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------PX  PDB: A:38-161 UniProt: 38-161                                                                                            PROSITE
               Transcript 1 Exon 1.1  PDB: A:28-161 UniProt: 1-162 [INCOMPLETE]                                                                                    Transcript 1
                 1ocu A  28 IYAEPENFLEIEVHNPKTHIPNGMDSKGMFTDYEIICRTNLPSFHKRVSKVRRRYSDFEFFRKcLIKEISMLNHPKVMVPHLPGKILLSNRFSNEVIEERRQGLNTWMQSVAGHPLLQSGSKVLVRFIEAEKFV 161
                                    37        47        57        67        77        87   |    97       107       117       127       137       147       157    
                                                                                          91-CME

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with SNX3_YEAST | Q08826 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:132
                                    40        50        60        70        80        90       100       110       120       130       140       150       160  
           SNX3_YEAST    31 EPENFLEIEVHNPKTHIPNGMDSKGMFTDYEIICRTNLPSFHKRVSKVRRRYSDFEFFRKCLIKEISMLNHPKVMVPHLPGKILLSNRFSNEVIEERRQGLNTWMQSVAGHPLLQSGSKVLVRFIEAEKFVG 162
               SCOP domains d1ocub_ B: Sorting nexin grd19                                                                                                       SCOP domains
               CATH domains 1ocuB00 B:31-162 PX Domain                                                                                                           CATH domains
           Pfam domains (1) --PX-1ocuB01 B:33-158                                                                                                           ---- Pfam domains (1)
           Pfam domains (2) --PX-1ocuB02 B:33-158                                                                                                           ---- Pfam domains (2)
         Sec.struct. author .....eeeeeeeeeee..........eeeeeeeeee........eeeeeehhhhhhhhhh.hhhhhhh...............hhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------PX  PDB: B:38-161 UniProt: 38-161                                                                                           - PROSITE
               Transcript 1 Exon 1.1  PDB: B:31-162 UniProt: 1-162 [INCOMPLETE]                                                                                  Transcript 1
                 1ocu B  31 EPENFLEIEVHNPKTHIPNGMDSKGMFTDYEIICRTNLPSFHKRVSKVRRRYSDFEFFRKcLIKEISMLNHPKVMVPHLPGKILLSNRFSNEVIEERRQGLNTWMQSVAGHPLLQSGSKVLVRFIEAEKFVG 162
                                    40        50        60        70        80        90|      100       110       120       130       140       150       160  
                                                                                       91-CME

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: PX domain (23)

Superfamily: PX domain (23)

Family: PX domain (9)

Protein domain: Sorting nexin grd19 (2)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d1ocua_	A:
1b	d1ocub_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: PX Domain (10)

Homologous Superfamily: PX Domain (10)

Baker's yeast (Saccharomyces cerevisiae) (3)

1a	1ocuB00	B:31-162
1b	1ocuA00	A:28-161

Asymmetric Unit

Clans(

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Families(

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Organisms( (-)

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Clan: no clan defined [family: PX] (17)

Family: PX (17)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (4)

1a	PX-1ocuB01	B:33-158
1b	PX-1ocuB02	B:33-158

Asymmetric Unit(hide GO term definitions)

Chain A,B (SNX3_YEAST | Q08826)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0035091	phosphatidylinositol binding	Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	GO:0032266	phosphatidylinositol-3-phosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
biological process
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	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:0034499	late endosome to Golgi transport	The directed movement of substances from late endosomes to the Golgi.
	GO:0008104	protein localization	Any process in which a protein is transported to, or maintained in, a specific location.
	GO:0032258	protein localization by the CVT pathway	A cytoplasm to vacuole targeting pathway that uses machinery common with autophagy. The CVT vesicle is formed when the receptor protein, Atg19, binds to the complexes of the target protein (aminopeptidase or alpha-mannosidase homododecamers), forming the Cvt complex. Atg11 binds to Atg9 and transports the CVT complex to the pre-autophagosome (PAS). The phagophore membrane expands around the CVT complex (excluding bulk cytoplasm) forming the CVT vesicle. This pathway is mostly observed in yeast.
	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.
	GO:0016050	vesicle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	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:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	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:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0000407	pre-autophagosomal structure	Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction.

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	SNX3_YEAST \| Q08826	:	1ocs

1ocs	CRYSTAL STRUCTURE OF THE YEAST PX-DOAMIN PROTEIN GRD19P (SORTING NEXIN3) COMPLEXED TO PHOSPHATIDYLINOSYTOL-3-PHOSPHATE.

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