2PJW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE VPS27/HSE1 COMPLEX IS A GAT DOMAIN-BASED SCAFFOLD FOR UBIQUITIN-DEPENDENT SORTING

Authors :   G. Prag, J. H. Hurley

Date :   16 Apr 07 (Deposition) - 05 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.01

Chains :   Asym. Unit : H,V
Biol. Unit 1: H,V  (1x)
Biol. Unit 2: H,V  (2x)

Keywords :   Gat Domain, Core Complex, Doamin Swap, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Prag, H. Watson, Y. C. Kim, B. M. Beach, R. Ghirlando, G. Hummer, J. S. Bonifacino, J. H. Hurley
The Vps27/Hse1 Complex Is A Gat Domain-Based Scaffold For Ubiquitin-Dependent Sorting.
Dev. Cell V. 12 973 2007
PubMed-ID: 17543868 | Reference-DOI: 10.1016/J.DEVCEL.2007.04.013
(for further references see the PDB file header)

Molecule 1 - UNCHARACTERIZED PROTEIN YHL002W
	Chains	:	H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PST39
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HSE1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 27
	Chains	:	V
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PST39
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	VPS27, GRD11
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric Unit	:	H	V
Biological Unit 1 (1x)	:	H	V
Biological Unit 2 (2x)	:	H	V

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 16)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2PJW)

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

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

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

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

Asymmetric Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YHL002W	1	YHL002W.1	VIII:102607-103965	1359	HSE1_YEAST	1-452	452	1	H:288-375	88

2.1	YNR006W	1	YNR006W.1	XIV:636989-638857	1869	VPS27_YEAST	1-622	622	1	V:348-438	91

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 H from PDB  Type:PROTEIN  Length:88
 aligned with HSE1_YEAST | P38753 from UniProtKB/Swiss-Prot  Length:452

    Alignment length:88
                                   297       307       317       327       337       347       357       367        
           HSE1_YEAST   288 KEAIVFSQKTTIDQLHNSLNAASKTGNSNEVLQDPHIGDMYGSVTPLRPQVTRMLGKYAKEKEDMLSLRQVLANAERSYNQLMDRAAN 375
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.....hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: H:288-375 UniProt: 1-452 [INCOMPLETE]                                     Transcript 1
                 2pjw H 288 KEAIVFSQKTTIDQLHNSLNAASKTGNSNEVLQDPHIGDmYGSVTPLRPQVTRmLGKYAKEKEDmLSLRQVLANAERSYNQLmDRAAN 375
                                   297       307       317       327       337   |   347    |  357       367  |     
                                                                 327-MSE       341-MSE    352-MSE           370-MSE

Chain V from PDB  Type:PROTEIN  Length:91
 aligned with VPS27_YEAST | P40343 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:91
                                   357       367       377       387       397       407       417       427       437 
          VPS27_YEAST   348 VDLSDEEKDSIYMFASLVEKMKSRPLNEILEDSKLQNLAQRVFASKARLNYALNDKAQKYNTLIEMNGKISEIMNIYDRLLEQQLQSINLS 438
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: V:348-438 UniProt: 1-622 [INCOMPLETE]                                        Transcript 2
                 2pjw V 348 VDLSDEEKDSIYmFASLVEKmKSRPLNEILEDSKLQNLAQRVFASKARLNYALNDKAQKYNTLIEmNGKISEImNIYDRLLEQQLQSINLS 438
                                   357  |    367|      377       387       397       407     | 417   |   427       437 
                                      360-MSE 368-MSE                                      413-MSE 421-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 2PJW)

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

(no "Pfam Domain" information available for 2PJW)

Asymmetric Unit(hide GO term definitions)

Chain H (HSE1_YEAST | P38753)

molecular function
	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:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
	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:0045324	late endosome to vacuole transport	The directed movement of substances from late endosomes to the vacuole. In yeast, after transport to the prevacuolar compartment, endocytic content is delivered to the late endosome and on to the vacuole. This pathway is analogous to endosome to lysosome transport.
	GO:0006623	protein targeting to vacuole	The process of directing proteins towards the vacuole, usually using signals contained within the protein.
	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:0033565	ESCRT-0 complex	A protein complex required for the recycling of Golgi proteins, formation of lumenal membranes and sorting of ubiquitinated proteins into those membranes. This complex includes Vps1p and Hse1p in yeast and the Hrs and STAM proteins in mammals.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain V (VPS27_YEAST | P40343)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	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:0043130	ubiquitin binding	Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
	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:0045324	late endosome to vacuole transport	The directed movement of substances from late endosomes to the vacuole. In yeast, after transport to the prevacuolar compartment, endocytic content is delivered to the late endosome and on to the vacuole. This pathway is analogous to endosome to lysosome transport.
	GO:0045053	protein retention in Golgi apparatus	The retention of proteins within the Golgi apparatus. Golgi-localized carbohydrate-modifying enzymes have a short N-terminal domain that faces the cytosol, a single transmembrane alpha helix, and a large C-terminal domain that faces the Golgi lumen and that contains the catalytic site. How the membrane-spanning alpha helix in a Golgi enzyme causes its localization and prevents its movement to the plasma membrane is not known.
	GO:0006623	protein targeting to vacuole	The process of directing proteins towards the vacuole, usually using signals contained within the protein.
cellular component
	GO:0033565	ESCRT-0 complex	A protein complex required for the recycling of Golgi proteins, formation of lumenal membranes and sorting of ubiquitinated proteins into those membranes. This complex includes Vps1p and Hse1p in yeast and the Hrs and STAM proteins in mammals.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	VPS27_YEAST \| P40343	:	1o06 1q0v 1q0w 1vfy 2kdi 3r42 5ucl

1yd8	HUMAN GGA3 GAT DOMAIN

Description

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Ligands, Modified Residues, Ions (1, 8)

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