2J9U - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   2 ANGSTROM X-RAY STRUCTURE OF THE YEAST ESCRT-I VPS28 C-TERMINUS IN COMPLEX WITH THE NZF-N DOMAIN FROM ESCRT-II

Authors :   D. J. Gill, H. L. Teo, J. Sun, O. Perisic, D. B. Veprintsev, S. D. Emr, R. L.

Date :   16 Nov 06 (Deposition) - 23 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Zinc-Finger, Metal-Binding, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Gill, H. L. Teo, J. Sun, O. Perisic, D. B. Veprintsev, S. D. Emr, R. L. Williams
Structural Insight Into The Escrt-I/-Ii Link And Its Role In Mvb Trafficking.
Embo J. V. 26 600 2007
PubMed-ID: 17215868 | Reference-DOI: 10.1038/SJ.EMBOJ.7601501

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POPC
	Expression System Strain	:	C41 (DE3)
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 148-242
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	VPS28

Molecule 2 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 36
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	POPC
	Expression System Strain	:	C41 (DE3)
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 110-176
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	VPS36

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS B:120 , CYS B:123 , CYS B:143 , CYS B:146	BINDING SITE FOR RESIDUE ZN B1162
2	AC2	SOFTWARE	CYS D:120 , CYS D:123 , CYS D:143 , CYS D:146	BINDING SITE FOR RESIDUE ZN D1162

(no "SS Bond" information available for 2J9U)

Asymmetric Unit

No.	Residues
1	Leu B:138	-	Pro B:139
2	Leu D:138	-	Pro D:139

(no "SAP(SNP)/Variant" information available for 2J9U)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VPS28_C	PS51310	VPS28 C-terminal domain profile.	VPS28_YEAST	148-242	2	A:148-241 C:148-241

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VPS28_C	PS51310	VPS28 C-terminal domain profile.	VPS28_YEAST	148-242	1	A:148-241 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VPS28_C	PS51310	VPS28 C-terminal domain profile.	VPS28_YEAST	148-242	1	- C:148-241

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLR417W	1	YLR417W.1	XII:955007-956707	1701	VPS36_YEAST	1-566	566	2	B:115-161 D:115-161	47 47

2.1	YPL065W	1	YPL065W.1	XVI:427924-428652	729	VPS28_YEAST	1-242	242	2	A:148-241 C:148-241	94 94

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:94
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:94
                                   157       167       177       187       197       207       217       227       237    
          VPS28_YEAST   148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
               SCOP domains d2j9ua_ A: automated matches                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE VPS28_C  PDB: A:148-241 UniProt: 148-242                                                       PROSITE
               Transcript 2 Exon 2.1  PDB: A:148-241 UniProt: 1-242 [INCOMPLETE]                                           Transcript 2
                 2j9u A 148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
                                   157       167       177       187       197       207       217       227       237

Chain B from PDB  Type:PROTEIN  Length:47
 aligned with VPS36_YEAST | Q06696 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:47
                                   124       134       144       154       
          VPS36_YEAST   115 VSTWVCPICMVSNETQGEFTKDTLPTPICINCGVPADYELTKSSINC 161
               SCOP domains d2j9ub1 B:115-161                               SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeee.....................hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:115-161 UniProt: 1-566         Transcript 1
                 2j9u B 115 VSTWVCPICMVSNETQGEFTKDTLPTPICINCGVPADYELTKSSINC 161
                                   124       134       144       154

Chain C from PDB  Type:PROTEIN  Length:94
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:94
                                   157       167       177       187       197       207       217       227       237    
          VPS28_YEAST   148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
               SCOP domains d2j9uc_ C: automated matches                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE VPS28_C  PDB: C:148-241 UniProt: 148-242                                                       PROSITE
               Transcript 2 Exon 2.1  PDB: C:148-241 UniProt: 1-242 [INCOMPLETE]                                           Transcript 2
                 2j9u C 148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
                                   157       167       177       187       197       207       217       227       237

Chain D from PDB  Type:PROTEIN  Length:47
 aligned with VPS36_YEAST | Q06696 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:47
                                   124       134       144       154       
          VPS36_YEAST   115 VSTWVCPICMVSNETQGEFTKDTLPTPICINCGVPADYELTKSSINC 161
               SCOP domains d2j9ud_ D: automated matches                    SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeee.....................hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:115-161 UniProt: 1-566         Transcript 1
                 2j9u D 115 VSTWVCPICMVSNETQGEFTKDTLPTPICINCGVPADYELTKSSINC 161
                                   124       134       144       154

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 "CATH Domain" information available for 2J9U)

(no "Pfam Domain" information available for 2J9U)

Asymmetric Unit(hide GO term definitions)

Chain A,C (VPS28_YEAST | Q02767)

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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006612	protein targeting to membrane	The process of directing proteins towards a membrane, usually using signals contained within the protein.
	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:0043328	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	The process of directing proteins towards the vacuole that contributes to protein catabolism via the multivesicular body (MVB) pathway.
	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:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.
cellular component
	GO:0000813	ESCRT I complex	An endosomal sorting complex required for transport. It consists of the class E vacuolar protein sorting (Vps) proteins and interacts with ubiquitinated cargoes.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	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.

Chain B,D (VPS36_YEAST | Q06696)

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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0016236	macroautophagy	The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
	GO:0000433	negative regulation of transcription from RNA polymerase II promoter by glucose	Any process involving glucose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
	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: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.
	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:0043328	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	The process of directing proteins towards the vacuole that contributes to protein catabolism via the multivesicular body (MVB) pathway.
	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:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.
cellular component
	GO:0000814	ESCRT II complex	An endosomal sorting complex required for transport and functions downstream of ESCRT I complex. It consists of the class E vacuolar protein sorting (Vps) proteins and is required for the membrane recruitment of ESCRT III complex and binds to ubiquitinated cargoes.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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.

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		Leu B:138 - Pro B:139	[ RasMol ]
		Leu D:138 - Pro D:139	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	2j9u
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	VPS28_YEAST \| Q02767
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	VPS36_YEAST \| Q06696
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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	VPS28_YEAST \| Q02767
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	VPS36_YEAST \| Q06696
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UniProtKB/Swiss-Prot
	VPS28_YEAST \| Q02767	:	2caz 2f66 2f6m 2g3k 2j9v 2p22
	VPS36_YEAST \| Q06696	:	1u5t 1w7p 2cay

1u5t	STRUCTURE OF THE ESCRT-II ENDOSOMAL TRAFFICKING COMPLEX
1w7p	ESCRT-II
2cay	VPS36 N-TERMINAL PH DOMAIN
2caz	ESCRT-I CORE
2g3k	CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF VPS28
2j9v	2 ANGSTROM X-RAY STRUCTURE OF THE YEAST ESCRT-I VPS28 C-TERMINUS
2j9w	STRUCTURAL INSIGHT INTO THE ESCRT-I-II LINK AND ITS ROLE IN MVB TRAFFICKING

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (2, 4)

Sequences/Alignments

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SCOP Domains (3, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (23, 33)

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