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Title :   STRUCTURE BASIS FOR ENDOSOMAL TARGETING BY THE BRO1 DOMAIN

Authors :   J. Kim, S. Sitaraman, A. Hierro, B. M. Beach, G. Odorizzi, J. H. Hurley

Date :   07 Apr 05 (Deposition) - 14 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Bro1, Aip1, Bro1 Domain, Snf7, Trafficking, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Kim, S. Sitaraman, A. Hierro, B. M. Beach, G. Odorizzi, J. H. Hurley
Structural Basis For Endosomal Targeting By The Bro1 Domain.
Dev. Cell V. 8 937 2005
PubMed-ID: 15935782 | Reference-DOI: 10.1016/J.DEVCEL.2005.04.001
(for further references see the PDB file header)

Molecule 1 - BRO1 PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGST-PARALLEL2
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	BRO1 DOMAIN
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ZB1)

(no "Site" information available for 1ZB1)

(no "SS Bond" information available for 1ZB1)

(no "Cis Peptide Bond" information available for 1ZB1)

(no "SAP(SNP)/Variant" information available for 1ZB1)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRO1	PS51180	BRO1 domain profile.	BRO1_YEAST	4-400	2	A:4-367 B:4-367

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRO1	PS51180	BRO1 domain profile.	BRO1_YEAST	4-400	1	A:4-367 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BRO1	PS51180	BRO1 domain profile.	BRO1_YEAST	4-400	1	- B:4-367

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YPL084W	1	YPL084W.1	XVI:394035-396569	2535	BRO1_YEAST	1-844	844	2	A:1-367 B:1-367	367 367

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:367
 aligned with BRO1_YEAST | P48582 from UniProtKB/Swiss-Prot  Length:844

    Alignment length:367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       
           BRO1_YEAST     1 MKPYLFDLKLKDTEKLDWKKGLSSYLKKSYGSSQWRTFYDEKATSELDHLRNNANGELAPSSLSEQNLKYYSFLEHLYFRLGSKGSRLKMDFTWYDAEYSSAQKGLKYTQHTLAFEKSCTLFNIAVIFTQIARENINEDYKNSIANLTKAFSCFEYLSENFLNSPSVDLQSENTRFLANICHAEAQELFVLKLLNDQISSKQYTLISKLSRATCNLFQKCHDFMKEIDDDVAIYGEPKWKTTVTCKLHFYKSLSAYYHGLHLEEENRVGEAIAFLDFSMQQLISSLPFKTWLVEFIDFDGFKETLEKKQKELIKDNDFIYHESVPAVVQVDSIKALDAIKSPTWEKILEPYMQDVANKCDSLYRGII 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...........eeee.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..........hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---BRO1  PDB: A:4-367 UniProt: 4-400                                                                                                                                                                                                                                                                                                                                            PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-367 UniProt: 1-844 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                              Transcript 1
                 1zb1 A   1 MKPYLFDLKLKDTEKLDWKKGLSSYLKKSYGSSQWRTFYDEKATSELDHLRNNANGELAPSSLSEQNLKYYSFLEHLYFRLGSKGSRLKMDFTWYDAEYSSAQKGLKYTQHTLAFEKSCTLFNIAVIFTQIARENINEDYKNSIANLTKAFSCFEYLSENFLNSPSVDLQSENTRFLANICHAEAQELFVLKLLNDQISSKQYTLISKLSRATCNLFQKCHDFMKEIDDDVAIYGEPKWKTTVTCKLHFYKSLSAYYHGLHLEEENRVGEAIAFLDFSMQQLISSLPFKTWLVEFIDFDGFKETLEKKQKELIKDNDFIYHESVPAVVQVDSIKALDAIKSPTWEKILEPYMQDVANKYDSLYRGII 367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

Chain B from PDB  Type:PROTEIN  Length:367
 aligned with BRO1_YEAST | P48582 from UniProtKB/Swiss-Prot  Length:844

    Alignment length:367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       
           BRO1_YEAST     1 MKPYLFDLKLKDTEKLDWKKGLSSYLKKSYGSSQWRTFYDEKATSELDHLRNNANGELAPSSLSEQNLKYYSFLEHLYFRLGSKGSRLKMDFTWYDAEYSSAQKGLKYTQHTLAFEKSCTLFNIAVIFTQIARENINEDYKNSIANLTKAFSCFEYLSENFLNSPSVDLQSENTRFLANICHAEAQELFVLKLLNDQISSKQYTLISKLSRATCNLFQKCHDFMKEIDDDVAIYGEPKWKTTVTCKLHFYKSLSAYYHGLHLEEENRVGEAIAFLDFSMQQLISSLPFKTWLVEFIDFDGFKETLEKKQKELIKDNDFIYHESVPAVVQVDSIKALDAIKSPTWEKILEPYMQDVANKCDSLYRGII 367
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---BRO1-1zb1B01 B:4-367                                                                                                                                                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) ---BRO1-1zb1B02 B:4-367                                                                                                                                                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...........eeee.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.........hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---BRO1  PDB: B:4-367 UniProt: 4-400                                                                                                                                                                                                                                                                                                                                            PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-367 UniProt: 1-844 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                              Transcript 1
                 1zb1 B   1 MKPYLFDLKLKDTEKLDWKKGLSSYLKKSYGSSQWRTFYDEKATSELDHLRNNANGELAPSSLSEQNLKYYSFLEHLYFRLGSKGSRLKMDFTWYDAEYSSAQKGLKYTQHTLAFEKSCTLFNIAVIFTQIARENINEDYKNSIANLTKAFSCFEYLSENFLNSPSVDLQSENTRFLANICHAEAQELFVLKLLNDQISSKQYTLISKLSRATCNLFQKCHDFMKEIDDDVAIYGEPKWKTTVTCKLHFYKSLSAYYHGLHLEEENRVGEAIAFLDFSMQQLISSLPFKTWLVEFIDFDGFKETLEKKQKELIKDNDFIYHESVPAVVQVDSIKALDAIKSPTWEKILEPYMQDVANKYDSLYRGII 367
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360

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 1ZB1)

(no "CATH Domain" information available for 1ZB1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: BRO1] (11)

Family: BRO1 (11)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (1)

1a	BRO1-1zb1B01	B:4-367
1b	BRO1-1zb1B02	B:4-367

Asymmetric Unit(hide GO term definitions)

Chain A,B (BRO1_YEAST | P48582)

molecular function
	GO:0035800	deubiquitinase activator activity	Increases the activity of deubiquitinase, an enzyme that catalyzes the hydrolysis of various forms of polymeric ubiquitin sequences.
	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).
biological process
	GO:0070676	intralumenal vesicle formation	The invagination of the endosome membrane and resulting formation of a vesicle within the lumen of the endosome.
	GO:2000158	positive regulation of ubiquitin-specific protease activity	Any process that activates or increases the frequency, rate or extent of ubiquitin-specific protease (deubiquitinase) activity.
	GO:0016579	protein deubiquitination	The removal of one or more ubiquitin groups from a protein.
	GO:0036010	protein localization to endosome	A process in which a protein is transported to, or maintained in, a location within an endosome.
	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:0007584	response to nutrient	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 nutrient stimulus.
	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:0006511	ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
	GO:0007034	vacuolar transport	The directed movement of substances into, out of or within a vacuole.
cellular component
	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.

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