1ZUK - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   YEAST BBC1 SH3 DOMAIN COMPLEXED WITH A PEPTIDE FROM LAS17

Authors :   P. Kursula, I. Kursula, F. Lehmann, P. Zou, Y. H. Song, M. Wilmanns

Date :   31 May 05 (Deposition) - 15 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Sh3 Domain, Pxxp Peptide, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Kursula, I. Kursula, F. Lehmann, P. Zou, Y. H. Song, M. Wilmanns
Structural Genomics Of Yeast Sh3 Domains
To Be Published
PubMed: search

Molecule 1 - MYOSIN TAIL REGION-INTERACTING PROTEIN MTI1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST-17
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SH3 DOMAIN
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	BBC1 PROTEIN

Molecule 2 - PROLINE-RICH PROTEIN LAS17
	Chains	:	C
	Engineered	:	YES
	Fragment	:	PXXP MOTIF
	Other Details	:	SYNTHETIC PEPTIDE
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:18 , ASP A:19 , HOH A:2011 , PRO B:15 , HOH B:2059 , HOH C:15	BINDING SITE FOR RESIDUE CL A 1001
2	AC2	SOFTWARE	GLU A:41 , HOH A:2007 , HOH A:2049 , HOH C:12 , HOH C:17 , HOH C:29 , HOH C:35	BINDING SITE FOR RESIDUE MG A 2001
3	AC3	SOFTWARE	HOH B:2012 , HOH B:2024 , HOH B:2029 , HOH B:2062 , HOH B:2076 , HOH B:2079	BINDING SITE FOR RESIDUE MG B 2002

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

Asymmetric/Biological Unit

No.	Residues
1	Val A:6	-	Pro A:7
2	Val B:6	-	Pro B:7

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	BBC1_YEAST	5-69	2	A:5-67 B:5-67

Asymmetric/Biological Unit (2, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YJL020C	1	YJL020C.1	X:402404-398931	3474	BBC1_YEAST	1-1157	1157	2	A:3-67 B:3-67	65 65

2.1	YOR181W	1	YOR181W.1	XV:675940-677841	1902	LAS17_YEAST	1-633	633	1	C:1-11	11

Asymmetric/Biological 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:65
 aligned with BBC1_YEAST | P47068 from UniProtKB/Swiss-Prot  Length:1157

    Alignment length:65
                                    12        22        32        42        52        62     
           BBC1_YEAST     3 EPEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAVQ  67
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..................eeeeeee....eeeeeee.....eeeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SH3  PDB: A:5-67 UniProt: 5-69                                  PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-67 UniProt: 1-1157 [INCOMPLETE]                Transcript 1
                 1zuk A   3 EPEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAVQ  67
                                    12        22        32        42        52        62

Chain B from PDB  Type:PROTEIN  Length:65
 aligned with BBC1_YEAST | P47068 from UniProtKB/Swiss-Prot  Length:1157

    Alignment length:65
                                    12        22        32        42        52        62     
           BBC1_YEAST     3 EPEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAVQ  67
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
           Pfam domains (1) --------SH3_1-1zukB01 B:11-61                              ------ Pfam domains (1)
           Pfam domains (2) --------SH3_1-1zukB02 B:11-61                              ------ Pfam domains (2)
         Sec.struct. author .....eeeee..................eeeeeee....eeeeeee.....eeeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SH3  PDB: B:5-67 UniProt: 5-69                                  PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-67 UniProt: 1-1157 [INCOMPLETE]                Transcript 1
                 1zuk B   3 EPEVPFKVVAQFPYKSDYEDDLNFEKDQEIIVTSVEDAEWYFGEYQDSNGDVIEGIFPKSFVAVQ  67
                                    12        22        32        42        52        62

Chain C from PDB  Type:PROTEIN  Length:11
 aligned with LAS17_YEAST | Q12446 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:11
                                   359 
          LAS17_YEAST   350 RGPAPPPPPHR 360
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
               Transcript 2 Exon 2.1    Transcript 2
                 1zuk C   1 RGPAPPPPPHR  11
                                    10

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 1ZUK)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SH3 (175)

Family: SH3_1 (141)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (24)

1a	SH3_1-1zukB01	B:11-61
1b	SH3_1-1zukB02	B:11-61

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BBC1_YEAST | P47068)

molecular function
	GO:0017024	myosin I binding	Interacting selectively and non-covalently with a class I myosin; myosin I heavy chains are single-headed, possess tails of various lengths, and do not self-associate into bipolar filaments.
	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:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0007010	cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
cellular component
	GO:0030479	actin cortical patch	An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

Chain C (LAS17_YEAST | Q12446)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	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:0051666	actin cortical patch localization	Any process in which actin cortical patches are transported to, or maintained in, a specific location. An actin cortical patch is a discrete actin-containing structure found just beneath the plasma membrane in fungal cells.
	GO:0007015	actin filament organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
	GO:0030041	actin filament polymerization	Assembly of actin filaments by the addition of actin monomers to a filament.
	GO:0045010	actin nucleation	The initial step in the formation of an actin filament, in which actin monomers combine to form a new filament. Nucleation is slow relative to the subsequent addition of more monomers to extend the filament.
	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:2000601	positive regulation of Arp2/3 complex-mediated actin nucleation	Any process that activates or increases the frequency, rate or extent of Arp2/3 complex-mediated actin nucleation.
	GO:0032233	positive regulation of actin filament bundle assembly	Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles.
cellular component
	GO:0030479	actin cortical patch	An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Val A:6 - Pro A:7	[ RasMol ]
		Val B:6 - Pro B:7	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1zuk
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	BBC1_YEAST \| P47068
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	LAS17_YEAST \| Q12446
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	BBC1_YEAST \| P47068
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	LAS17_YEAST \| Q12446
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	BBC1_YEAST \| P47068	:	1tg0 1wdx 2dyf

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (2, 3)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (15, 17)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File