2BZ8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   N-TERMINAL SH3 DOMAIN OF CIN85 BOUND TO CBL-B PEPTIDE

Authors :   N. Cardenes, G. Moncalian, J. Bravo

Date :   12 Aug 05 (Deposition) - 05 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Sh3 Domain, Cin85 Adaptor Protein, Cbl Ubiquitin Ligase, Endocytosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Jozic, N. Cardenes, Y. Lissanu-Deribe, G. Moncalian, D. Hoeller, Y. Groemping, I. Dikic, K. Rittinger, J. Bravo
Cbl Promotes Clustering Of Endocytic Adaptor Proteins
Nat. Struct. Mol. Biol. V. 12 972 2005
PubMed-ID: 16228008 | Reference-DOI: 10.1038/NSMB1000

Molecule 1 - SH3-DOMAIN KINASE BINDING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET29B
	Expression System Strain	:	ROSETTA(DE3)PLYS
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL SH3 DOMAIN RESIDUES 1-58
	Organ	:	BRAIN, KIDNEY, HEART, PLACENTA, LUNG, LIVER, SKELETAL MUSCLE, PANCREAS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CBL-INTERACTING PROTEIN OF 85KDA, HUMAN SRC-FAMILY KINASE BINDING PROTEIN 1, HSB-1, CD2 BINDING PROTEIN 3, CD2BP3, CIN85

Molecule 2 - SIGNAL TRANSDUCTION PROTEIN CBL-B SH3-BINDING PROTEIN CBL-B, RING FINGER PROTEIN 56, CBL-B
	Chains	:	C
	Fragment	:	POLYPROLINE RICH REGION RESIDUES 902-912
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:50 , VAL A:53 , HOH A:2004 , HOH A:2033 , HOH A:2038	BINDING SITE FOR RESIDUE NA A1058
2	AC2	SOFTWARE	ASP B:50 , VAL B:53 , HOH B:2015 , HOH B:2030	BINDING SITE FOR RESIDUE NA B1059

(no "SS Bond" information available for 2BZ8)

(no "Cis Peptide Bond" information available for 2BZ8)

(no "SAP(SNP)/Variant" information available for 2BZ8)

(no "PROSITE Motif" information available for 2BZ8)

Asymmetric/Biological Unit (4, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2d	ENST00000264122	2d	ENSE00001340691	chr3:105587887-105587580	308	CBLB_HUMAN	-	0	0	-	-
1.3	ENST00000264122	3	ENSE00002109512	chr3:105586435-105586254	182	CBLB_HUMAN	1-56	56	0	-	-
1.4	ENST00000264122	4	ENSE00002192869	chr3:105572508-105572258	251	CBLB_HUMAN	57-140	84	0	-	-
1.5	ENST00000264122	5	ENSE00001686511	chr3:105495386-105495240	147	CBLB_HUMAN	140-189	50	0	-	-
1.6	ENST00000264122	6	ENSE00001628201	chr3:105470462-105470306	157	CBLB_HUMAN	189-241	53	0	-	-
1.7	ENST00000264122	7	ENSE00001692048	chr3:105464882-105464761	122	CBLB_HUMAN	242-282	41	0	-	-
1.8	ENST00000264122	8	ENSE00001696958	chr3:105459475-105459338	138	CBLB_HUMAN	282-328	47	0	-	-
1.9	ENST00000264122	9	ENSE00001616258	chr3:105456102-105456015	88	CBLB_HUMAN	328-357	30	0	-	-
1.10	ENST00000264122	10	ENSE00001694160	chr3:105452984-105452853	132	CBLB_HUMAN	358-401	44	0	-	-
1.11	ENST00000264122	11	ENSE00001654827	chr3:105439094-105438891	204	CBLB_HUMAN	402-469	68	0	-	-
1.12	ENST00000264122	12	ENSE00001767402	chr3:105423017-105422832	186	CBLB_HUMAN	470-531	62	0	-	-
1.13a	ENST00000264122	13a	ENSE00001607504	chr3:105421303-105420938	366	CBLB_HUMAN	532-653	122	0	-	-
1.14	ENST00000264122	14	ENSE00000774846	chr3:105412432-105412338	95	CBLB_HUMAN	654-685	32	0	-	-
1.15	ENST00000264122	15	ENSE00000774845	chr3:105404310-105404164	147	CBLB_HUMAN	685-734	50	0	-	-
1.16b	ENST00000264122	16b	ENSE00000774844	chr3:105400662-105400568	95	CBLB_HUMAN	734-766	33	0	-	-
1.16d	ENST00000264122	16d	ENSE00000774843	chr3:105400454-105400323	132	CBLB_HUMAN	766-810	45	0	-	-
1.17	ENST00000264122	17	ENSE00000774842	chr3:105397415-105397275	141	CBLB_HUMAN	810-857	48	0	-	-
1.18b	ENST00000264122	18b	ENSE00000774841	chr3:105389196-105389077	120	CBLB_HUMAN	857-897	41	0	-	-
1.19d	ENST00000264122	19d	ENSE00001755904	chr3:105378073-105374305	3769	CBLB_HUMAN	897-982	86	1	C:902-912	11

2.1a	ENST00000397821	1a	ENSE00002155133	X:19905719-19905425	295	SH3K1_HUMAN	1-2	2	2	A:2-2 B:2-2	1 1
2.2	ENST00000397821	2	ENSE00001789519	X:19854400-19854243	158	SH3K1_HUMAN	2-54	53	2	A:2-54 B:2-54	53 53
2.5a	ENST00000397821	5a	ENSE00001709790	X:19764559-19764436	124	SH3K1_HUMAN	55-96	42	2	A:55-58 B:55-58	4 4
2.8	ENST00000397821	8	ENSE00001200119	X:19725102-19724999	104	SH3K1_HUMAN	96-130	35	0	-	-
2.9a	ENST00000397821	9a	ENSE00001200111	X:19713859-19713730	130	SH3K1_HUMAN	131-174	44	0	-	-
2.12b	ENST00000397821	12b	ENSE00002170582	X:19702146-19701941	206	SH3K1_HUMAN	174-242	69	0	-	-
2.15b	ENST00000397821	15b	ENSE00001752859	X:19663593-19663518	76	SH3K1_HUMAN	243-268	26	0	-	-
2.16	ENST00000397821	16	ENSE00001789134	X:19650076-19649982	95	SH3K1_HUMAN	268-299	32	0	-	-
2.17	ENST00000397821	17	ENSE00001667936	X:19626163-19626056	108	SH3K1_HUMAN	300-335	36	0	-	-
2.19	ENST00000397821	19	ENSE00001798573	X:19613118-19613067	52	SH3K1_HUMAN	336-353	18	0	-	-
2.20b	ENST00000397821	20b	ENSE00001780198	X:19610265-19610185	81	SH3K1_HUMAN	353-380	28	0	-	-
2.21b	ENST00000397821	21b	ENSE00001781910	X:19606920-19606761	160	SH3K1_HUMAN	380-433	54	0	-	-
2.22	ENST00000397821	22	ENSE00001696322	X:19587306-19587221	86	SH3K1_HUMAN	433-462	30	0	-	-
2.23	ENST00000397821	23	ENSE00001670343	X:19568201-19568092	110	SH3K1_HUMAN	462-498	37	0	-	-
2.24	ENST00000397821	24	ENSE00001757635	X:19564168-19564040	129	SH3K1_HUMAN	499-541	43	0	-	-
2.25	ENST00000397821	25	ENSE00001659172	X:19560311-19560043	269	SH3K1_HUMAN	542-631	90	0	-	-
2.26	ENST00000397821	26	ENSE00001632685	X:19555898-19555835	64	SH3K1_HUMAN	631-652	22	0	-	-
2.27e	ENST00000397821	27e	ENSE00001938509	X:19554576-19552093	2484	SH3K1_HUMAN	653-665	13	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:57
 aligned with SH3K1_HUMAN | Q96B97 from UniProtKB/Swiss-Prot  Length:665

    Alignment length:57
                                    11        21        31        41        51       
          SH3K1_HUMAN     2 VEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKK  58
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains 2bz8A00 A:2-58 SH3 Domains                                CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..................eeeeee.....eeeeee..eeeeee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
           Transcript 2 (1) 2----------------------------------------------------2.5a Transcript 2 (1)
           Transcript 2 (2) Exon 2.2  PDB: A:2-54 UniProt: 2-54                  ---- Transcript 2 (2)
                 2bz8 A   2 VEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKK  58
                                    11        21        31        41        51

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with SH3K1_HUMAN | Q96B97 from UniProtKB/Swiss-Prot  Length:665

    Alignment length:57
                                    11        21        31        41        51       
          SH3K1_HUMAN     2 VEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKK  58
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains 2bz8B00 B:2-58 SH3 Domains                                CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..................eeeeee.....eeeee....eeeee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
           Transcript 2 (1) 2----------------------------------------------------2.5a Transcript 2 (1)
           Transcript 2 (2) Exon 2.2  PDB: B:2-54 UniProt: 2-54                  ---- Transcript 2 (2)
                 2bz8 B   2 VEAIVEFDYQAQHDDELTISVGEIITNIRKEDGGWWEGQINGRRGLFPDNFVREIKK  58
                                    11        21        31        41        51

Chain C from PDB  Type:PROTEIN  Length:11
 aligned with CBLB_HUMAN | Q13191 from UniProtKB/Swiss-Prot  Length:982

    Alignment length:11
                                   911 
           CBLB_HUMAN   902 PARPPKPRPRR 912
               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 1 Exon 1.19d  Transcript 1
                 2bz8 C 902 PARPPKPRPRR 912
                                   911

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 2BZ8)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

Human (Homo sapiens) (133)

1a	2bz8A00	A:2-58
1b	2bz8B00	B:2-58

(no "Pfam Domain" information available for 2BZ8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SH3K1_HUMAN | Q96B97)

molecular function
	GO:0017124	SH3 domain binding	Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
	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:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	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.
	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:0042059	negative regulation of epidermal growth factor receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
cellular component
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0030659	cytoplasmic vesicle membrane	The lipid bilayer surrounding a cytoplasmic vesicle.
	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.
	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:0030139	endocytic vesicle	A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

Chain C (CBLB_HUMAN | Q13191)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0001784	phosphotyrosine residue binding	Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006607	NLS-bearing protein import into nucleus	The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0000209	protein polyubiquitination	Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0023051	regulation of signaling	Any process that modulates the frequency, rate or extent of a signaling process.
	GO:0009629	response to gravity	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 gravitational stimulus.
	GO:0009725	response to hormone	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 hormone stimulus.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	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:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 2BZ8)

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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Exons (4, 7)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File