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Description

Title :   CRYSTAL STRUCTURE OF THE RAT ENDOPHILIN-A1 SH3 DOMAIN

Authors :   J. F. Trempe, G. Kozlov, E. M. Camacho, K. Gehring

Date :   20 Aug 09 (Deposition) - 10 Nov 09 (Release) - 26 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Sh3, Endophilin, Coiled Coil, Cytoplasm, Endocytosis, Lipid- Binding, Membrane, Phosphoprotein, Sh3 Domain, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Trempe, C. X. Chen, K. Grenier, E. M. Camacho, G. Kozlov, P. S. Mcpherson, K. Gehring, E. A. Fon
Sh3 Domains From A Subset Of Bar Proteins Define A Ubl-Binding Domain And Implicate Parkin In Synaptic Ubiquitination.
Mol. Cell V. 36 1034 2009
PubMed-ID: 20064468 | Reference-DOI: 10.1016/J.MOLCEL.2009.11.021
(for further references see the PDB file header)

Compounds

Molecule 1 - ENDOPHILIN-A1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2TK
	Expression System Strain	:	K12 BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SH3D2A, SH3GL2, SH3P4
	Organism Common	:	BROWN RAT,RAT,RATS
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	ENDOPHILIN-1, SH3 DOMAIN-CONTAINING GRB2-LIKE PROTEIN 2, SH3 DOMAIN PROTEIN 2A, SH3P4

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:352 , HOH B:168 , GLU B:302 , LYS B:312 , GLU B:345 , ILE B:346	BINDING SITE FOR RESIDUE CL A 1
2	AC2	SOFTWARE	GLU A:302 , LYS A:312 , GLU A:345 , ILE A:346 , HIS B:352	BINDING SITE FOR RESIDUE CL B 2

SS Bonds (0, 0)

(no "SS Bond" information available for 3IQL)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 3IQL)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 3IQL)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	SH3G2_RAT	290-349	2	A:291-349 B:291-349

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	SH3G2_RAT	290-349	1	A:291-349 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	SH3G2_RAT	290-349	1	- B:291-349

Exons (1, 2)

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENSRNOT00000008999	2a	ENSRNOE00000436067	chr5:104268400-104268471	72	SH3G2_RAT	1-24	24	0	-	-
1.3	ENSRNOT00000008999	3	ENSRNOE00000457989	chr5:104276496-104276568	73	SH3G2_RAT	25-49	25	0	-	-
1.4	ENSRNOT00000008999	4	ENSRNOE00000062036	chr5:104295141-104295284	144	SH3G2_RAT	49-97	49	0	-	-
1.5a	ENSRNOT00000008999	5a	ENSRNOE00000062149	chr5:104296193-104296326	134	SH3G2_RAT	97-141	45	0	-	-
1.6	ENSRNOT00000008999	6	ENSRNOE00000062311	chr5:104298663-104298821	159	SH3G2_RAT	142-194	53	0	-	-
1.7	ENSRNOT00000008999	7	ENSRNOE00000062475	chr5:104300776-104300879	104	SH3G2_RAT	195-229	35	0	-	-
1.8	ENSRNOT00000008999	8	ENSRNOE00000062624	chr5:104305039-104305169	131	SH3G2_RAT	229-273	45	0	-	-
1.9	ENSRNOT00000008999	9	ENSRNOE00000062798	chr5:104307549-104308099	551	SH3G2_RAT	273-338	66	2	A:287-338 B:286-338	52 53

Sequences/Alignments

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:66
 aligned with SH3G2_RAT | O35179 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:66
                                   296       306       316       326       336       346      
            SH3G2_RAT   287 GVQMDQPCCRALYDFEPENEGELGFKEGDIITLTNQIDENWYEGMLHGQSGFFPINYVEILVALPH 352
               SCOP domains d3iqla_ A: automated matches                                       SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeee..................eeeeeee....eeeeee..eeeeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---SH3  PDB: A:291-349 UniProt: 290-349                        --- PROSITE
               Transcript 1 Exon 1.9  PDB: A:287-338 UniProt: 273-338           -------------- Transcript 1
                 3iql A 287 SVGSDQPCCRALYDFEPENEGELGFKEGDIITLTNQIDENWYEGMLHGQSGFFPINYVEILVALPH 352
                                   296       306       316       326       336       346

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with SH3G2_RAT | O35179 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:67
                                   295       305       315       325       335       345       
            SH3G2_RAT   286 AGVQMDQPCCRALYDFEPENEGELGFKEGDIITLTNQIDENWYEGMLHGQSGFFPINYVEILVALPH 352
               SCOP domains d3iqlb_ B: automated matches                                        SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..................eeeeeee....eeeeee..eeeeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SH3  PDB: B:291-349 UniProt: 290-349                        --- PROSITE
               Transcript 1 Exon 1.9  PDB: B:286-338 UniProt: 273-338            -------------- Transcript 1
                 3iql B 286 ASVGSDQPCCRALYDFEPENEGELGFKEGDIITLTNQIDENWYEGMLHGQSGFFPINYVEILVALPH 352
                                   295       305       315       325       335       345

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: SH3-domain (369)

Family: automated matches (114)

Protein domain: automated matches (114)

Norway rat (Rattus norvegicus) [TaxId: 10116] (3)

1a	d3iqla_	A:
1b	d3iqlb_	B:

CATH Domains (0, 0)

(no "CATH Domain" information available for 3IQL)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 3IQL)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SH3G2_RAT | O35179)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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: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:0002090	regulation of receptor internalization	Any process that modulates the frequency, rate or extent of receptor internalization.
	GO:0048488	synaptic vesicle endocytosis	Clathrin-mediated endocytosis of presynaptic membrane that recycles synaptic vesicle membrane and its components following synaptic vesicle exocytosis. This process starts with coating of the membrane with adaptor proteins and clathrin prior to invagination and ends when uncoating has finished.
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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

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Related Entries

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UniProtKB/Swiss-Prot
	SH3G2_RAT \| O35179	:	2c08 2knb

Related Entries Specified in the PDB File

2knb	SOLUTION NMR STRUCTURE OF THE COMPLEX FORMED BY THE ENDOPHILIN-A1 SH3 DOMAIN AND THE PARKIN UBL DOMAIN