2JIK - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PDZ DOMAIN OF SYNAPTOJANIN-2 BINDING PROTEIN

Authors :   J. Tickle, C. Phillips, A. C. W. Pike, C. Cooper, E. Salah, J. Elkins, A. P. Turnbull, A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, D. Doyle

Date :   28 Jun 07 (Deposition) - 10 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

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

Keywords :   Transmembrane, Outer Membrane, Mitochondria Distribution, Pdz, Membrane, Scaffold, Mitochondrion, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Tickle, C. Phillips, A. C. W. Pike, C. Cooper, E. Salah, J. Elkins, A. P. Turnbull, A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, D. Doyle
Crystal Structure Of Pdz Domain Of Synaptojanin-2 Binding Protein
To Be Published
PubMed: search

Molecule 1 - SYNAPTOJANIN-2 BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Fragment	:	PDZ DOMAIN, RESIDUES 6-100
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MITOCHONDRIAL OUTER MEMBRANE PROTEIN 25

		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 2JIK)

(no "Site" information available for 2JIK)

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

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051394	V	9	I	SYJ2B_HUMAN	Polymorphism	4356408	A/B	V	9	I

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051394	V	9	I	SYJ2B_HUMAN	Polymorphism	4356408	A	V	9	I

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051394	V	9	I	SYJ2B_HUMAN	Polymorphism	4356408	B	V	9	I

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	SYJ2B_HUMAN	13-100	2	A:13-100 B:13-100

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	SYJ2B_HUMAN	13-100	1	A:13-100 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	SYJ2B_HUMAN	13-100	1	- B:13-100

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000256366	1	ENSE00000807865	chr14:70883807-70883617	191	SYJ2B_HUMAN	1-22	22	2	A:-1-22 B:-1-22	19 19
1.2	ENST00000256366	2	ENSE00000658851	chr14:70855323-70855187	137	SYJ2B_HUMAN	22-67	46	2	A:22-67 B:22-67 (gaps)	46 46
1.3	ENST00000256366	3	ENSE00000658850	chr14:70842488-70842393	96	SYJ2B_HUMAN	68-99	32	2	A:68-99 B:68-99	32 32
1.4	ENST00000256366	4	ENSE00000807864	chr14:70839848-70833217	6632	SYJ2B_HUMAN	100-145	46	2	A:100-104 (gaps) B:100-104 (gaps)	8 8

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:101
 aligned with SYJ2B_HUMAN | P57105 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:104
                                    13        23        33        43        53        63        73        83        93       103    
          SYJ2B_HUMAN     4 RVDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQNGPI 107
               SCOP domains d2jika_ A: automated matches                                                                             SCOP domains
               CATH domains 2jikA00 A:-1-104  [code=2.30.42.10, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeeeeeeee.......eeeee............eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeeeee...---.. Sec.struct. author
                 SAPs(SNPs) -----I-------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PDZ  PDB: A:13-100 UniProt: 13-100                                                      ------- PROSITE
           Transcript 1 (1) Exon 1.1           ---------------------------------------------Exon 1.3  PDB: A:68-99          Exon 1.4 Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.2  PDB: A:22-67 UniProt: 22-67         ---------------------------------------- Transcript 1 (2)
                 2jik A  -1 SMDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLES---SI 104
                             ||     13        23        33        43        53        63        73        83        93        |-  | 
                             0|                                                                                             102 103 
                              6

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with SYJ2B_HUMAN | P57105 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:104
                                    13        23        33        43        53        63        73        83        93       103    
          SYJ2B_HUMAN     4 RVDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQNGPI 107
               SCOP domains d2jikb_ B: automated matches                                                                             SCOP domains
               CATH domains 2jikB00 B:-1-104  [code=2.30.42.   10, no name defined]                                                  CATH domains
           Pfam domains (1) ---------PDZ-2jikB01 B:13-97                                                                  -----   -- Pfam domains (1)
           Pfam domains (2) ---------PDZ-2jikB02 B:13-97                                                                  -----   -- Pfam domains (2)
         Sec.struct. author .hhh.eeeeeeeee.......eeeee......---...eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeeeee...---.. Sec.struct. author
                 SAPs(SNPs) -----I-------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PDZ  PDB: B:13-100 UniProt: 13-100                                                      ------- PROSITE
           Transcript 1 (1) Exon 1.1           ---------------------------------------------Exon 1.3  PDB: B:68-99          Exon 1.4 Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.2  PDB: B:22-67 (gaps) UniProt: 22-67  ---------------------------------------- Transcript 1 (2)
                 2jik B  -1 SMDYLVTEEEINLTRGPSGLGFNIVGGTDQQY---DSGIYVSRIKENGAAALDGRLQEGDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLES---SI 104
                             ||     13        23        33 |   |  43        53        63        73        83        93        |-  | 
                             0|                           35  39                                                            102 103 
                              6

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: automated matches (94)

Protein domain: automated matches (94)

Human (Homo sapiens) [TaxId: 9606] (71)

1a	d2jika_	A:
1b	d2jikb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Pdz3 Domain (191)

Homologous Superfamily: [code=2.30.42.10, no name defined] (191)

Human (Homo sapiens) (120)

1a	2jikB00	B:-1-104
1b	2jikA00	A:-1-104

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

1a	PDZ-2jikB01	B:13-97
1b	PDZ-2jikB02	B:13-97

Asymmetric Unit(hide GO term definitions)

Chain A,B (SYJ2B_HUMAN | P57105)

molecular function
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0070699	type II activin receptor binding	Interacting selectively and non-covalently with a type II activin receptor.
biological process
	GO:0007266	Rho protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
	GO:0048312	intracellular distribution of mitochondria	Any process that establishes the spatial arrangement of mitochondria within the cell.
	GO:0070373	negative regulation of ERK1 and ERK2 cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0032926	negative regulation of activin receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of any activin receptor signaling pathway.
	GO:0016525	negative regulation of angiogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
	GO:0010596	negative regulation of endothelial cell migration	Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0001937	negative regulation of endothelial cell proliferation	Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation.
	GO:1903671	negative regulation of sprouting angiogenesis	Any process that stops, prevents or reduces the frequency, rate or extent of sprouting angiogenesis.
	GO:0032927	positive regulation of activin receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of the activity of any activin receptor signaling pathway.
	GO:2000010	positive regulation of protein localization to cell surface	Any process that activates or increases the frequency, rate or extent of protein localization to the cell surface.
	GO:0002092	positive regulation of receptor internalization	Any process that activates or increases the frequency, rate or extent of receptor internalization.
	GO:0006605	protein targeting	The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
	GO:0008593	regulation of Notch signaling pathway	Any process that modulates the frequency, rate or extent of the Notch signaling pathway.
	GO:0030100	regulation of endocytosis	Any process that modulates the frequency, rate or extent of endocytosis.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0031307	integral component of mitochondrial outer membrane	The component of the mitochondrial outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	SYJ2B_HUMAN \| P57105	:	2eno 2jin

2jin	CRYSTAL STRUCTURE OF PDZ DOMAIN OF SYNAPTOJANIN-2 BINDING PROTEIN

Description

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Ligands, Modified Residues, Ions (0, 0)

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Exons (4, 8)

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