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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE FIRST PDZ DOMAIN OF HUMAN SCRIB1

Authors :   V. Hozjan, E. S. Pilka, A. K. Roos, W. W Yue, C. Phillips, J. Bray, C. Cooper, E. Salah, J. M. Elkins, J. R. C. Muniz, C. H. Arrowsmith, J. Weigelt, A. M. Edwards, F. Von Delft, C. Bountra, D. A. Doyle, U. Oppermann

Date :   25 Nov 08 (Deposition) - 09 Dec 08 (Release) - 09 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

Keywords :   Structural Protein, Phosphoprotein, Ubl Conjugation, Leucine-Rich Repeat, Alternative Splicing, Cytoplasm, Circletail, Coiled Coil, Polymorphism, Lap4, Crib1, Scrb1, Vartul, Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Hozjan, E. S. Pilka, A. K. Roos, W. W Yue, C. Phillips, J. Bray, C. Cooper, E. Salah, J. M. Elkins, J. R. C. Muniz, C. H. Arrowsmith, J. Weigelt, A. M. Edwards, F. Von Delft, C. Bountra, D. A. Doyle, U. Oppermann
Crystal Structure Of The First Pdz Domain Of Human Scrib1
To Be Published
PubMed: search

Molecule 1 - PROTEIN LAP4
	Chains	:	A
	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	:	RESIDUES 725-815
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PDZ DOMAIN OF SCRIB1 VARIANT N1, PROTEIN SCRIBBLE HOMOLOG, HSCRIB

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:743 , GLY A:744 , THR A:749 , HIS A:793 , ARG A:815 , HOH A:2082	BINDING SITE FOR RESIDUE EDO A1820
2	AC2	SOFTWARE	TYR A:751 , GLY A:777 , HIS A:793 , HIS A:794 , HOH A:2027 , HOH A:2085 , HOH A:2091 , HOH A:2092 , HOH A:2093	BINDING SITE FOR RESIDUE EDO A1821
3	AC3	SOFTWARE	ILE A:758 , LEU A:780 , GLN A:789 , HOH A:2055 , HOH A:2094	BINDING SITE FOR RESIDUE EDO A1822

(no "SS Bond" information available for 2W4F)

(no "Cis Peptide Bond" information available for 2W4F)

(no "SAP(SNP)/Variant" information available for 2W4F)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	SCRIB_HUMAN	728-815 862-950 1004-1093 1100-1188	1	A:728-815 - - -

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000320476	1	ENSE00001421242	chr8:144897549-144897384	166	SCRIB_HUMAN	1-53	53	0	-	-
1.3	ENST00000320476	3	ENSE00001710051	chr8:144896288-144896171	118	SCRIB_HUMAN	54-93	40	0	-	-
1.4	ENST00000320476	4	ENSE00001280634	chr8:144896066-144895988	79	SCRIB_HUMAN	93-119	27	0	-	-
1.5	ENST00000320476	5	ENSE00001280624	chr8:144895896-144895807	90	SCRIB_HUMAN	119-149	31	0	-	-
1.6	ENST00000320476	6	ENSE00001280614	chr8:144895696-144895640	57	SCRIB_HUMAN	149-168	20	0	-	-
1.7	ENST00000320476	7	ENSE00001280605	chr8:144895544-144895481	64	SCRIB_HUMAN	168-189	22	0	-	-
1.8	ENST00000320476	8	ENSE00001280596	chr8:144895274-144895200	75	SCRIB_HUMAN	190-214	25	0	-	-
1.9	ENST00000320476	9	ENSE00001280589	chr8:144895131-144894987	145	SCRIB_HUMAN	215-263	49	0	-	-
1.10	ENST00000320476	10	ENSE00001280580	chr8:144894554-144894436	119	SCRIB_HUMAN	263-302	40	0	-	-
1.11	ENST00000320476	11	ENSE00001280573	chr8:144893515-144893316	200	SCRIB_HUMAN	303-369	67	0	-	-
1.12	ENST00000320476	12	ENSE00001280566	chr8:144893242-144893076	167	SCRIB_HUMAN	369-425	57	0	-	-
1.13	ENST00000320476	13	ENSE00001280559	chr8:144892986-144892856	131	SCRIB_HUMAN	425-468	44	0	-	-
1.14	ENST00000320476	14	ENSE00001280549	chr8:144892774-144892649	126	SCRIB_HUMAN	469-510	42	0	-	-
1.15	ENST00000320476	15	ENSE00001280543	chr8:144891888-144891721	168	SCRIB_HUMAN	511-566	56	0	-	-
1.16a	ENST00000320476	16a	ENSE00001280537	chr8:144891195-144890779	417	SCRIB_HUMAN	567-705	139	0	-	-
1.17	ENST00000320476	17	ENSE00001280531	chr8:144889784-144889722	63	SCRIB_HUMAN	706-726	21	1	A:725-726	2
1.18	ENST00000320476	18	ENSE00001280522	chr8:144889183-144889094	90	SCRIB_HUMAN	727-756	30	1	A:727-756	30
1.19	ENST00000320476	19	ENSE00001280512	chr8:144888654-144888577	78	SCRIB_HUMAN	757-782	26	1	A:757-782	26
1.20b	ENST00000320476	20b	ENSE00001280505	chr8:144887605-144887282	324	SCRIB_HUMAN	783-890	108	1	A:783-819 (gaps)	41
1.21	ENST00000320476	21	ENSE00001280498	chr8:144887184-144887104	81	SCRIB_HUMAN	891-917	27	0	-	-
1.22	ENST00000320476	22	ENSE00001280489	chr8:144886995-144886738	258	SCRIB_HUMAN	918-1003	86	0	-	-
1.23a	ENST00000320476	23a	ENSE00001280482	chr8:144886326-144886216	111	SCRIB_HUMAN	1004-1040	37	0	-	-
1.24	ENST00000320476	24	ENSE00001280475	chr8:144886110-144885817	294	SCRIB_HUMAN	1041-1138	98	0	-	-
1.25	ENST00000320476	25	ENSE00001280467	chr8:144885741-144885553	189	SCRIB_HUMAN	1139-1201	63	0	-	-
1.26	ENST00000320476	26	ENSE00001280460	chr8:144877700-144877590	111	SCRIB_HUMAN	1202-1238	37	0	-	-
1.27	ENST00000320476	27	ENSE00001280713	chr8:144877503-144877447	57	SCRIB_HUMAN	1239-1257	19	0	-	-
1.28	ENST00000320476	28	ENSE00001280704	chr8:144877282-144877208	75	SCRIB_HUMAN	1258-1282	25	0	-	-
1.29	ENST00000320476	29	ENSE00001280697	chr8:144876132-144876070	63	SCRIB_HUMAN	1283-1303	21	0	-	-
1.30b	ENST00000320476	30b	ENSE00001280801	chr8:144875253-144875146	108	SCRIB_HUMAN	1304-1339	36	0	-	-
1.31a	ENST00000320476	31a	ENSE00001280748	chr8:144875037-144874878	160	SCRIB_HUMAN	1340-1393	54	0	-	-
1.31c	ENST00000320476	31c	ENSE00001280742	chr8:144874805-144874655	151	SCRIB_HUMAN	1393-1443	51	0	-	-
1.32a	ENST00000320476	32a	ENSE00001280685	chr8:144874575-144874390	186	SCRIB_HUMAN	1443-1505	63	0	-	-
1.33	ENST00000320476	33	ENSE00001280794	chr8:144874303-144874161	143	SCRIB_HUMAN	1505-1553	49	0	-	-
1.34	ENST00000320476	34	ENSE00001280669	chr8:144874083-144874046	38	SCRIB_HUMAN	1553-1565	13	0	-	-
1.36b	ENST00000320476	36b	ENSE00001346693	chr8:144873610-144873559	52	SCRIB_HUMAN	1566-1583	18	0	-	-
1.37c	ENST00000320476	37c	ENSE00001280723	chr8:144873478-144873090	389	SCRIB_HUMAN	1583-1630	48	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
	(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:95
 aligned with SCRIB_HUMAN | Q14160 from UniProtKB/Swiss-Prot  Length:1630

    Alignment length:99
                                   734       744       754       764       774       784       794       804       814         
          SCRIB_HUMAN   725 EELTLTILRQTGGLGISIAGGKGSTPYKGDDEGIFISRVSEEGPAARAGVRVGDKLLEVNGVALQGAEHHEAVEALRGAGTAVQMRVWRERMVEPENAV 823
               SCOP domains d2w4fa_ A: automated matches                                                                        SCOP domains
               CATH domains 2w4fA00 A:725-819  [code=2.30.42.10, no name defined]                                               CATH domains
               Pfam domains ---PDZ-2w4fA01 A:728-812                                                                ----------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeee.............eeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhhh...eeeeeee...----.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: A:728-815 UniProt: 728-815                                                    -------- PROSITE
               Transcript 1 1.Exon 1.18  PDB: A:727-756     Exon 1.19  PDB: A:757-782 Exon 1.20b  PDB: A:783-819 (gaps)         Transcript 1
                 2w4f A 725 EELTLTILRQTGGLGISIAGGKGSTPYKGDDEGIFISRVSEEGPAARAGVRVGDKLLEVNGVALQGAEHHEAVEALRGAGTAVQMRVWRER----ETSV 819
                                   734       744       754       764       774       784       794       804       814|    |   
                                                                                                                    815  816

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: PDZ domain (180)

Protein domain: automated matches (53)

Human (Homo sapiens) [TaxId: 9606] (34)

d2w4fa_

Asymmetric/Biological 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)

2w4fA00

A:725-819

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

PDZ-2w4fA01

A:728-812

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SCRIB_HUMAN | Q14160)

molecular function
	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:0090630	activation of GTPase activity	Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
	GO:0060561	apoptotic process involved in morphogenesis	Any apoptotic process that contributes to the shaping of an anatomical structure.
	GO:0043615	astrocyte cell migration	The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord.
	GO:0008105	asymmetric protein localization	Any process in which a protein is transported to, or maintained in, a specific location such that it is distributed asymmetrically.
	GO:0002093	auditory receptor cell morphogenesis	Any process that alters the size or shape of an auditory receptor cell.
	GO:0060088	auditory receptor cell stereocilium organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of auditory hair cells.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	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:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0021747	cochlear nucleus development	The process whose specific outcome is the progression of the cochlear nucleus over time, from its formation to the mature structure.
	GO:0035089	establishment of apical/basal cell polarity	The specification and formation of the polarity of a cell along its apical/basal axis.
	GO:0060603	mammary gland duct morphogenesis	The process in which anatomical structures of the mammary ducts are generated and organized. Mammary ducts are epithelial tubes that transport milk.
	GO:0016331	morphogenesis of embryonic epithelium	The process in which the anatomical structures of embryonic epithelia are generated and organized.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0045930	negative regulation of mitotic cell cycle	Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
	GO:0001843	neural tube closure	The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
	GO:0050918	positive chemotaxis	The directed movement of a motile cell or organism towards a higher concentration of a chemical.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0001921	positive regulation of receptor recycling	Any process that activates or increases the frequency, rate or extent of receptor recycling.
	GO:0071896	protein localization to adherens junction	Any process in which a protein is transported to, and/or maintained at the adherens junction.
	GO:0016337	single organismal cell-cell adhesion	The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
	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.
	GO:0016080	synaptic vesicle targeting	The process in which synaptic vesicles are directed to specific destination membranes, mediated by molecules at the vesicle membrane and target membrane surfaces.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0034750	Scrib-APC-beta-catenin complex	A protein complex that contains the Scribble protein (a cell polarity determinant), the tumor suppressor protein adenomatous polyposis coli (APC), and beta-catenin; may be involved in the control of cell proliferation.
	GO:0005912	adherens junction	A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
	GO:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
	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:0031252	cell leading edge	The area of a motile cell closest to the direction of movement.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005913	cell-cell adherens junction	An adherens junction which connects a cell to another cell.
	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: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:0030027	lamellipodium	A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork 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:0035748	myelin sheath abaxonal region	The region of the myelin sheath furthest from the axon.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0045211	postsynaptic membrane	A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
	GO:0098793	presynapse	The part of a synapse that is part of the presynaptic cell.
	GO:0042734	presynaptic membrane	A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

Asymmetric/Biological Unit
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	SCRIB_HUMAN \| Q14160	:	1uju 1wha 1x5q 4wyt 4wyu

1uju	SOLUTION STRUCTURE OF THE FOURTH PDZ DOMAIN OF HUMANSCRIBBLE (KIAA0147 PROTEIN)
1wha	SOLUTION STRUCTURE OF THE SECOND PDZ DOMAIN OF HUMANSCRIBBLE (KIAA0147 PROTEIN).
1x5q	SOLUTION STRUCTURE OF THE FIRST PDZ DOMAIN OF SCRIBBLEHOMOLOG PROTEIN (HSCRIB)

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