1FHX - JenaLib

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Title :   STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM GRP1 IN COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE

Authors :   K. M. Ferguson, J. M. Kavran, V. G. Sankaran, E. Fournier, S. J. Isakoff, E. Y. Skolnik, M. A. Lemmon

Date :   02 Aug 00 (Deposition) - 23 Aug 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Pleckstrin, 3-Phosphoinositides, Inositol Tetrakisphosphate Signal Transduction Protein, Guanine Nucleotide Exchange Factor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Ferguson, J. M. Kavran, V. G. Sankaran, E. Fournier, S. J. Isakoff E. Y. Skolnik, M. A. Lemmon
Structural Basis For Discrimination Of 3-Phosphoinositides By Pleckstrin Homology Domains
Mol. Cell V. 6 373 2000
PubMed-ID: 10983984 | Reference-DOI: 10.1016/S1097-2765(00)00037-X

Molecule 1 - GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PLECKSTRIN HOMOLOGY DOMAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE
	Synonym	:	GRP1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	4IP	2	Ligand/Ion	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	4IP	1	Ligand/Ion	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	4IP	1	Ligand/Ion	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 7)

No.	Name	Count	Type	Full Name
1	4IP	2	Ligand/Ion	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:24 , HOH B:61 , ARG B:284 , GLU B:297	BINDING SITE FOR RESIDUE SO4 B 2001
2	AC2	SOFTWARE	ASN A:312 , ASN A:331 , HIS A:334 , HIS B:334 , LYS B:340	BINDING SITE FOR RESIDUE SO4 B 2002
3	AC3	SOFTWARE	HOH A:10 , HOH A:37 , LYS A:273 , GLY A:275 , GLY A:276 , ARG A:277 , VAL A:278 , THR A:280 , LYS A:282 , ARG A:284 , TYR A:295 , LYS A:343 , ASN A:354 , HIS A:355	BINDING SITE FOR RESIDUE 4IP A 1001
4	AC4	SOFTWARE	GLU A:366 , GLU A:369 , LYS A:373 , HOH B:6 , HOH B:18 , HOH B:75 , LYS B:273 , GLY B:275 , GLY B:276 , ARG B:277 , VAL B:278 , THR B:280 , LYS B:282 , ARG B:284 , TYR B:295 , ARG B:305 , LYS B:343 , ASN B:354 , HIS B:355	BINDING SITE FOR RESIDUE 4IP B 1002

Asymmetric Unit

No.	Residues
1	A:342	-	B:342

(no "Cis Peptide Bond" information available for 1FHX)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PH_DOMAIN	PS50003	PH domain profile.	CYH3_MOUSE	264-380	2	A:264-380 B:264-380

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PH_DOMAIN	PS50003	PH domain profile.	CYH3_MOUSE	264-380	1	A:264-380 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PH_DOMAIN	PS50003	PH domain profile.	CYH3_MOUSE	264-380	1	- B:264-380

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PH_DOMAIN	PS50003	PH domain profile.	CYH3_MOUSE	264-380	2	A:264-380 B:264-380

(no "Exon" information available for 1FHX)

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
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Chain A from PDB  Type:PROTEIN  Length:123
 aligned with CYH3_MOUSE | O08967 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:123
                                   273       283       293       303       313       323       333       343       353       363       373       383   
           CYH3_MOUSE   264 NPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRISAPSPEEKEEWMKSIKASISRDPFYD 386
               SCOP domains d1fhxa_ A: Grp1                                                                                                             SCOP domains
               CATH domains 1fhxA00 A:264-386 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......eeeeeeeee..eeeee.........eeee....eeee........eeeeehhhhh......eee.....eee.....eeee..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PH_DOMAIN  PDB: A:264-380 UniProt: 264-380                                                                           ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fhx A 264 NPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRISAPSPEEKEEWmKSIKASISRDPFYD 386
                                   273       283       293       303       313       323       333       343       353       363       373       383   
                                                                                                                                      372-MSE

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with CYH3_MOUSE | O08967 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:126
                                   273       283       293       303       313       323       333       343       353       363       373       383      
           CYH3_MOUSE   264 NPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRISAPSPEEKEEWMKSIKASISRDPFYDMLA 389
               SCOP domains d1fhxb_ B: Grp1                                                                                                                SCOP domains
               CATH domains 1fhxB00 B:264-389 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee......eeeeeeeee..eeeee.........eeee....eeeee.......eeeee...........eee.....eee....eeeee..hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE PH_DOMAIN  PDB: B:264-380 UniProt: 264-380                                                                           --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fhx B 264 NPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRISAPSPEEKEEWmKSIKASISRDPFYDmLA 389
                                   273       283       293       303       313       323       333       343       353       363       373       383   |  
                                                                                                                                      372-MSE        387-MSE

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PH domain-like barrel (258)

Superfamily: PH domain-like (257)

Family: Pleckstrin-homology domain (PH domain) (102)

Protein domain: Grp1 (6)

Mouse (Mus musculus) [TaxId: 10090] (6)

1a	d1fhxa_	A:
1b	d1fhxb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: PH-domain like (150)

Homologous Superfamily: Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) (147)

House mouse (Mus musculus) (39)

1a	1fhxA00	A:264-386
1b	1fhxB00	B:264-389

(no "Pfam Domain" information available for 1FHX)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYH3_MOUSE | O08967)

molecular function
	GO:0005086	ARF guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with the GTPase ARF. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0005547	phosphatidylinositol-3,4,5-trisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions.
	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:0048193	Golgi vesicle transport	The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles.
	GO:0090162	establishment of epithelial cell polarity	The specification and formation of anisotropic intracellular organization of an epithelial cell.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0045785	positive regulation of cell adhesion	Any process that activates or increases the frequency, rate or extent of cell adhesion.
	GO:0032012	regulation of ARF protein signal transduction	Any process that modulates the frequency, rate or extent of ARF protein signal transduction.
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:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	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.
	GO:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.

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	CYH3_MOUSE \| O08967	:	1fgy 1fgz 1fhw 1u2b 2r09 2r0d

1fhw	STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM GRP1 IN COMPLEX WITH INOSITOL(1,3,4,5,6)PENTAKISPHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (4, 4)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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