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(-) Description

Title :  CRYSTAL STRUCTURE OF AUTOINHIBITED FORM OF GRP1 ARF GTPASE EXCHANGE FACTOR
 
Authors :  J. P. Dinitto, A. Delprato, M. T. Gabe Lee, T. C. Cronin, S. Huang, A. Gui M. P. Czech, D. G. Lambright
Date :  18 Aug 07  (Deposition) - 04 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Grp1, General Receptor For Phosphoinositides, Arf Gtpase, Exchange Factor, Pip3, 3-Phosphoinositide, Guanine-Nucleotide Releasing Factor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. P. Dinitto, A. Delprato, M. T. Gabe Lee, T. C. Cronin, S. Huang, A. Guilherme, M. P. Czech, D. G. Lambright
Structural Basis And Mechanism Of Autoregulation In 3-Phosphoinositide-Dependent Grp1 Family Arf Gtpase Exchang Factors.
Mol. Cell V. 28 569 2007
PubMed-ID: 18042453  |  Reference-DOI: 10.1016/J.MOLCEL.2007.09.017

(-) Compounds

Molecule 1 - CYTOHESIN-3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSEC7-PH DOMAINS
    GenePSCD3, GRP1
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPH, SEC7 AND COILED-COIL DOMAIN-CONTAINING PROTEIN 3, CLM3, SEC7 HOMOLOG C, MSEC7-3, ARF NUCLEOTIDE-BINDING SITE OPENER 3, PROTEIN ARNO3, GENERAL RECEPTOR OF PHOSPHOINOSITIDES 1, GRP1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
14IP2Ligand/IonINOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
14IP1Ligand/IonINOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
14IP1Ligand/IonINOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:147 , ARG A:150 , SER A:242 , GLN A:337 , HOH A:450 , HOH A:540 , HOH A:576 , HOH A:594 , HOH A:762BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREHOH A:596 , HIS B:55 , HIS B:56 , HIS B:57 , HOH B:410 , HOH B:504 , HOH B:512 , HOH B:530BINDING SITE FOR RESIDUE SO4 B 1
3AC3SOFTWAREHIS A:57 , HIS A:58 , HIS A:60 , LEU B:272 , LYS B:323 , PRO B:324BINDING SITE FOR RESIDUE SO4 A 400
4AC4SOFTWAREARG A:217 , HOH A:525 , HOH A:716 , HIS B:60BINDING SITE FOR RESIDUE SO4 A 401
5AC5SOFTWARELYS A:107 , 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 , ARG A:305 , LYS A:343 , ASN A:354 , HIS A:355 , HOH A:409 , HOH A:412 , HOH A:414 , HOH A:431 , HOH A:488 , HOH A:498 , HOH A:538 , HOH A:567 , HOH A:572 , HOH A:752BINDING SITE FOR RESIDUE 4IP A 402
6AC6SOFTWARELYS B:107 , 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 , HOH B:407 , HOH B:408 , HOH B:418 , HOH B:440 , HOH B:475 , HOH B:491 , HOH B:496 , HOH B:506 , HOH B:524BINDING SITE FOR RESIDUE 4IP B 400
7AC7SOFTWARETYR A:385 , LEU A:388 , LYS A:392 , HOH A:749BINDING SITE FOR RESIDUE PEG A 403
8AC8SOFTWAREGLY A:269 , TRP A:270 , ARG A:283 , TRP A:285 , GLY B:54BINDING SITE FOR RESIDUE PEG A 404
9AC9SOFTWARELYS B:340 , CYS B:342BINDING SITE FOR RESIDUE PEG B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R0D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R0D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R0D)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SEC7PS50190 SEC7 domain profile.CYH3_MOUSE59-246
 
  2A:63-246
B:63-246
2PH_DOMAINPS50003 PH domain profile.CYH3_MOUSE264-380
 
  2A:264-380
B:264-380
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SEC7PS50190 SEC7 domain profile.CYH3_MOUSE59-246
 
  1A:63-246
-
2PH_DOMAINPS50003 PH domain profile.CYH3_MOUSE264-380
 
  1A:264-380
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SEC7PS50190 SEC7 domain profile.CYH3_MOUSE59-246
 
  1-
B:63-246
2PH_DOMAINPS50003 PH domain profile.CYH3_MOUSE264-380
 
  1-
B:264-380

(-) Exons   (0, 0)

(no "Exon" information available for 2R0D)

(-) 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:343
 aligned with CYH3_MOUSE | O08967 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:343
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393   
           CYH3_MOUSE    54 NLTSVEESKTTQRNKQIAMGRKKFNMDPKKGIQFLIENDLLQSSPEDVAQFLYKGEGLNKTVIGDYLGERDDFNIKVLQAFVELHEFADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCNPGVFQSTDTCYVLSFAIIMLNTSLHNHNVRDKPTAERFITMNRGINEGGDLPEELLRNLYESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRISAPSPEEKEEWMKSIKASISRDPFYDMLATRKRRIA 396
               SCOP domains -----------d2r0da1 A:65-252 Cytohesin-1/b2-1                                                                                                                                                           -------------d2r0da2 A:266-391 Grp1                                                                                                        ----- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhhhhhhhhhhh..........hhhhh.....eeeeeeee......eeeeeeeee..eeeee.........eeee....eeeee.......eeeee...........eee.....eee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SEC7  PDB: A:63-246 UniProt: 59-246                                                                                                                                                         -----------------PH_DOMAIN  PDB: A:264-380 UniProt: 264-380                                                                           ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r0d A  54 GHHHHHHGSTTQRNAQIAMGRKKFNMDPKKGIQFLIENDLLQSSPEDVAQFLYKGEGLNKTVIGDYLGERDDFNIKVLQAFVELHEFADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCNPGVFQSTDTCYVLSFAIIMLNTSLHNHNVRDKPTAERFITMNRGINEGGDLPEELLRNLYESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRISAPSPEEKEEWMKSIKASISRDPFYDMLATRKRRIA 396
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393   

Chain B from PDB  Type:PROTEIN  Length:341
 aligned with CYH3_MOUSE | O08967 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:341
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393 
           CYH3_MOUSE    54 NLTSVEESKTTQRNKQIAMGRKKFNMDPKKGIQFLIENDLLQSSPEDVAQFLYKGEGLNKTVIGDYLGERDDFNIKVLQAFVELHEFADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCNPGVFQSTDTCYVLSFAIIMLNTSLHNHNVRDKPTAERFITMNRGINEGGDLPEELLRNLYESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRISAPSPEEKEEWMKSIKASISRDPFYDMLATRKRR 394
               SCOP domains -----------d2r0db1 B:65-252 Cytohesin-1/b2-1                                                                                                                                                           -------------d2r0db2 B:266-391 Grp1                                                                                                        --- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------Sec7-2r0dB03 B:63-248                                                                                                                                                                     ----------------PH-2r0dB01 B:265-380                                                                                                -------------- Pfam domains (1)
           Pfam domains (2) ---------Sec7-2r0dB04 B:63-248                                                                                                                                                                     ----------------PH-2r0dB02 B:265-380                                                                                                -------------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.........hhhhhhhhhhhhhhh..........hhhhh.....eeeeeeee......eeeeeeeee..eeeee.........eeee....eeeee.......eeeee...........eee.....eee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SEC7  PDB: B:63-246 UniProt: 59-246                                                                                                                                                         -----------------PH_DOMAIN  PDB: B:264-380 UniProt: 264-380                                                                           -------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r0d B  54 GHHHHHHGSTTQRNAQIAMGRKKFNMDPKKGIQFLIENDLLQSSPEDVAQFLYKGEGLNKTVIGDYLGERDDFNIKVLQAFVELHEFADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCNPGVFQSTDTCYVLSFAIIMLNTSLHNHNVRDKPTAERFITMNRGINEGGDLPEELLRNLYESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRISAPSPEEKEEWMKSIKASISRDPFYDMLATRKRR 394
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393 

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R0D)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: PH (111)
(-)
Family: PH (71)
1aPH-2r0dB01B:265-380
1bPH-2r0dB02B:265-380
(-)
Family: Sec7 (12)

(-) Gene Ontology  (16, 16)

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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CYH3_MOUSE | O089671fgy 1fgz 1fhw 1fhx 1u2b 2r09

(-) Related Entries Specified in the PDB File

2r09