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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF A BINARY ROP-PRONE COMPLEX
 
Authors :  C. Thomas, I. Fricke, M. Weyand, A. Berken
Date :  02 Mar 09  (Deposition) - 14 Apr 09  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Membrane, Prenylation, Methylation, Nucleotide- Binding, Signaling Protein, Nucleotide-Binding, Complex Of Prone-Gef With Rop Substrate, Lipoprotein, Gtp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Thomas, I. Fricke, M. Weyand, A. Berken
3D Structure Of A Binary Rop-Prone Complex: The Final Intermediate For A Complete Set Of Molecular Snapshots Of The Ropgef Reaction.
Biol. Chem. V. 390 427 2009
PubMed-ID: 19335195  |  Reference-DOI: 10.1515/BC.2009.049
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHO OF PLANTS GUANINE NUCLEOTIDE EXCHANGE FACTOR 8
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21-CODONPLUS-RIL
    Expression System Taxid: 511693
    Fragment: PRONE DOMAIN, RESIDUES 76-440
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: ROPGEF8
    Synonym: EMB|CAB41934.1
    Variant: COL-0
 
Molecule 2 - RAC-LIKE GTP-BINDING PROTEIN ARAC2
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21-CODONPLUS-RIL
    Expression System Taxid: 511693
    Fragment: RESIDUES 1-180
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: ROP7
    Synonym: RHO7 OF PLANTS, GTPASE PROTEIN ROP7
    Variant: LANDSBERG ERECTA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2WBL)

(-) Sites  (0, 0)

(no "Site" information available for 2WBL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu B:222 -Gly B:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WBL)

(-) Exons   (0, 0)

(no "Exon" information available for 2WBL)

(-) Sequences/Alignments

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:329
 aligned with ROGF8_ARATH | Q9LV40 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:354
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434    
          ROGF8_ARATH    85 DMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKRKLHTKDTKSSWGSAVSLEKRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDTLALKQTL 438
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.......ee..........-------.......ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.------------------.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wbl A  10 DMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQ-------DKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKR------------------KRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDTLALKQTL 363
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        |-         -       289       299       309       319       329       339       349       359    
                                                                                                                                                                     149     157                                                                                                            268                287                                                                            


Chain B from PDB  Type:PROTEIN  Length:329
 aligned with ROGF8_ARATH | Q9LV40 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:353
                                    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       403       413       423       433   
          ROGF8_ARATH    84 ADMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKRKLHTKDTKSSWGSAVSLEKRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDTLALKQ 436
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) PRONE-2wblB01 B:9-361                                                                                                                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) PRONE-2wblB02 B:9-361                                                                                                                                                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.......ee............------......ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhh....hhhhhhhhhhhhhhhhhhhh..------------------hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wbl B   9 ADMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQAR------KWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKRK------------------RELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDTLALKQ 361
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148  |    158       168       178       188       198       208       218       228       238       248       258       268|        -       288       298       308       318       328       338       348       358   
                                                                                                                                                                        151    158                                                                                                            269                288                                                                         


Chain C from PDB  Type:PROTEIN  Length:168
 aligned with RAC2_ARATH | Q38903 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174      
           RAC2_ARATH     5 RFIKCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGSTVNLGLWDTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENIHKKWLPELKHYAPGIPIVLVGTKLDLRDDKQFLKDHPGAASITTAQGEELRKMIGAVRYLECSSKTQQNVKAVFDTAIRVALRP 180
               SCOP domains d2wblc_ C: automated mat        ches                                                                                                                                             SCOP domains
               CATH domains 2wblC00 C:5-180 P-loop c        ontaining nucleotide triphosphate hydrolases                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhh--------......eeeeeee..eeeeeeee.......hhhhh........eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhh......hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wbl C   5 RFIKCVTVGDGAVGKTCMLISYTG--------PTVFDNFSANVVVDGSTVNLGLWDTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENIHKKWLPELKHYAPGIPIVLVGTKLDLRDDKQFLKDHPGAASITTAQGEELRKMIGAVRYLECSSKTQQNVKAVFDTAIRVALRP 180
                                    14        24   |     -  |     44        54        64        74        84        94       104       114       124       134       144       154       164       174      
                                                  28       37                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:169
 aligned with RAC2_ARATH | Q38903 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:177
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       
           RAC2_ARATH     4 ARFIKCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGSTVNLGLWDTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENIHKKWLPELKHYAPGIPIVLVGTKLDLRDDKQFLKDHPGAASITTAQGEELRKMIGAVRYLECSSKTQQNVKAVFDTAIRVALRP 180
               SCOP domains d2wbld_ D: automated matc        hes                                                                                                                                              SCOP domains
               CATH domains 2wblD00 D:4-180 P-loop co        ntaining nucleotide triphosphate hydrolases                                                                                                      CATH domains
           Pfam domains (1) ----Ras-2wblD01 D:8-179                                                                                                                                                         - Pfam domains (1)
           Pfam domains (2) ----Ras-2wblD02 D:8-179                                                                                                                                                         - Pfam domains (2)
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhh--------......eeeeeee..eeeeeeee.......hhhhh........eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhh......hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wbl D   4 ARFIKCVTVGDGAVGKTCMLISYTG--------PTVFDNFSANVVVDGSTVNLGLWDTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENIHKKWLPELKHYAPGIPIVLVGTKLDLRDDKQFLKDHPGAASITTAQGEELRKMIGAVRYLECSSKTQQNVKAVFDTAIRVALRP 180
                                    13        23    |    -   |    43        53        63        73        83        93       103       113       123       133       143       153       163       173       
                                                   28       37
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: PRONE] (3)

(-) Gene Ontology  (11, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ROGF8_ARATH | Q9LV40)
molecular function
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. 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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
cellular component
    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.

Chain C,D   (RAC2_ARATH | Q38903)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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    Leu B:222 - Gly B:223   [ RasMol ]  
 

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  2wbl
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 Related Entries

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

UniProtKB/Swiss-Prot
        ROGF8_ARATH | Q9LV40: 2ntx 2nty

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2WBL)