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(-) Description

Title :  PRONE8
 
Authors :  C. Thomas, I. Fricke, A. Scrima, A. Berken, A. Wittinghofer
Date :  08 Nov 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Dimer, Guanine Nucleotide Exchange Factor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Thomas, I. Fricke, A. Scrima, A. Berken, A. Wittinghofer
Structural Evidence For A Common Intermediate In Small G Protein-Gef Reactions
Mol. Cell V. 25 141 2007
PubMed-ID: 17218277  |  Reference-DOI: 10.1016/J.MOLCEL.2006.11.023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EMB|CAB41934.1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 76-440
    Gene: AT3G24620
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Strain: COLUMBIA
    Synonym: PRONE8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 28)

Asymmetric Unit (1, 28)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 28)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 56)
No.NameCountTypeFull Name
1MSE56Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2NTX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NTX)

(-) 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:314
 aligned with ROGF8_ARATH | Q9LV40 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:359
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428         
          ROGF8_ARATH    79 SERQQADMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKRKLHTKDTKSSWGSAVSLEKRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDTLALKQT 437
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh..-.....hhhhhhhhhhhhhhhhhhhhh.eeeee.----------..eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.--------------------...ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh--------------hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ntx A   4 SERQQADmEmmKDRFAKLLLGEDmSGGGKGVSSALALSNAITNLAASIFGEQ-KLQPmPQDRQARWKKEIDWLLSVTDHIVEFVPS----------EImVTRQRGDLLmNIPALRKLDAmLIDTLDNFRGHNEFWYV--------------------LPPVKVPPGGLSEPSRRmLYFQKDSVTQVQKAAmAINAQVLSEmEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAmLDmSTEHKVLDLKNRIEASVVIWKRK--------------SLEKRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVmSRIEDVLYTDTLALKQT 362
                                   |13|       23   |    33        43        53 | |   |63        73        83     |   -      |103       113       123       133      |  -         -       163       173    |  183       193|      203|      213       223       233       243  |    253       263     |   -         -|      293       303       313       323       333       343 |     353         
                                  11-MSE          27-MSE                      55 |   |                          89        100 |       112-MSE    123-MSE          140                  161              178-MSE         194-MSE   204-MSE                                243-MSE                   269            284                                                          345-MSE             
                                    13-MSE                                      57   |                                      102-MSE                                                                                                                                         246-MSE                                                                                                                
                                     14-MSE                                         61-MSE                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:287
 aligned with ROGF8_ARATH | Q9LV40 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:354
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427    
          ROGF8_ARATH    78 RSERQQADMEMMKDRFAKLLLGEDMSGGGKGVSSALALSNAITNLAASIFGEQTKLQPMPQDRQARWKKEIDWLLSVTDHIVEFVPSQQTSKDGVCTEIMVTRQRGDLLMNIPALRKLDAMLIDTLDNFRGHNEFWYVSRDSEEGQQARNDRTNDKWWLPPVKVPPGGLSEPSRRMLYFQKDSVTQVQKAAMAINAQVLSEMEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAMLDMSTEHKVLDLKNRIEASVVIWKRKLHTKDTKSSWGSAVSLEKRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVMSRIEDVLYTDT 431
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---PRONE-2ntxB01 B:6-356                                                                                                                                                                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) ---PRONE-2ntxB02 B:6-356                                                                                                                                                                                                                                                                                                                                           Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh..-.....hhhhhhhhhhhhhhhhhhhhh.eeee..-----------..eeeehhhhhhhhhhhhhhhhhhhhhhhh.-----------------------------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh--------------hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ntx B   3 RSERQQADmEmmKDRFAKLLLGEDmSGGGKGVSSALALSNAITNLAASIFGEQ-KLQPmPQDRQARWKKEIDWLLSVTDHIVEFVPS-----------ImVTRQRGDLLmNIPALRKLDAmLIDTLDNF-----------------------------------------EPSRRmLYFQKDSVTQVQKAAmAINAQVLSEmEIPESYIDSLPKNGRASLGDSIYKSITEEWFDPEQFLAmLDmSTEHKVLDLKNRIEASVVIWKRK--------------SLEKRELFEERAETILVLLKQKFPGLPQSSLDISKIQFNKDVGQAVLESYSRILESLAYTVmSRIEDVLYTDT 356
                                    12||      22    |   32        42        52  | |   62        72        82      |  -       102       112       122|       |-         -         -         -         -|    | 182       192 |     202 |     212       222       232       242|  |   252       262      |  -         - |     292       302       312       322       332       342  |    352    
                                   11-MSE          27-MSE                      55 |   |                          89         101|       112-MSE    123-MSE 131                                       173    |             194-MSE   204-MSE                                243-MSE                   269            284                                                          345-MSE       
                                     13-MSE                                      57   |                                      102-MSE                                                                     178-MSE                                                             246-MSE                                                                                                          
                                      14-MSE                                         61-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2NTX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: PRONE] (3)

(-) Gene Ontology  (7, 7)

Asymmetric 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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2nty THE SAME PROTEIN WITH ROP4 SUBSTRATE