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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RAB5, RABEX-5DELTA AND RABAPTIN-5C21 COMPLEX
 
Authors :  Z. Zhang, T. Zhang, J. Ding
Date :  01 May 14  (Deposition) - 23 Jul 14  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.62
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Rab5, Rabex-5, Rabaptin-5, Gef Activity, Endocytosis, Early Endosomes, Vps9, Coiled-Coil, Gef, Effector, Small Gtpases (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Zhang, T. Zhang, S. Wang, Z. Gong, C. Tang, J. Chen, J. Ding
Molecular Mechanism For Rabex-5 Gef Activation By Rabaptin-
Elife V. 3 02687 2014
PubMed-ID: 24957337  |  Reference-DOI: 10.7554/ELIFE.02687

(-) Compounds

Molecule 1 - RAB5 GDP/GTP EXCHANGE FACTOR
    ChainsA, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETDUET1
    Expression System StrainBL21(DE3) CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 132-455
    GeneRABGEF1, RABEX5
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRABEX-5DELTA, RAP1, RABAPTIN-5-ASSOCIATED EXCHANGE FACTOR FOR RAB5, RABEX-5
 
Molecule 2 - RAS-RELATED PROTEIN RAB-5A
    ChainsB, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETDUET1
    Expression System StrainBL21(DE3) CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 15-184
    GeneRAB5A, RAB5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRABAPTIN-5C21
 
Molecule 3 - RAB GTPASE-BINDING EFFECTOR PROTEIN 1
    ChainsC, D, G, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3) CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 552-642
    GeneRABEP1, RAB5EP, RABPT5, RABPT5A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAB5, RABAPTIN-4, RABAPTIN-5, RABAPTIN-5ALPHA, RENAL CARCINOMA ANTIGEN NY-REN-17

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABCDEFGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4Q9U)

(-) Sites  (0, 0)

(no "Site" information available for 4Q9U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q9U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q9U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q9U)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q9U)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q9u A 134 ETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQDFYHNVAERMQTRGKPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKLDAQSLNLSQEDFDRYMSGQTSPRKQMYKNLDLLSQLNERQERIMNEAKKLEKDLIDWTDGIAREVQDI 437
                                   143       153       163       173       183       193    || 204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
                                                                                          198|                                                                                                                                                                                                                                             
                                                                                           200                                                                                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhh..........ee......ee.eeee.........hhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhh.......eeee...hhhhh..hhhhhhhhhhhh.............hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q9u B  20 QFKLVLLGESAVGKSSLVLRFSTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLP 182
                                    29        39||      59        69        79        89        99       109       119       129       139       149       159       169       179   
                                               40|                                                                                                                                   
                                                51                                                                                                                                   

Chain C from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 4q9u C 552 ETRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQS 634
                                   561       571       581       591       601       611       621       631   

Chain D from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4q9u D 558 KKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLM 632
                                   567       577       587       597       607       617       627     

Chain E from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q9u E 134 ETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQDFYHNVAERMQTRGKVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKLDAQSLNLSQEDFDRYMSGQTSPRKQMYKNLDLLSQLNERQERIMNEAKKLEKDLIDWTDGIAREVQDI 437
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     ||321       331       341       351       361       371       381       391       401       411       421       431      
                                                                                                                                                                                                         309|                                                                                                                       
                                                                                                                                                                                                          318                                                                                                                       

Chain F from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..hhhhhhh.....ee...eee................eeeee...hhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh..eee.......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q9u F  21 FKLVLSSLVLRFVIGAAFLTQKFEIWDTAGQERYHSLAPMAQAAIVVYDNEESFARAKNWVKELQRQASPNIVIALSGNRAVDFQEAQSYADDNSLFMETSAKTSMNVNEIFMAIAKKLP 182
                                ||  38  ||    59||      78        88|      104       114       124       141       151    || 162       172       182
                               25|     41|     60|                88|     101|                          133|            156|                        
                                34      53      70                 93      104                           141             158                        

Chain G from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 4q9u G 552 ETRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQSR 635
                                   561       571       581       591       601       611       621       631    

Chain H from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 4q9u H 553 TRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQS 634
                                   562       572       582       592       602       612       622       632  

   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 4Q9U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q9U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q9U)

(-) Gene Ontology  (75, 93)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB5A_HUMAN | P203391n6h 1n6i 1n6k 1n6l 1n6n 1n6o 1n6p 1n6r 1r2q 1tu3 1tu4 3mjh
        RABE1_HUMAN | Q152761p4u 1tu3 1x79 4n3y 4n3z
        RABX5_HUMAN | Q9UJ411txu 2c7m 2c7n 2ot3 4n3x 4n3y 4n3z

(-) Related Entries Specified in the PDB File

4n3x CRYSTAL STRUCTURE OF RABEX-5 CC DOMAIN
4n3y CRYSTAL STRUCTURE OF RABEX-5CC AND RABAPTIN-5C21 COMPLEX
4n3z CRYSTAL STRUCTURE OF RABEX-5DELTA AND RABAPTIN-5C21 COMPLEX