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(-) Description

Title :  CRYSTAL STRUCTURE OF RABEX-5DELTA AND RABAPTIN-5C21 COMPLEX
 
Authors :  Z. Zhang, T. Zhang, J. Ding
Date :  08 Oct 13  (Deposition) - 23 Jul 14  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rab5, Rabex-5, Rabaptin-5, Gef Activity, Endocytosis, Early Endosome (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
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETDUET1
    Expression System StrainBL21(DE3) CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES, ISOFORM 2, 132-455
    GeneRABEX5
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRABEX-5DELTA, RAP1, RABAPTIN-5-ASSOCIATED EXCHANGE FACTOR FOR RAB5, RABEX-5
 
Molecule 2 - RAB GTPASE-BINDING EFFECTOR PROTEIN 1
    ChainsB, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETDUET1
    Expression System StrainBL21(DE3) CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 552-642
    GeneRABEP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRABAPTIN-5C21, RABAPTIN-4, RABAPTIN-5, RABAPTIN-5ALPHA, RENAL CARCINOMA ANTIGEN NY-REN-17

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:270 , HIS A:297BINDING SITE FOR RESIDUE PO4 A 501
2AC2SOFTWAREASP B:591 , HIS C:594BINDING SITE FOR RESIDUE PO4 B 701
3AC3SOFTWAREGLN B:627 , GLN C:625 , MET C:628 , ALA C:629 , MET C:632BINDING SITE FOR RESIDUE PO4 C 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N3Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N3Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4N3Z)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.hhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n3z A 141 EFIEFLKTHKTGQEIYKQTFLEGMHYKRDLIEEQSECAQDFYHNVEKIMDQIEKYIMTRLDEKKDLAIQKRIRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKNLDLLSQLNERQERIMNEAKKLEKDLIDWTDGIAREVQDI 430
                                   151       163       173|      184    || 209       219|      240       250       260       270       280       290       300       310       320       330       340       350       360       392       402       412       422        
                                 148|       160|       173|           189|           219|                                                                                                                                      368|                                       
                                  150        163        175            205            231                                                                                                                                       391                                       

Chain B from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 4n3z B 553 TRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQS 634
                                   562       572       582       592       602       612       622       632  

Chain C from PDB  Type:PROTEIN  Length:83
                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 4n3z C 553 TRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVLMQSR 635
                                   562       572       582       592       602       612       622       632   

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  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 4N3Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N3Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N3Z)

(-) Gene Ontology  (37, 46)

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
        RABE1_HUMAN | Q152761p4u 1tu3 1x79 4n3y 4q9u
        RABX5_HUMAN | Q9UJ411txu 2c7m 2c7n 2ot3 4n3x 4n3y 4q9u

(-) Related Entries Specified in the PDB File

4n3x 4n3y