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(-) Description

Title :  CRYSTAL STRUCTURE OF A BOVINE RABEX-5 FRAGMENT COMPLEXED WITH UBIQUITIN
 
Authors :  S. Lee, J. H. Hurley
Date :  29 Dec 05  (Deposition) - 07 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Zinc Finger, Helix, Protein Turnover-Endocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lee, Y. C. Tsai, R. Mattera, W. J. Smith, M. S. Kostelansky, A. M. Weissman, J. S. Bonifacino, J. H. Hurley
Structural Basis For Ubiquitin Recognition And Autoubiquitination By Rabex-5
Nat. Struct. Mol. Biol. V. 13 264 2006
PubMed-ID: 16462746  |  Reference-DOI: 10.1038/NSMB1064

(-) Compounds

Molecule 1 - UBIQUITIN
    Chains: A, C, E
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
 
Molecule 2 - RAB5 GDP/GTP EXCHANGE FACTOR
    Chains: B, D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PARALLEL GST2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: A20 ZINC FINGER AND INVERTED UBIQUITIN INTERACTING MOTIF DOMAINS
    Gene: RABGEF1, RABEX5
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: RABEX-5

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN3Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:19 , CYS B:23 , CYS B:35 , CYS B:38BINDING SITE FOR RESIDUE ZN B 901
2AC2SOFTWARECYS D:19 , CYS D:23 , CYS D:35 , CYS D:38BINDING SITE FOR RESIDUE ZN D 902
3AC3SOFTWARECYS F:19 , CYS F:23 , CYS F:35 , CYS F:38BINDING SITE FOR RESIDUE ZN F 903
4AC4SOFTWAREARG A:42 , ARG A:72 , LYS C:11 , GLU C:34BINDING SITE FOR RESIDUE SO4 A 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RS27A_BOVIN1-76
 
 		  3A:1-73
C:1-73
E:1-73
RL40_BOVIN1-76
 
 		  3A:1-73
C:1-73
E:1-73
UBB_BOVIN1-76
77-152
153-228
229-304
 
 		  3-
-
-
A:1-73
C:1-73
E:1-73
UBC_BOVIN1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
 
 		  3-
-
-
-
-
-
-
-
A:1-73
C:1-73
E:1-73
2UBIQUITIN_1PS00299 Ubiquitin domain signature.RS27A_BOVIN27-52
 
 		  3A:27-52
C:27-52
E:27-52
RL40_BOVIN27-52
 
 		  3A:27-52
C:27-52
E:27-52
UBB_BOVIN27-52
103-128
179-204
255-280
 
 		  3-
-
-
A:27-52
C:27-52
E:27-52
UBC_BOVIN27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
 
 		  3-
-
-
-
-
-
-
-
A:27-52
C:27-52
E:27-52
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RS27A_BOVIN1-76
 
 		  1A:1-73
-
-
RL40_BOVIN1-76
 
 		  1A:1-73
-
-
UBB_BOVIN1-76
77-152
153-228
229-304
 
 		  1-
-
-
A:1-73
-
-
UBC_BOVIN1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
 
 		  1-
-
-
-
-
-
-
-
A:1-73
-
-
2UBIQUITIN_1PS00299 Ubiquitin domain signature.RS27A_BOVIN27-52
 
 		  1A:27-52
-
-
RL40_BOVIN27-52
 
 		  1A:27-52
-
-
UBB_BOVIN27-52
103-128
179-204
255-280
 
 		  1-
-
-
A:27-52
-
-
UBC_BOVIN27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
 
 		  1-
-
-
-
-
-
-
-
A:27-52
-
-
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RS27A_BOVIN1-76
 
 		  1-
C:1-73
-
RL40_BOVIN1-76
 
 		  1-
C:1-73
-
UBB_BOVIN1-76
77-152
153-228
229-304
 
 		  1-
-
-
-
C:1-73
-
UBC_BOVIN1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
 
 		  1-
-
-
-
-
-
-
-
-
C:1-73
-
2UBIQUITIN_1PS00299 Ubiquitin domain signature.RS27A_BOVIN27-52
 
 		  1-
C:27-52
-
RL40_BOVIN27-52
 
 		  1-
C:27-52
-
UBB_BOVIN27-52
103-128
179-204
255-280
 
 		  1-
-
-
-
C:27-52
-
UBC_BOVIN27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
 
 		  1-
-
-
-
-
-
-
-
-
C:27-52
-
Biological Unit 3 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.RS27A_BOVIN1-76
 
 		  1-
-
E:1-73
RL40_BOVIN1-76
 
 		  1-
-
E:1-73
UBB_BOVIN1-76
77-152
153-228
229-304
 
 		  1-
-
-
-
-
E:1-73
UBC_BOVIN1-76
77-152
153-228
229-304
305-380
381-456
457-532
533-608
609-684
 
 		  1-
-
-
-
-
-
-
-
-
-
E:1-73
2UBIQUITIN_1PS00299 Ubiquitin domain signature.RS27A_BOVIN27-52
 
 		  1-
-
E:27-52
RL40_BOVIN27-52
 
 		  1-
-
E:27-52
UBB_BOVIN27-52
103-128
179-204
255-280
 
 		  1-
-
-
-
-
E:27-52
UBC_BOVIN27-52
103-128
179-204
255-280
331-356
407-432
483-508
559-584
635-660
 
 		  1-
-
-
-
-
-
-
-
-
-
E:27-52

(-) Exons   (0, 0)

(no "Exon" information available for 2FIF)

(-) 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:73
 aligned with RL40_BOVIN | P63048 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:73
                                    10        20        30        40        50        60        70   
           RL40_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d2fifa_ A: Ubiquitin                                                      SCOP domains
               CATH domains 2fifA00 A:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: A:1-73 UniProt: 1-76                                    PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) ------------------------------------------------------------------------- PROSITE (7)
                PROSITE (8) --------------------------UBIQUITIN_1  PDB: A:27-52 --------------------- PROSITE (8)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain A from PDB  Type:PROTEIN  Length:73
 aligned with RS27A_BOVIN | P62992 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:73
                                    10        20        30        40        50        60        70   
          RS27A_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d2fifa_ A: Ubiquitin                                                      SCOP domains
               CATH domains 2fifA00 A:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) UBIQUITIN_2  PDB: A:1-73 UniProt: 1-76                                    PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) --------------------------UBIQUITIN_1  PDB: A:27-52 --------------------- PROSITE (7)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain A from PDB  Type:PROTEIN  Length:73
 aligned with UBB_BOVIN | P0CG53 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:73
                                   238       248       258       268       278       288       298   
            UBB_BOVIN   229 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 301
               SCOP domains d2fifa_ A: Ubiquitin                                                      SCOP domains
               CATH domains 2fifA00 A:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------UBIQUITIN_1  PDB: A:27-52 --------------------- PROSITE (3)
                PROSITE (1) UBIQUITIN_2  PDB: A:1-73 UniProt: 229-304                                 PROSITE (1)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain A from PDB  Type:PROTEIN  Length:73
 aligned with UBC_BOVIN | P0CH28 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:73
                                   618       628       638       648       658       668       678   
            UBC_BOVIN   609 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 681
               SCOP domains d2fifa_ A: Ubiquitin                                                      SCOP domains
               CATH domains 2fifA00 A:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: A:27-52 --------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (1) UBIQUITIN_2  PDB: A:1-73 UniProt: 609-684                                 PROSITE (1)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif A   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain B from PDB  Type:PROTEIN  Length:59
 aligned with RABX5_BOVIN | O18973 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:59
                                    24        34        44        54        64         
          RABX5_BOVIN    15 SELLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASSQ  73
               SCOP domains d2fifb_ B: RabGEF1 (Rabex-5), ubiquitin-binding domain      SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 2fif B  15 SELLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASSQ  73
                                    24        34        44        54        64         


Chain C from PDB  Type:PROTEIN  Length:73
 aligned with RL40_BOVIN | P63048 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:73
                                    10        20        30        40        50        60        70   
           RL40_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d2fifc_ C: Ubiquitin                                                      SCOP domains
               CATH domains 2fifC00 C:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: C:1-73 UniProt: 1-76                                    PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) ------------------------------------------------------------------------- PROSITE (7)
                PROSITE (8) --------------------------UBIQUITIN_1  PDB: C:27-52 --------------------- PROSITE (8)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif C   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain C from PDB  Type:PROTEIN  Length:73
 aligned with RS27A_BOVIN | P62992 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:73
                                    10        20        30        40        50        60        70   
          RS27A_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d2fifc_ C: Ubiquitin                                                      SCOP domains
               CATH domains 2fifC00 C:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) UBIQUITIN_2  PDB: C:1-73 UniProt: 1-76                                    PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) --------------------------UBIQUITIN_1  PDB: C:27-52 --------------------- PROSITE (7)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif C   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain C from PDB  Type:PROTEIN  Length:73
 aligned with UBB_BOVIN | P0CG53 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:73
                                   238       248       258       268       278       288       298   
            UBB_BOVIN   229 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 301
               SCOP domains d2fifc_ C: Ubiquitin                                                      SCOP domains
               CATH domains 2fifC00 C:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------UBIQUITIN_1  PDB: C:27-52 --------------------- PROSITE (3)
                PROSITE (1) UBIQUITIN_2  PDB: C:1-73 UniProt: 229-304                                 PROSITE (1)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif C   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain C from PDB  Type:PROTEIN  Length:73
 aligned with UBC_BOVIN | P0CH28 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:73
                                   618       628       638       648       658       668       678   
            UBC_BOVIN   609 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 681
               SCOP domains d2fifc_ C: Ubiquitin                                                      SCOP domains
               CATH domains 2fifC00 C:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: C:27-52 --------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (1) UBIQUITIN_2  PDB: C:1-73 UniProt: 609-684                                 PROSITE (1)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif C   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain D from PDB  Type:PROTEIN  Length:58
 aligned with RABX5_BOVIN | O18973 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:58
                                    25        35        45        55        65        
          RABX5_BOVIN    16 ELLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASSQ  73
               SCOP domains d2fifd_ D: RabGEF1 (Rabex-5), ubiquitin-binding domain     SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 2fif D  16 ELLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASSQ  73
                                    25        35        45        55        65        


Chain E from PDB  Type:PROTEIN  Length:73
 aligned with RL40_BOVIN | P63048 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:73
                                    10        20        30        40        50        60        70   
           RL40_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d2fife_ E: Ubiquitin                                                      SCOP domains
               CATH domains 2fifE00 E:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhh....hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) UBIQUITIN_2  PDB: E:1-73 UniProt: 1-76                                    PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) ------------------------------------------------------------------------- PROSITE (7)
                PROSITE (8) --------------------------UBIQUITIN_1  PDB: E:27-52 --------------------- PROSITE (8)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif E   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain E from PDB  Type:PROTEIN  Length:73
 aligned with RS27A_BOVIN | P62992 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:73
                                    10        20        30        40        50        60        70   
          RS27A_BOVIN     1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
               SCOP domains d2fife_ E: Ubiquitin                                                      SCOP domains
               CATH domains 2fifE00 E:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhh....hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) UBIQUITIN_2  PDB: E:1-73 UniProt: 1-76                                    PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                PROSITE (7) --------------------------UBIQUITIN_1  PDB: E:27-52 --------------------- PROSITE (7)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif E   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain E from PDB  Type:PROTEIN  Length:73
 aligned with UBB_BOVIN | P0CG53 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:73
                                   238       248       258       268       278       288       298   
            UBB_BOVIN   229 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 301
               SCOP domains d2fife_ E: Ubiquitin                                                      SCOP domains
               CATH domains 2fifE00 E:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhh....hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------UBIQUITIN_1  PDB: E:27-52 --------------------- PROSITE (3)
                PROSITE (1) UBIQUITIN_2  PDB: E:1-73 UniProt: 229-304                                 PROSITE (1)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif E   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain E from PDB  Type:PROTEIN  Length:73
 aligned with UBC_BOVIN | P0CH28 from UniProtKB/Swiss-Prot  Length:690

    Alignment length:73
                                   618       628       638       648       658       668       678   
            UBC_BOVIN   609 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL 681
               SCOP domains d2fife_ E: Ubiquitin                                                      SCOP domains
               CATH domains 2fifE00 E:1-73                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhh....hhh.eeeee..ee.....hhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------UBIQUITIN_1  PDB: E:27-52 --------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------- PROSITE (4)
                PROSITE (1) UBIQUITIN_2  PDB: E:1-73 UniProt: 609-684                                 PROSITE (1)
                PROSITE (5) ------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ------------------------------------------------------------------------- PROSITE (6)
                 Transcript ------------------------------------------------------------------------- Transcript
                 2fif E   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL  73
                                    10        20        30        40        50        60        70   


Chain F from PDB  Type:PROTEIN  Length:56
 aligned with RABX5_BOVIN | O18973 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:56
                                    26        36        46        56        66      
          RABX5_BOVIN    17 LLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASS  72
               SCOP domains d2fiff_ F: RabGEF1 (Rabex-5), ubiquitin-binding domain   SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 2fif F  17 LLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASS  72
                                    26        36        46        56        66
   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, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FIF)

(-) Gene Ontology  (18, 32)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E   (RS27A_BOVIN | P62992)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain A,C,E   (UBB_BOVIN | P0CG53)
molecular function
    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).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain A,C,E   (RL40_BOVIN | P63048)
molecular function
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain A,C,E   (UBC_BOVIN | P0CH28)
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B,D,F   (RABX5_BOVIN | O18973)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.

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  2fif
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  RL40_BOVIN | P63048
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  RS27A_BOVIN | P62992
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  UBB_BOVIN | P0CG53
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 Related Entries

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

UniProtKB/Swiss-Prot
        RABX5_BOVIN | O18973: 2fid
        RL40_BOVIN | P63048: 1aar 1cmx 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2hd5 2oob 2qho 2wwz 2wx0 2wx1 3h1u 3m3j 4ljo 4ljp 4s22
        RS27A_BOVIN | P62992: 1aar 1cmx 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2hd5 2oob 2qho 2wwz 2wx0 2wx1 3h1u 3m3j 4m0w 4y1h 4z9s 5bz0 5fer 5jqs 5mn9
        UBB_BOVIN | P0CG53: 1aar 1cmx 1e0q 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2hd5 2oob 2qho 2wwz 2wx0 2wx1 2xbb 3h1u 3m3j 4bbn
        UBC_BOVIN | P0CH28: 1aar 1cmx 1e0q 1gjz 1p3q 1ud7 1uzx 1v80 1v81 1wr6 1wrd 1yd8 2c7m 2c7n 2d3g 2dx5 2fid 2hd5 2oob 2qho 2wwz 2wx0 2wx1 2xbb 2zcc 3h1u 3m3j 4bbn 4xkh 4xyz 5ait

(-) Related Entries Specified in the PDB File

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