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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RAB11-RABIN8-FIP3
 
Authors :  M. Vetter, E. Lorentzen
Date :  08 Apr 15  (Deposition) - 12 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Transport Protein, Ciliary Targeting Complex, Cilium, Vesicu Transport, Membrane Trafficking, Rabin8, Rab11, Fip3 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Vetter, R. Stehle, C. Basquin, E. Lorentzen
Structure Of Rab11-Fip3-Rabin8 Reveals Simultaneous Binding Of Fip3 And Rabin8 Effectors To Rab11.
Nat. Struct. Mol. Biol. V. 22 695 2015
PubMed-ID: 26258637  |  Reference-DOI: 10.1038/NSMB.3065

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-11A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: GTPASE DOMAIN, RESIDUES 6-186
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAB-11, YL8, RAB-11, YL8, RAB11A
 
Molecule 2 - RAB-3A-INTERACTING PROTEIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, RESIDUES 286-476
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAB3A-INTERACTING PROTEIN, RABIN-3, SSX2-INTERACTING PROTEIN, RAB3A-INTERACTING PROTEIN, RABIN-3, SSX2-INTERACTING PROTEIN, RABIN8

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO4-1Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:20 , GLY A:21 , VAL A:22 , GLY A:23 , LYS A:24 , SER A:25 , ASN A:26 , PHE A:36 , ASN A:37 , LEU A:38 , SER A:40 , SER A:42 , THR A:43 , ALA A:68 , GLY A:69 , ASN A:124 , LYS A:125 , ASP A:127 , LEU A:128 , SER A:154 , ALA A:155 , LEU A:156 , MG A:202 , HOH A:2006 , HOH A:2007 , HOH A:2027 , TYR C:423BINDING SITE FOR RESIDUE GNP A 201
2AC2SOFTWARESER A:25 , THR A:43 , ASP A:66 , GNP A:201 , HOH A:2006 , HOH A:2007BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREASP A:92 , ALA A:94 , LYS A:95 , LYS A:125BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWARESER B:20 , GLY B:21 , VAL B:22 , GLY B:23 , LYS B:24 , SER B:25 , ASN B:26 , PHE B:36 , ASN B:37 , LEU B:38 , SER B:40 , SER B:42 , THR B:43 , THR B:67 , ALA B:68 , GLY B:69 , ASN B:124 , LYS B:125 , ASP B:127 , LEU B:128 , SER B:154 , ALA B:155 , LEU B:156 , MG B:202 , HOH B:2006 , HOH B:2007 , TYR D:423BINDING SITE FOR RESIDUE GNP B 201
5AC5SOFTWARESER B:25 , THR B:43 , GNP B:201 , HOH B:2006 , HOH B:2007BINDING SITE FOR RESIDUE MG B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UJ5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:122 -Gly A:123
2Asp C:396 -Ser C:397

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UJ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UJ5)

(-) Exons   (0, 0)

(no "Exon" information available for 4UJ5)

(-) 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:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee....hhhhhhhhhhh............eeeeeeeeee..eeeeeeeeee......hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeee..........hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uj5 A   4 ASDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGLRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQK 179
                                    13        23        33        43        53        63      ||76        86        96       106       116       126       136       146       156       166       176   
                                                                                             70|                                                                                                         
                                                                                              74                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh............eeeeeeeeee..eeeeeeeeee..................eeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeee..........hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uj5 B   7 EYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVSQ 178
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176  


Chain C from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...eeee.............................eeee......eeeehhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uj5 C 288 QPIVKDCKEADLSLYNEFRLWKDEPTMDRTCPFLDKIYQEDIFPCLTFSKSELASAVLEAVENNTLSIEPVGLQPIRFVKAECGGPKKCALTGQSKSCKHRIKLGDSSNYYYISPFCRYRITSVCNFFTYIRYIQQGLVKQQDVDQMFWEVMQLRKEMSLAKLGYFKEE 459
                                   297       307       317       327       337       347       357       367||     380       390       400       410       420       430       440       450         
                                                                                                          368|                                                                                       
                                                                                                           372                                                                                       


Chain D from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...eeee...........eeee......eeeehhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uj5 D 286 VIQPIVKDCKEADLSLYNEFRLWKDEPTMDRTCPFLDKIYQEDIFPCLTFSKSELASAVLEAVENNTLSIEPVGLTGQSKSCKHRIKLGDSSNYYYISPFCRYRITSVCNFFTYIRYIQQGLVKQQDVDQMFWEVMQLRKEMSLAKLGYFKEEL 460
                                   295       305       315       325       335       345       355   ||  386       396       406       416       426       436       446       456    
                                                                                                   359|                                                                               
                                                                                                    381
   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 4UJ5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UJ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UJ5)

(-) Gene Ontology  (68, 74)

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  RB11A_HUMAN | P62491
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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB3I_HUMAN | Q96QF0: 4lhx 4lhy 4lhz 4uj3 4uj4 5oag
        RB11A_HUMAN | P62491: 1oiv 1oiw 1oix 1yzk 2d7c 2gzd 2gzh 2hv8 4c4p 4d0l 4d0m 4lwz 4lx0 4uj3 4uj4 5c46 5c4g 5euq 5ez5 5fbl 5fbq 5fbr 5fbv 5fbw 5jcz

(-) Related Entries Specified in the PDB File

4uj3 CRYSTAL STRUCTURE OF HUMAN RAB11-RABIN8-FIP3
4uj4 CRYSTAL STRUCTURE OF HUMAN RAB11-RABIN8-FIP3