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(-) Description

Title :  STRUCTURE OF THE CANCER ASSOCIATED RAB25 PROTEIN IN COMPLEX WITH FIP2
 
Authors :  S. Oda, P. Y. Lall, M. W. Mccaffrey, A. R. Khan
Date :  13 Sep 11  (Deposition) - 19 Sep 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ras Gtpase Fold (Rab25), Vesicle Trafficking, Endosome, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Oda, P. Y. Lall, M. W. Mccaffrey, A. R. Khan
Structure Of The Cancer Associated Rab25 Protein In Complex With Fip2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-25
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 7-180
    Gene: RAB25, CATX8
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CATX-8
 
Molecule 2 - RAB11 FAMILY-INTERACTING PROTEIN 2
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 440-512
    Gene: RAB11FIP2, KIAA0941
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAB11-FIP2, NRIP11

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2GOL5Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:26 , THR A:44 , GNP A:201 , HOH A:368 , HOH A:377BINDING SITE FOR RESIDUE MG A 200
02AC2SOFTWARESER A:21 , GLY A:22 , VAL A:23 , GLY A:24 , LYS A:25 , THR A:26 , ASN A:27 , PHE A:37 , SER A:38 , HIS A:39 , ASP A:40 , SER A:41 , THR A:43 , THR A:44 , ALA A:69 , GLY A:70 , ASN A:125 , LYS A:126 , ASP A:128 , LEU A:129 , SER A:155 , ALA A:156 , LEU A:157 , MG A:200 , HOH A:329 , HOH A:344 , HOH A:359 , HOH A:368 , HOH A:377BINDING SITE FOR RESIDUE GNP A 201
03AC3SOFTWAREASN A:35 , GLU A:36 , PHE A:37 , ASP B:158 , THR B:160BINDING SITE FOR RESIDUE GOL A 202
04AC4SOFTWAREILE A:45 , GLY A:46 , LEU A:71 , ARG A:73 , ARG A:75 , ILE D:481 , ASP D:482BINDING SITE FOR RESIDUE GOL A 203
05AC5SOFTWAREILE A:18 , ALA A:69 , LEU A:71 , ARG A:75 , THR A:78 , TYR A:81 , TYR A:82 , TRP A:106 , GLU A:109BINDING SITE FOR RESIDUE GOL A 204
06AC6SOFTWAREGLU A:163 , LEU A:164 , GLU A:167 , HOH A:300 , GLU B:138BINDING SITE FOR RESIDUE PO4 A 205
07AC7SOFTWARETYR A:100 , ALA A:101 , GLU A:104BINDING SITE FOR RESIDUE PO4 A 206
08AC8SOFTWARETHR B:26 , THR B:44 , GNP B:201 , HOH B:352 , HOH B:353BINDING SITE FOR RESIDUE MG B 200
09AC9SOFTWARESER B:21 , GLY B:22 , VAL B:23 , GLY B:24 , LYS B:25 , THR B:26 , ASN B:27 , PHE B:37 , SER B:38 , HIS B:39 , SER B:41 , THR B:43 , THR B:44 , ALA B:69 , GLY B:70 , ASN B:125 , LYS B:126 , ASP B:128 , LEU B:129 , SER B:155 , ALA B:156 , LEU B:157 , MG B:200 , HOH B:349 , HOH B:352 , HOH B:353BINDING SITE FOR RESIDUE GNP B 201
10BC1SOFTWAREILE B:45 , GLY B:46 , ARG B:73 , ARG B:75 , GLU C:478 , ILE C:481 , ASP C:482BINDING SITE FOR RESIDUE GOL B 202
11BC2SOFTWAREILE B:18 , ALA B:69 , LEU B:71 , ARG B:75 , THR B:78 , TRP B:106 , GLU B:109BINDING SITE FOR RESIDUE GOL B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TSO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val C:498 -Pro C:499
2Val D:498 -Pro D:499

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TSO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TSO)

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003556241ENSE00001123753chr10:119806114-119805322793RFIP2_HUMAN1-1181180--
1.2aENST000003556242aENSE00001095234chr10:119800076-119799634443RFIP2_HUMAN118-2661490--
1.3aENST000003556243aENSE00001133266chr10:119798951-119798483469RFIP2_HUMAN266-4221570--
1.5ENST000003556245ENSE00000987833chr10:119774621-11977457646RFIP2_HUMAN422-437160--
1.6cENST000003556246cENSE00001952026chr10:119768736-1197644274310RFIP2_HUMAN438-512752C:449-502
D:449-502		54
54
2.1aENST000003610841aENSE00001842111chr1:156030951-156031234284RAB25_HUMAN1-15152A:10-15
B:11-15		6
5
2.2aENST000003610842aENSE00000855863chr1:156035702-156035897196RAB25_HUMAN15-80662A:15-80
B:15-80		66
66
2.3bENST000003610843bENSE00000788616chr1:156038061-156038254194RAB25_HUMAN80-145662A:80-145
B:80-145		66
66
2.4aENST000003610844aENSE00000788617chr1:156039462-15603954281RAB25_HUMAN145-172282A:145-172
B:145-172		28
28
2.5bENST000003610845bENSE00001862439chr1:156039951-156040295345RAB25_HUMAN172-213422A:172-178
B:172-177		7
6

(-) 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:169
 aligned with RAB25_HUMAN | P57735 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:169
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
          RAB25_HUMAN    10 NFVFKVVLIGESGVGKTNLLSRFTRNEFSHDSRTTIGVEFSTRTVMLGTAAVKAQIWDTAGLERYRAITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREVPTEEARMFAENNGLLFLETSALDSTNVELAFETVLKEIFAKVS 178
               SCOP domains d3tsoa_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee........hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhh......eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) 2.1a  ----------------------------------------------------------------Exon 2.3b  PDB: A:80-145 UniProt: 80-145                          --------------------------2.5b    Transcript 2 (1)
           Transcript 2 (2) -----Exon 2.2a  PDB: A:15-80 UniProt: 15-80                            ----------------------------------------------------------------Exon 2.4a  PDB: A:145-172   ------ Transcript 2 (2)
                 3tso A  10 NFVFKVVLIGESGVGKTNLLSRFTRNEFSHDSRTTIGVEFSTRTVMLGTAAVKAQIWDTAGLERYRAITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREVPTEEARMFAENNGLLFLETSALDSTNVELAFETVLKEIFAKVS 178
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with RAB25_HUMAN | P57735 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:167
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
          RAB25_HUMAN    11 FVFKVVLIGESGVGKTNLLSRFTRNEFSHDSRTTIGVEFSTRTVMLGTAAVKAQIWDTAGLERYRAITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREVPTEEARMFAENNGLLFLETSALDSTNVELAFETVLKEIFAKV 177
               SCOP domains d3tsob_ B: automated matches                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee........hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) 2.1a ----------------------------------------------------------------Exon 2.3b  PDB: B:80-145 UniProt: 80-145                          --------------------------2.5b   Transcript 2 (1)
           Transcript 2 (2) ----Exon 2.2a  PDB: B:15-80 UniProt: 15-80                            ----------------------------------------------------------------Exon 2.4a  PDB: B:145-172   ----- Transcript 2 (2)
                 3tso B  11 FVFKVVLIGESGVGKTNLLSRFTRNEFSHDSRTTIGVEFSTRTVMLGTAAVKAQIWDTAGLERYRAITSAYYRGAVGALLVFDLTKHQTYAVVERWLKELYDHAEATIVVMLVGNKSDLSQAREVPTEEARMFAENNGLLFLETSALDSTNVELAFETVLKEIFAKV 177
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain C from PDB  Type:PROTEIN  Length:54
 aligned with RFIP2_HUMAN | Q7L804 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:54
                                   458       468       478       488       498    
          RFIP2_HUMAN   449 RSLTYEEVLQELVKHKELLRRKDTHIRELEDYIDNLLVRVMEETPSILRVPYEP 502
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.6c  PDB: C:449-502 UniProt: 438-512             Transcript 1
                 3tso C 449 RSLTYEEVLQELVKHKELLRRKDTHIRELEDYIDNLLVRVMEETPSILRVPYEP 502
                                   458       468       478       488       498    


Chain D from PDB  Type:PROTEIN  Length:54
 aligned with RFIP2_HUMAN | Q7L804 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:54
                                   458       468       478       488       498    
          RFIP2_HUMAN   449 RSLTYEEVLQELVKHKELLRRKDTHIRELEDYIDNLLVRVMEETPSILRVPYEP 502
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.6c  PDB: D:449-502 UniProt: 438-512             Transcript 1
                 3tso D 449 RSLTYEEVLQELVKHKELLRRKDTHIRELEDYIDNLLVRVMEETPSILRVPYEP 502
                                   458       468       478       488       498
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TSO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TSO)

(-) Gene Ontology  (31, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RAB25_HUMAN | P57735)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0031489    myosin V binding    Interacting selectively and non-covalently with a class V myosin; myosin V is a dimeric molecule involved in intracellular transport.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0003382    epithelial cell morphogenesis    The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010634    positive regulation of epithelial cell migration    Any process that activates or increases the frequency, rate or extent of epithelial cell migration.
    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:0031268    pseudopodium organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pseudopodium, a temporary protrusion or retractile process of a cell, associated with cellular movement.
    GO:0060627    regulation of vesicle-mediated transport    Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0031143    pseudopodium    A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.
    GO:0031260    pseudopodium membrane    The portion of the plasma membrane surrounding a pseudopodium.

Chain C,D   (RFIP2_HUMAN | Q7L804)
molecular function
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0030010    establishment of cell polarity    The specification and formation of anisotropic intracellular organization or cell growth patterns.
    GO:0035773    insulin secretion involved in cellular response to glucose stimulus    The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin, in response to a glucose stimulus.
    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:0045055    regulated exocytosis    A process of exocytosis in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand.
    GO:0003091    renal water homeostasis    Renal process involved in the maintenance of an internal steady state of water in the body.
    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:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0055038    recycling endosome membrane    The lipid bilayer surrounding a recycling endosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB25_HUMAN | P57735: 2oil
        RFIP2_HUMAN | Q7L804: 2gzd 2gzh 2k6s 4c4p

(-) Related Entries Specified in the PDB File

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