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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RAB5B IN COMPLEX WITH GDP
 
Authors :  B. Hong, L. Shen, J. Wang, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  21 Jun 06  (Deposition) - 04 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  G-Protein, Rab, Structural Genomics, Structural Genomics Consortium, Sgc, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Hong, L. Shen, J. Wang, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of Human Rab5B In Complex With Gdp
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-5B
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP28A-LIC
    Expression System StrainBL21-CODONPLUS (DE-3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRAB5B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1D1D2Ligand/Ion(4S,5S)-1,2-DITHIANE-4,5-DIOL
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:30 , VAL A:31 , GLY A:32 , LYS A:33 , SER A:34 , SER A:35 , PHE A:45 , GLU A:47 , TYR A:48 , SER A:51 , ALA A:77 , ASN A:133 , LYS A:134 , ASP A:136 , LEU A:137 , SER A:163 , ALA A:164 , LYS A:165 , HOH A:221 , HOH A:223 , HOH A:244 , HOH A:266BINDING SITE FOR RESIDUE GDP A 201
2AC2SOFTWARETHR A:76 , GLN A:79 , GLU A:80 , HIS A:83 , ALA A:86 , TYR A:89 , TYR A:90 , TRP A:114 , GLU A:117BINDING SITE FOR RESIDUE D1D A 202
3AC3SOFTWAREALA B:30 , VAL B:31 , GLY B:32 , LYS B:33 , SER B:34 , SER B:35 , PHE B:45 , GLU B:47 , TYR B:48 , SER B:51 , ALA B:77 , ASN B:133 , LYS B:134 , ASP B:136 , LEU B:137 , SER B:163 , ALA B:164 , LYS B:165 , HOH B:310 , HOH B:315 , HOH B:338 , HOH B:360 , HOH B:361BINDING SITE FOR RESIDUE GDP B 301
4AC4SOFTWARETHR B:76 , GLN B:79 , GLU B:80 , HIS B:83 , ALA B:86 , TYR B:89 , TRP B:114 , GLU B:117BINDING SITE FOR RESIDUE D1D B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HEI)

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003602991ENSE00001517581chr12:56367862-5636792362RAB5B_HUMAN-00--
1.2aENST000003602992aENSE00001416149chr12:56380653-56380907255RAB5B_HUMAN1-55552A:18-55
B:17-55
38
39
1.3ENST000003602993ENSE00000938754chr12:56383731-56383882152RAB5B_HUMAN55-105512A:55-105 (gaps)
B:55-105 (gaps)
51
51
1.4ENST000003602994ENSE00000938756chr12:56384466-56384588123RAB5B_HUMAN106-146412A:106-146
B:106-146
41
41
1.5ENST000003602995ENSE00001607598chr12:56385144-5638523794RAB5B_HUMAN147-178322A:147-178
B:147-178
32
32
1.6bENST000003602996bENSE00001305108chr12:56385881-563884692589RAB5B_HUMAN178-215382A:178-183
B:178-183
6
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:163
 aligned with RAB5B_HUMAN | P61020 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:166
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177      
          RAB5B_HUMAN    18 ICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANKRMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPK 183
               SCOP domains d2heia_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains 2heiA00 A:18-183 P-loop containing nucleotide t   riphosphate hydrolases                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh..............eeeee..---.eeeeee.......hhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:18-55 UniProt: 1-55 --------------------------------------------------Exon 1.4  PDB: A:106-146 UniProt: 106-146Exon 1.5  PDB: A:147-178        ----- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.3  PDB: A:55-105 (gaps) UniProt: 55-105     ------------------------------------------------------------------------1.6b   Transcript 1 (2)
                 2hei A  18 ICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCL---TVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANKRMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPK 183
                                    27        37        47        57      |  -|       77        87        97       107       117       127       137       147       157       167       177      
                                                                         64  68                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with RAB5B_HUMAN | P61020 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:167
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       
          RAB5B_HUMAN    17 KICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANKRMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPK 183
               SCOP domains d2heib_ B: automated matches                                                                                                                                            SCOP domains
               CATH domains 2heiB00 B:17-183 P-loop containing nucleotide tr  iphosphate hydrolases                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....hhhhhhhhhhhh..............eeeee..--.eeeeeeee......hhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:17-55 UniProt: 1-55  --------------------------------------------------Exon 1.4  PDB: B:106-146 UniProt: 106-146Exon 1.5  PDB: B:147-178        ----- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.3  PDB: B:55-105 (gaps) UniProt: 55-105     ------------------------------------------------------------------------1.6b   Transcript 1 (2)
                 2hei B  17 KICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCL--TTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANKRMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPK 183
                                    26        36        46        56       | -|       76        86        96       106       116       126       136       146       156       166       176       
                                                                          64 67                                                                                                                    

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RAB5B_HUMAN | P61020)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0030742    GTP-dependent 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) using energy from the hydrolysis of GTP.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0007032    endosome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.
    GO:0048227    plasma membrane to endosome transport    Transport of a vesicle from the plasma membrane to the endosome.
    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:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    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: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:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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: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:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    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.

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