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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RAB9B IN COMPLEX WITH A GTP ANALOGUE
 
Authors :  B. Hong, L. Shen, J. R. Walker, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  20 Dec 06  (Deposition) - 02 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  G-Protein, Rab, Gtpase, Gtp Analogue, Structural Genomics, Structural Genomics Consortium, Sgc, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Hong, L. Shen, J. R. Walker, W. Tempel, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of Human Rab9B In Complex With A Gtp Analogue
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-9B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28ALIC
    Expression System Strain: BL21(DE3)CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RAB9B, RAB9L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAB-9L, RAB9-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3UNX7Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:21 , THR A:39 , GNP A:201 , HOH A:302 , HOH A:303BINDING SITE FOR RESIDUE MG A 202
2AC2SOFTWAREGLY A:16 , GLY A:17 , VAL A:18 , GLY A:19 , LYS A:20 , SER A:21 , SER A:22 , PHE A:32 , ASP A:33 , SER A:34 , ALA A:36 , HIS A:38 , THR A:39 , GLY A:65 , ASN A:124 , LYS A:125 , ASP A:127 , LYS A:128 , SER A:154 , ALA A:155 , LYS A:156 , MG A:202 , HOH A:302 , HOH A:303 , HOH A:304 , HOH A:318 , HOH A:334BINDING SITE FOR RESIDUE GNP A 201
3AC3SOFTWARETYR A:107BINDING SITE FOR RESIDUE UNX A 1001
4AC4SOFTWAREVAL A:126 , ASP A:157 , THR A:159BINDING SITE FOR RESIDUE UNX A 1002
5AC5SOFTWARETHR A:134 , GLU A:136BINDING SITE FOR RESIDUE UNX A 1003
6AC6SOFTWAREASN A:160 , VAL A:163 , HOH A:332BINDING SITE FOR RESIDUE UNX A 1004
7AC7SOFTWAREARG A:68BINDING SITE FOR RESIDUE UNX A 1005
8AC8SOFTWAREGLU A:104BINDING SITE FOR RESIDUE UNX A 1006
9AC9SOFTWAREGLU A:43 , PHE A:44 , MET A:143 , ASP A:147BINDING SITE FOR RESIDUE UNX A 1007

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002432981ENSE00001105684X:103087158-103086990169RAB9B_HUMAN-00--
1.2ENST000002432982ENSE00001105686X:103082008-10308193574RAB9B_HUMAN-00--
1.3ENST000002432983ENSE00000840323X:103080756-1030772523505RAB9B_HUMAN1-2152151A:3-175173

(-) 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:173
 aligned with RAB9B_HUMAN | Q9NP90 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   
          RAB9B_HUMAN     3 GKSLLLKVILLGDGGVGKSSLMNRYVTNKFDSQAFHTIGVEFLNRDLEVDGRFVTLQIWDTAGQERFKSLRTPFYRGADCCLLTFSVDDRQSFENLGNWQKEFIYYADVKDPEHFPFVVLGNKVDKEDRQVTTEEAQTWCMENGDYPYLETSAKDDTNVTVAFEEAVRQVLAV 175
               SCOP domains d2ocba_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Ras-2ocbA01 A:9-174                                                                                                                                                   - Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhh.........eeeeee.........hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: A:3-175 UniProt: 1-215 [INCOMPLETE]                                                                                                                            Transcript 1
                 2ocb A   3 GKSLLLKVILLGDGGVGKSSLMNRYVTNKFDSQAFHTIGVEFLNRDLEVDGRFVTLQIWDTAGQERFKSLRTPFYRGADCCLLTFSVDDRQSFENLGNWQKEFIYYADVKDPEHFPFVVLGNKVDKEDRQVTTEEAQTWCMENGDYPYLETSAKDDTNVTVAFEEAVRQVLAV 175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OCB)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: Ras (176)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RAB9B_HUMAN | Q9NP90)
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: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: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:0042147    retrograde transport, endosome to Golgi    The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
    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:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045335    phagocytic vesicle    A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    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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