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(-) Description

Title :  CRYSTAL STRUCTURE OF RABEX-5 VPS9 DOMAIN IN COMPLEX WITH NUCLEOTIDE FREE RAB21
 
Authors :  A. Delprato, D. Lambright
Date :  07 Feb 07  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rabex-5, Vps9 Domain, Rab21, Vesicular Traffic, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Delprato, D. G. Lambright
Structural Basis For Rab Gtpase Activation By Vps9 Domain Exchange Factors.
Nat. Struct. Mol. Biol. V. 14 406 2007
PubMed-ID: 17450153  |  Reference-DOI: 10.1038/NSMB1232
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAB5 GDP/GTP EXCHANGE FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 132-297
    Gene: RABGEF1, RABEX5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RABEX-5, RABAPTIN-5-ASSOCIATED EXCHANGE FACTOR FOR RAB5, RAP1
 
Molecule 2 - RAS-RELATED PROTEIN RAB-21
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 16-183
    Gene: RAB21, KIAA0118
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2OT3)

(-) Sites  (0, 0)

(no "Site" information available for 2OT3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OT3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OT3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OT3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS9PS51205 VPS9 domain profile.RABX5_HUMAN449-592  1A:232-375

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002612631ENSE00001194681chr12:72148658-72149068411RAB21_HUMAN1-53531B:17-53 (gaps)37
1.2ENST000002612632ENSE00001098832chr12:72163580-7216363960RAB21_HUMAN54-73201B:54-7320
1.3ENST000002612633ENSE00001098835chr12:72164372-72164479108RAB21_HUMAN74-109361B:74-10936
1.4ENST000002612634ENSE00001098834chr12:72167739-7216780264RAB21_HUMAN110-131221B:110-13122
1.5ENST000002612635ENSE00001098836chr12:72175811-7217586555RAB21_HUMAN131-149191B:131-14919
1.6ENST000002612636ENSE00001098837chr12:72176350-7217643889RAB21_HUMAN149-179311B:149-17931
1.7ENST000002612637ENSE00001431792chr12:72179311-721811501840RAB21_HUMAN179-225471B:179-1824

(-) 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:253
 aligned with RABX5_HUMAN | Q9UJ41 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:292
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606  
          RABX5_HUMAN   317 SKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQDFYHNVAERMQTRGKERRFHHVGQAGLELLTSGDPPASASQSAGNTGVEPPHPAVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKLDAQSLNLSQEDFDRYMSGQTSP 608
               SCOP domains d2ot3a_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------VPS9-2ot3A01 A:268-371                                                                                  -------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...hh.hhh.hhhhhhhh..........hhhhhhhhh.hhh........---------------------------------------........hhhhhhhhhhhhhh.hhh.....hhhhhhhhhh.hhhhhh..............hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------VPS9  PDB: A:232-375 UniProt: 449-592                                                                                                           ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ot3 A 139 SKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQDFYHNVAERMQTRGK---------------------------------------VPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAVAFIEKLDAQSLNLSQEDFDRYMSGQTSP 391
                                   148       158       168       178       188       198         -         -         -       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389  
                                                                                     198                                     199                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with RAB21_HUMAN | Q9UL25 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:166
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176      
          RAB21_HUMAN    17 AYSFKVVLLGEGCVGKTSLVLRYCENKFNDKHITTLQASFLTKKLNIGGKRVNLAIWDTAGQERFHALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRMIE 182
               SCOP domains d2ot3b1 B:17-182 Rab21                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Ras-2ot3B01 B:21-182                                                                                                                                               Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhh---------......eeee.........eeeeee...hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh.......eeeeeee..........hhhhhhhhh.....eeee..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:17-53 (gaps)        Exon 1.2            Exon 1.3  PDB: B:74-109             Exon 1.4              -----------------Exon 1.6  PDB: B:149-179       --- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------Exon 1.5           -----------------------------1.7  Transcript 1 (2)
                 2ot3 B  17 AYSFKVVLLGEGCVGKTSLVLRYC---------TTLQASFLTKKLNIGGKRVNLAIWDTAGQERFHALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRMIE 182
                                    26        36   |     -   |    56        66        76        86        96       106       116       126       136       146       156       166       176      
                                                  40        50
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OT3)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: Ras (176)
(-)
Clan: no clan defined [family: VPS9] (2)

(-) Gene Ontology  (57, 61)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RABX5_HUMAN | Q9UJ41)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0017112    Rab guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rab family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    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:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    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:1900235    negative regulation of Kit signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of Kit signaling pathway.
    GO:0046580    negative regulation of Ras protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:1900165    negative regulation of interleukin-6 secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interleukin-6 secretion.
    GO:0002686    negative regulation of leukocyte migration    Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte migration.
    GO:0033004    negative regulation of mast cell activation    Any process that stops, prevents, or reduces the frequency, rate, or extent of mast cell activation.
    GO:0043305    negative regulation of mast cell degranulation    Any process that stops, prevents, or reduces the rate of mast cell degranulation.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0048261    negative regulation of receptor-mediated endocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    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:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0060368    regulation of Fc receptor mediated stimulatory signaling pathway    Any process that modulates the rate, frequency or extent of the Fc receptor mediated stimulatory signaling pathway. The Fc receptor mediated stimulatory signaling pathway is a series of molecular signals generated as a consequence of a the binding of the Fc portion of an immunoglobulin by an Fc receptor capable of activating or perpetuating an immune response. The Fc portion of an immunoglobulin is its C-terminal constant region.
    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.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

Chain B   (RAB21_HUMAN | Q9UL25)
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: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:0008089    anterograde axonal transport    The directed movement of organelles or molecules along microtubules from the cell body toward the cell periphery in nerve cell axons.
    GO:0050775    positive regulation of dendrite morphogenesis    Any process that activates or increases the frequency, rate or extent of dendrite morphogenesis.
    GO:2000643    positive regulation of early endosome to late endosome transport    Any process that activates or increases the frequency, rate or extent of early endosome to late endosome transport.
    GO:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    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:0030516    regulation of axon extension    Any process that modulates the rate, direction or extent of axon extension.
    GO:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:1904115    axon cytoplasm    Any cytoplasm that is part of a axon.
    GO:0032154    cleavage furrow    The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
    GO:0098559    cytoplasmic side of early endosome membrane    The side (leaflet) of the early endosome membrane that faces the cytoplasm.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.
    GO:0012506    vesicle membrane    The lipid bilayer surrounding any membrane-bounded vesicle in the cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB21_HUMAN | Q9UL25: 1yzt 1yzu 1z08 1z0i
        RABX5_HUMAN | Q9UJ41: 1txu 2c7m 2c7n 4n3x 4n3y 4n3z 4q9u

(-) Related Entries Specified in the PDB File

1txu CRYSTAL STRUCTURE OF THE VPS9 DOMAIN OF RABEX-5
1z0i GDP-BOUND RAB21 GTPASE