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(-) Description

Title :  GPPNHP-BOUND RAB21 GTPASE AT 2.05 A RESOLUTION
 
Authors :  S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright
Date :  28 Feb 05  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rab Gtpase, Rab21, Vesicular Trafficking, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eathiraj, X. Pan, C. Ritacco, D. G. Lambright
Structural Basis Of Family-Wide Rab Gtpase Recognition By Rabenosyn-5.
Nature V. 436 415 2005
PubMed-ID: 16034420  |  Reference-DOI: 10.1038/NATURE03798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAB-21
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T1
    Expression System Strain: BL21 (DE3) CODON PLUS-RIL CELLS
    Expression System Taxid: 562
    Expression System Vector Type: GST FUSION, PGEX
    Gene: RAB21, KIAA0118
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:33 , THR A:51 , GNP A:701 , HOH A:704 , HOH A:716BINDING SITE FOR RESIDUE MG A 700
2AC2SOFTWARETHR B:33 , THR B:51 , GNP B:801 , HOH B:803 , HOH B:870BINDING SITE FOR RESIDUE MG B 800
3AC3SOFTWAREGLY A:28 , GLY A:31 , LYS A:32 , THR A:33 , SER A:34 , PHE A:44 , ASN A:45 , ASP A:46 , HIS A:48 , THR A:50 , THR A:51 , GLY A:77 , ASN A:132 , LYS A:133 , ASP A:135 , LEU A:136 , SER A:162 , ALA A:163 , LYS A:164 , MG A:700 , HOH A:704 , HOH A:711 , HOH A:716 , HOH A:731 , HOH A:750 , HOH A:771 , HOH A:907BINDING SITE FOR RESIDUE GNP A 701
4AC4SOFTWAREGLY B:28 , CYS B:29 , GLY B:31 , LYS B:32 , THR B:33 , SER B:34 , PHE B:44 , ASN B:45 , ASP B:46 , HIS B:48 , THR B:50 , THR B:51 , ASN B:132 , LYS B:133 , ASP B:135 , LEU B:136 , SER B:162 , ALA B:163 , LYS B:164 , MG B:800 , HOH B:803 , HOH B:808 , HOH B:813 , HOH B:830 , HOH B:846 , HOH B:870 , HOH B:898BINDING SITE FOR RESIDUE GNP B 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YZT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YZT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YZT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YZT)

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002612631ENSE00001194681chr12:72148658-72149068411RAB21_HUMAN1-53532A:17-53
B:17-53
37
37
1.2ENST000002612632ENSE00001098832chr12:72163580-7216363960RAB21_HUMAN54-73202A:54-73
B:54-73
20
20
1.3ENST000002612633ENSE00001098835chr12:72164372-72164479108RAB21_HUMAN74-109362A:74-109 (gaps)
B:74-109 (gaps)
36
36
1.4ENST000002612634ENSE00001098834chr12:72167739-7216780264RAB21_HUMAN110-131222A:110-131
B:110-131
22
22
1.5ENST000002612635ENSE00001098836chr12:72175811-7217586555RAB21_HUMAN131-149192A:131-149
B:131-149
19
19
1.6ENST000002612636ENSE00001098837chr12:72176350-7217643889RAB21_HUMAN149-179312A:149-179
B:149-179
31
31
1.7ENST000002612637ENSE00001431792chr12:72179311-721811501840RAB21_HUMAN179-225472A:179-183
B:179-183
5
5

(-) 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:155
 aligned with RAB21_HUMAN | Q9UL25 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:167
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       
          RAB21_HUMAN    17 AYSFKVVLLGEGCVGKTSLVLRYCENKFNDKHITTLQASFLTKKLNIGGKRVNLAIWDTAGQERFHALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRMIET 183
               SCOP domains d1yzta1 A:17-183 Rab21                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh............eeeeeeeee..eeeeeeeee...------------....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhheeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:17-53 UniProt: 1-53 Exon 1.2            Exon 1.3  PDB: A:74-109 (gaps)      Exon 1.4              -----------------Exon 1.6  PDB: A:149-179       ---- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------Exon 1.5           -----------------------------1.7   Transcript 1 (2)
                 1yzt A  17 AYSFKVVLLGEGCVGKTSLVLRYCENKFNDKHITTLQASFLTKKLNIGGKRVNLAIWDTAG------------RDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRMIET 183
                                    26        36        46        56        66        76|        -   |    96       106       116       126       136       146       156       166       176       
                                                                                       77           90                                                                                             

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with RAB21_HUMAN | Q9UL25 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:167
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       
          RAB21_HUMAN    17 AYSFKVVLLGEGCVGKTSLVLRYCENKFNDKHITTLQASFLTKKLNIGGKRVNLAIWDTAGQERFHALGPIYYRDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRMIET 183
               SCOP domains d1yztb_ B: automated matches                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Ras-1yztB01 B:21-182                                                                                                                                              - Pfam domains (1)
           Pfam domains (2) ----Ras-1yztB02 B:21-182                                                                                                                                              - Pfam domains (2)
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh............eeeeeeeee..eeeeeeeee..-------------....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhheeeeeee.hhhhhhh..hhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:17-53 UniProt: 1-53 Exon 1.2            Exon 1.3  PDB: B:74-109 (gaps)      Exon 1.4              -----------------Exon 1.6  PDB: B:149-179       ---- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------Exon 1.5           -----------------------------1.7   Transcript 1 (2)
                 1yzt B  17 AYSFKVVLLGEGCVGKTSLVLRYCENKFNDKHITTLQASFLTKKLNIGGKRVNLAIWDTA-------------RDSNGAILVYDITDEDSFQKVKNWVKELRKMLGNEICLCIVGNKIDLEKERHVSIQEAESYAESVGAKHYHTSAKQNKGIEELFLDLCKRMIET 183
                                    26        36        46        56        66        76         -   |    96       106       116       126       136       146       156       166       176       
                                                                                      76            90                                                                                             

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YZT)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: Ras (176)
1aRas-1yztB01B:21-182
1bRas-1yztB02B:21-182

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,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: 1yzu 1z08 1z0i 2ot3

(-) Related Entries Specified in the PDB File

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