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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYTOSOLIC DOMAIN OF HUMAN ATLASTIN-1 IN COMPLEX WITH GDP, HEXAGONAL FORM
 
Authors :  X. Liu
Date :  09 Feb 11  (Deposition) - 02 Mar 11  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Gtpase, Homotypic Fusion, Ras-Like Gtpase, Membrane Fusion, Gdp, Gtp, Endopalsmic Reticulum, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Bian, R. W. Klemm, T. Y. Liu, M. Zhang, S. Sun, X. Sui, X. Liu, T. A. Rapoport, J. Hu
Structures Of The Atlastin Gtpase Provide Insight Into Homotypic Fusion Of Endoplasmic Reticulum Membranes.
Proc. Natl. Acad. Sci. Usa V. 108 3976 2011
PubMed-ID: 21368113  |  Reference-DOI: 10.1073/PNAS.1101643108

(-) Compounds

Molecule 1 - ATLASTIN-1
    ChainsA
    EC Number3.6.5.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentATLASTIN ECTO-DOMAIN (UNP RESIDUES 18-447)
    GeneATL1, GBP3, SPG3A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBRAIN-SPECIFIC GTP-BINDING PROTEIN, GTP-BINDING PROTEIN 3, GBP-3, HGBP3, GUANINE NUCLEOTIDE-BINDING PROTEIN 3, SPASTIC PARAPLEGIA 3 PROTEIN A

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:76 , ARG A:77 , LYS A:78 , GLY A:79 , LYS A:80 , SER A:81 , PHE A:82 , ARG A:113 , ARG A:217 , ASP A:218 , PRO A:272 , VAL A:276 , ASN A:279 , PRO A:280 , HOH A:448 , HOH A:452 , HOH A:459 , MG A:599BINDING SITE FOR RESIDUE GDP A 593
2AC2SOFTWARESER A:81 , GDP A:593BINDING SITE FOR RESIDUE MG A 599

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QNU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (18, 18)

Asymmetric Unit (18, 18)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_058963D43EATLA1_HUMANPolymorphism17850684AD43E
02UniProtVAR_065508E66QATLA1_HUMANDisease (HSN1D)200314808AE66Q
03UniProtVAR_071874R118QATLA1_HUMANDisease (SPG3)606231265AR118Q
04UniProtVAR_067655Q154EATLA1_HUMANDisease (SPG3)  ---AQ154E
05UniProtVAR_065509L157WATLA1_HUMANDisease (SPG3)119476051AL157W
06UniProtVAR_019446A161PATLA1_HUMANDisease (SPG3)  ---AA161P
07UniProtVAR_058964F193CATLA1_HUMANPolymorphism17850683AF193C
08UniProtVAR_067656Y196CATLA1_HUMANUnclassified  ---AY196C
09UniProtVAR_017146R217QATLA1_HUMANDisease (SPG3)119476049AR217Q
10UniProtVAR_017147R239CATLA1_HUMANDisease (SPG3)119476046AR239C
11UniProtVAR_017148H258RATLA1_HUMANDisease (SPG3)119476048AH258R
12UniProtVAR_017149S259YATLA1_HUMANDisease (SPG3)119476047AS259Y
13UniProtVAR_065510N355KATLA1_HUMANDisease (HSN1D)  ---AN355K
14UniProtVAR_065511M408VATLA1_HUMANDisease (SPG3)28939094AM408V
15UniProtVAR_067658F413VATLA1_HUMANDisease (SPG3)  ---AF413V
16UniProtVAR_071708R415QATLA1_HUMANDisease (SPG3)397514712AR415Q
17UniProtVAR_065512R415WATLA1_HUMANDisease (SPG3)119476050AR415W
18UniProtVAR_071709R416CATLA1_HUMANDisease (SPG3)387906941AR416C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (18, 36)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_058963D43EATLA1_HUMANPolymorphism17850684AD43E
02UniProtVAR_065508E66QATLA1_HUMANDisease (HSN1D)200314808AE66Q
03UniProtVAR_071874R118QATLA1_HUMANDisease (SPG3)606231265AR118Q
04UniProtVAR_067655Q154EATLA1_HUMANDisease (SPG3)  ---AQ154E
05UniProtVAR_065509L157WATLA1_HUMANDisease (SPG3)119476051AL157W
06UniProtVAR_019446A161PATLA1_HUMANDisease (SPG3)  ---AA161P
07UniProtVAR_058964F193CATLA1_HUMANPolymorphism17850683AF193C
08UniProtVAR_067656Y196CATLA1_HUMANUnclassified  ---AY196C
09UniProtVAR_017146R217QATLA1_HUMANDisease (SPG3)119476049AR217Q
10UniProtVAR_017147R239CATLA1_HUMANDisease (SPG3)119476046AR239C
11UniProtVAR_017148H258RATLA1_HUMANDisease (SPG3)119476048AH258R
12UniProtVAR_017149S259YATLA1_HUMANDisease (SPG3)119476047AS259Y
13UniProtVAR_065510N355KATLA1_HUMANDisease (HSN1D)  ---AN355K
14UniProtVAR_065511M408VATLA1_HUMANDisease (SPG3)28939094AM408V
15UniProtVAR_067658F413VATLA1_HUMANDisease (SPG3)  ---AF413V
16UniProtVAR_071708R415QATLA1_HUMANDisease (SPG3)397514712AR415Q
17UniProtVAR_065512R415WATLA1_HUMANDisease (SPG3)119476050AR415W
18UniProtVAR_071709R416CATLA1_HUMANDisease (SPG3)387906941AR416C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GB1_RHD3PS51715 GB1/RHD3-type guanine nucleotide-binding (G) domain profile.ATLA1_HUMAN64-309  1A:64-309
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GB1_RHD3PS51715 GB1/RHD3-type guanine nucleotide-binding (G) domain profile.ATLA1_HUMAN64-309  2A:64-309

(-) Exons   (0, 0)

(no "Exon" information available for 3QNU)

(-) 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:395
 aligned with ATLA1_HUMAN | Q8WXF7 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:404
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
          ATLA1_HUMAN    31 KAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLMDFMLRYMYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSMLQATAEANNLAAVATAKDTYNKKMEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKMGGEEFSRRYLQQLESEIDELYIQYIK 434
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------GBP-3qnuA01 A:43-314                                                                                                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.........hhhhhhhhhh........eeeeeeeee...hhhhhhhhhhhhhhh............................eeeee...eeee.....eeeeeeeeeee...hhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhh........eeeeeeeeeee........hhhhhhhhhhhhhh...---------..hhhhheeeeeeeeee..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
             SAPs(SNPs) (1) ------------E----------------------Q---------------------------------------------------Q-----------------------------------E--W---P-------------------------------C--C--------------------Q---------------------C------------------RY-----------------------------------------------------------------------------------------------K----------------------------------------------------V----V-QC------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------G_GB1_RHD3  PDB: A:64-309 UniProt: 64-309                                                                                                                                                                                                             ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnu A  31 KAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLMDFMLRYMYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSG---------RKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSMLQATAEANNLAAVATAKDTYNKKMEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKMGGEEFSRRYLQQLESEIDELYIQYIK 434
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   |     -   |   260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430    
                                                                                                                                                                                                                                               244       254                                                                                                                                                                                    

   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  (0, 0)

(no "SCOP Domain" information available for 3QNU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (ATLA1_HUMAN | Q8WXF7)
molecular function
    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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0007029    endoplasmic reticulum organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
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:0000137    Golgi cis cisterna    The Golgi cisterna closest to the endoplasmic reticulum; the first processing compartment through which proteins pass after export from the ER.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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        ATLA1_HUMAN | Q8WXF73q5d 3q5e 3qof 4idn 4ido 4idp 4idq

(-) Related Entries Specified in the PDB File

3qof