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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ATLASTIN-1 (RESIDUES 1-447) BOUND TO GDP, CRYSTAL FORM 1
 
Authors :  L. J. Byrnes, H. Sondermann
Date :  28 Dec 10  (Deposition) - 19 Jan 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  G Protein, Gtpase, Gdp/Gtp Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Byrnes, H. Sondermann
Structural Basis For The Nucleotide-Dependent Dimerization Of The Large G Protein Atlastin-1/Spg3A.
Proc. Natl. Acad. Sci. Usa V. 108 2216 2011
PubMed-ID: 21220294  |  Reference-DOI: 10.1073/PNAS.1012792108

(-) Compounds

Molecule 1 - ATLASTIN-1
    ChainsA
    EC Number3.6.5.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentG AND MIDDLE DOMAIN, UNP RESIDUES 1-447
    GeneATL1, ATLASTIN-1 (RESIDUES 1-447), 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 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 20)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:77 , LYS A:78 , GLY A:79 , LYS A:80 , SER A:81 , PHE A:82 , GLN A:148 , ARG A:217 , ASP A:218 , HIS A:271 , PRO A:272 , VAL A:276 , ASN A:279 , PRO A:280 , MG A:448 , HOH A:449BINDING SITE FOR RESIDUE GDP A 3850
2AC2SOFTWARESER A:81 , GLU A:117 , GDP A:3850BINDING SITE FOR RESIDUE MG A 448

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q5D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:243 -Gly A:244
2Gly A:244 -Asn A:245
3Gln A:246 -His A:247
4Gly A:376 -Gly A:377

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (20, 20)

Asymmetric Unit (20, 20)
  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_019447H247PATLA1_HUMANDisease (SPG3)  ---AH247P
12UniProtVAR_067657V253IATLA1_HUMANDisease (SPG3)864622520AV253I
13UniProtVAR_017148H258RATLA1_HUMANDisease (SPG3)119476048AH258R
14UniProtVAR_017149S259YATLA1_HUMANDisease (SPG3)119476047AS259Y
15UniProtVAR_065510N355KATLA1_HUMANDisease (HSN1D)  ---AN355K
16UniProtVAR_065511M408VATLA1_HUMANDisease (SPG3)28939094AM408V
17UniProtVAR_067658F413VATLA1_HUMANDisease (SPG3)  ---AF413V
18UniProtVAR_071708R415QATLA1_HUMANDisease (SPG3)397514712AR415Q
19UniProtVAR_065512R415WATLA1_HUMANDisease (SPG3)119476050AR415W
20UniProtVAR_071709R416CATLA1_HUMANDisease (SPG3)387906941AR416C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (20, 20)
  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_019447H247PATLA1_HUMANDisease (SPG3)  ---AH247P
12UniProtVAR_067657V253IATLA1_HUMANDisease (SPG3)864622520AV253I
13UniProtVAR_017148H258RATLA1_HUMANDisease (SPG3)119476048AH258R
14UniProtVAR_017149S259YATLA1_HUMANDisease (SPG3)119476047AS259Y
15UniProtVAR_065510N355KATLA1_HUMANDisease (HSN1D)  ---AN355K
16UniProtVAR_065511M408VATLA1_HUMANDisease (SPG3)28939094AM408V
17UniProtVAR_067658F413VATLA1_HUMANDisease (SPG3)  ---AF413V
18UniProtVAR_071708R415QATLA1_HUMANDisease (SPG3)397514712AR415Q
19UniProtVAR_065512R415WATLA1_HUMANDisease (SPG3)119476050AR415W
20UniProtVAR_071709R416CATLA1_HUMANDisease (SPG3)387906941AR416C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (20, 40)
  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_019447H247PATLA1_HUMANDisease (SPG3)  ---AH247P
12UniProtVAR_067657V253IATLA1_HUMANDisease (SPG3)864622520AV253I
13UniProtVAR_017148H258RATLA1_HUMANDisease (SPG3)119476048AH258R
14UniProtVAR_017149S259YATLA1_HUMANDisease (SPG3)119476047AS259Y
15UniProtVAR_065510N355KATLA1_HUMANDisease (HSN1D)  ---AN355K
16UniProtVAR_065511M408VATLA1_HUMANDisease (SPG3)28939094AM408V
17UniProtVAR_067658F413VATLA1_HUMANDisease (SPG3)  ---AF413V
18UniProtVAR_071708R415QATLA1_HUMANDisease (SPG3)397514712AR415Q
19UniProtVAR_065512R415WATLA1_HUMANDisease (SPG3)119476050AR415W
20UniProtVAR_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, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_GB1_RHD3PS51715 GB1/RHD3-type guanine nucleotide-binding (G) domain profile.ATLA1_HUMAN64-309  1A:64-309
Biological Unit 2 (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 3Q5D)

(-) 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:410
 aligned with ATLA1_HUMAN | Q8WXF7 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:410
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438
          ATLA1_HUMAN    29 VKKAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLMDFMLRYMYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSMLQATAEANNLAAVATAKDTYNKKMEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKMGGEEFSRRYLQQLESEIDELYIQYIKHNDS 438
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------GBP-3q5dA01 A:43-314                                                                                                                                                                                                                                                            ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.....eeehhhhhhhhhh........eeeeeeee....hhhhhhhhhhhhhhh............................eeeee...eeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhh........eeeeeeeeeee........hhhhhhhhhhhhhhh.........hhhhhhhhheeeeeeeeee..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --------------E----------------------Q---------------------------------------------------Q-----------------------------------E--W---P-------------------------------C--C--------------------Q---------------------C-------P-----I----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
                 3q5d A  29 VKKAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLmDFmLRYmYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLmDTQGTFDSQSTLRDSATVFALSTmISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAmEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSmLQATAEANNLAAVATAKDTYNKKmEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKmGGEEFSRRYLQQLESEIDELYIQYIKHNDS 438
                                    38        48        58        68        78     |  88  |     98       108       118       128       138      |148       158       168|      178       188       198  |    208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368  |    378       388       398       408       418       428       438
                                                                                  84-MSE  |                                                   145-MSE                 169-MSE                         201-MSE                                                                                                                                           347-MSE                 371-MSE                              408-MSE                          
                                                                                     87-MSE                                                                                                                                                                                                                                                                                                                                                           
                                                                                         91-MSE                                                                                                                                                                                                                                                                                                                                                       

   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 3Q5D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q5D)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        ATLA1_HUMAN | Q8WXF73q5e 3qnu 3qof 4idn 4ido 4idp 4idq

(-) Related Entries Specified in the PDB File

3q5e