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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS ACD11 (ACCELERATED-CELL-DEATH 11) COMPLEXED WITH LYSO-SPHINGOMYELIN (D18:1) AT 2.4 ANGSTROM RESOLUTION
 
Authors :  D. K. Simanshu, R. E. Brown, D. J. Patel
Date :  29 Nov 13  (Deposition) - 05 Feb 14  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Lipid Complexes, Gltp-Fold, Lipid Transfer Protein, Cell Death, Lysosm, Lysosphingomyelin, Ceramide-1-Phosphate, C1P, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Simanshu, X. Zhai, D. Munch, D. Hofius, J. E. Markham, J. Bielawski, A. Bielawska, L. Malinina, J. G. Molotkovsky, J. W. Mundy, D. J. Patel, R. E. Brown
Arabidopsis Accelerated Cell Death 11, Acd11, Is A Ceramide-1-Phosphate Transfer Protein And Intermediary Regulator Of Phytoceramide Levels.
Cell Rep V. 6 388 2014
PubMed-ID: 24412362  |  Reference-DOI: 10.1016/J.CELREP.2013.12.023

(-) Compounds

Molecule 1 - ACCELERATED-CELL-DEATH 11
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ACD11, AT2G34690
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: GLYCOLIPID TRANSFER PROTEIN, AT2G34690

 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
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SO45Ligand/IonSULFATE ION
3SPU2Ligand/Ion2-{[(R)-{[(2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YL]OXY}(HYDROXY)PHOSPHORYL]OXY}-N,N,N-TRIMETHYLETHANAMINIUM

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:60 , HIS A:143 , GLY A:144 , ILE A:147 , LEU A:153 , SPU A:302 , SO4 A:307 , HOH A:426BINDING SITE FOR RESIDUE SPU A 301
2AC2SOFTWARETRP A:145 , ILE A:147 , LYS A:149 , TYR A:156 , SPU A:301 , SO4 A:304 , SO4 A:307BINDING SITE FOR RESIDUE SPU A 302
3AC3SOFTWARELYS A:64 , ARG A:99 , ARG A:103 , HOH A:475BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREARG A:148 , LYS A:149 , SPU A:302BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWARESER A:181 , ASN A:184BINDING SITE FOR RESIDUE SO4 A 305
6AC6SOFTWAREARG A:11BINDING SITE FOR RESIDUE SO4 A 306
7AC7SOFTWARETRP A:145 , ARG A:148 , SPU A:301 , SPU A:302BINDING SITE FOR RESIDUE SO4 A 307
8AC8SOFTWAREILE A:52 , ALA A:53 , PHE A:54 , LYS A:55 , PHE A:56 , VAL A:151BINDING SITE FOR RESIDUE EDO A 308
9AC9SOFTWAREVAL A:79 , ASP A:83 , LEU A:196 , LYS A:200BINDING SITE FOR RESIDUE EDO A 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NT2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NT2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NT2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NT2)

(-) Exons   (0, 0)

(no "Exon" information available for 4NT2)

(-) 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:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt2 A   7 DKPLRKISAAFKKLAIIVNSPNPEVPVTQFSHACSLVSPLFGCLGIAFKFAEMDYVAKVDDLVRASSSISTLVVMMDKDIEADCVRKAGSHTRNLLRVKRGLDMVKVLFEQIIASEGDNSLKDPATKSYAQVFAPHHGWAIRKAVSLGMYALPTRAHLLNMLKEDEAAAKIHMQSYVNSSAPLITYLDNLFLSKQLGIDW 206
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4NT2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NT2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NT2)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACD11_ARATH | O64587: 4nt1 4ntg 4nti 4nto

(-) Related Entries Specified in the PDB File

4nt1 4ntg 4nti 4nto