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(-) Description

Title :  CRYSTAL STRUCTURE OF APO-FORM OF ARABIDOPSIS ACD11 (ACCELERATED-CELL-DEATH 11) AT 1.8 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 :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Protein-Lipid Complexes, Gltp-Fold, Lipid Transfer Protein, Cell Death, Ceramide-1-Phosphate, C1P, Lysine Carboxylation, 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, B, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2NA-1Ligand/IonSODIUM ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:34 , SER A:72 , ILE A:75 , HOH A:401 , HOH A:508BINDING SITE FOR RESIDUE NA A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NT1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NT1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NT1)

(-) Exons   (0, 0)

(no "Exon" information available for 4NT1)

(-) 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    
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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 .hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt1 A   7 DKPLRKISAAFKKLAIIVNSPNPEVPVTQFSHACSLVSPLFGCLGIAFKFAEMDYVAkVDDLVRASSSISTLVVMMDKDIEADCVRKAGSHTRNLLRVKRGLDMVKVLFEQIIASEGDNSLKDPATKSYAQVFAPHHGWAIRKAVSLGMYALPTRAHLLNMLKEDEAAAKIHMQSYVNSSAPLITYLDNLFLSKQLGIDW 206
                                    16        26        36        46        56       |66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
                                                                                    64-KCX                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt1 B   7 DKPLRKISAAFKKLAIIVNSPNPEVPVTQFSHACSLVSPLFGCLGIAFKFAEMDYVAkVDDLVRASSSISTLVVMMDKDIEADCVRKAGSHTRNLLRVKRGLDMVKVLFEQIIASEGDNSLKDPATKSYAQVFAPHHGWAIRKAVSLGMYALPTRAHLLNMLKEDEAAAKIHMQSYVNSSAPLITYLDNLFLSKQLGIDW 206
                                    16        26        36        46        56       |66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
                                                                                    64-KCX                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt1 C   7 DKPLRKISAAFKKLAIIVNSPNPEVPVTQFSHACSLVSPLFGCLGIAFKFAEMDYVAkVDDLVRASSSISTLVVMMDKDIEADCVRKAGSHTRNLLRVKRGLDMVKVLFEQIIASEGDNSLKDPATKSYAQVFAPHHGWAIRKAVSLGMYALPTRAHLLNMLKEDEAAAKIHMQSYVNSSAPLITYLDNLFLSKQLGIDW 206
                                    16        26        36        46        56       |66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
                                                                                    64-KCX                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nt1 D   6 ADKPLRKISAAFKKLAIIVNSPNPEVPVTQFSHACSLVSPLFGCLGIAFKFAEMDYVAkVDDLVRASSSISTLVVMMDKDIEADCVRKAGSHTRNLLRVKRGLDMVKVLFEQIIASEGDNSLKDPATKSYAQVFAPHHGWAIRKAVSLGMYALPTRAHLLNMLKEDEAAAKIHMQSYVNSSAPLITYLDNLFLSK 200
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195     
                                                                                     64-KCX
   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 4NT1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NT1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NT1)

(-) Gene Ontology  (15, 15)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACD11_ARATH | O64587: 4nt2 4ntg 4nti 4nto

(-) Related Entries Specified in the PDB File

4nt2 4ntg 4nti 4nto