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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE CERAMIDE-1-PHOSPHATE TRANSFER PROTEIN (APO-FORM)
 
Authors :  D. K. Simanshu, R. E. Brown, D. J. Patel
Date :  23 Apr 13  (Deposition) - 17 Jul 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Biol. Unit 9:  A,C  (1x)
Biol. Unit 10:  B,E  (1x)
Biol. Unit 11:  D (1x),G (1x)
Biol. Unit 12:  F (1x),H (1x)
Keywords :  Lipid Transfer Protein, Gltp-Fold, Cptp, C1P, Ceramide-1-Phosphate, Protein-Lipid Complex, Eicosanoid, Lipid Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Simanshu, R. K. Kamlekar, D. S. Wijesinghe, X. Zou, X. Zhai, S. K. Mishra, J. G. Molotkovsky, L. Malinina, E. H. Hinchcliffe, C. E. Chalfant, R. E. Brown, D. J. Patel
Non-Vesicular Trafficking By A Ceramide-1-Phosphate Transfe Protein Regulates Eicosanoids.
Nature V. 500 463 2013
PubMed-ID: 23863933  |  Reference-DOI: 10.1038/NATURE12332

(-) Compounds

Molecule 1 - GLYCOLIPID TRANSFER PROTEIN DOMAIN-CONTAINING PROTEIN 1
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: BL21(DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GLTPD1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A       
Biological Unit 2 (1x):  B      
Biological Unit 3 (1x):   C     
Biological Unit 4 (1x):    D    
Biological Unit 5 (1x):     E   
Biological Unit 6 (1x):      F  
Biological Unit 7 (1x):       G 
Biological Unit 8 (1x):        H
Biological Unit 9 (1x): A C     
Biological Unit 10 (1x):  B  E   
Biological Unit 11 (1x):    D (1x)  G (1x) 
Biological Unit 12 (1x):      F (1x) H (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1PO48Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 7 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 8 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 9 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 10 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
Biological Unit 11 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 12 (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:60 , ARG A:108BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWARELYS B:60 , ARG B:108 , ARG B:112BINDING SITE FOR RESIDUE PO4 B 301
3AC3SOFTWARELYS C:60 , ARG C:108 , ARG C:112BINDING SITE FOR RESIDUE PO4 C 301
4AC4SOFTWARELYS D:60 , ARG D:108 , ARG D:112BINDING SITE FOR RESIDUE PO4 D 301
5AC5SOFTWAREARG E:108 , ARG E:112BINDING SITE FOR RESIDUE PO4 E 301
6AC6SOFTWARELYS F:60 , ARG F:108 , ARG F:112BINDING SITE FOR RESIDUE PO4 F 301
7AC7SOFTWARELYS G:60 , ARG G:108 , ARG G:112BINDING SITE FOR RESIDUE PO4 G 301
8AC8SOFTWARELYS H:60 , ARG H:108 , ARG H:112BINDING SITE FOR RESIDUE PO4 H 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KBR)

(-) 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:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbr A   8 FNLKVVLVSFKQCLTDKGEVLLDHYIAGWKGLVRFLNSLGAVFSFISKDVVAKLQIMERLRSSPQSEHYTSLQSMVAYEVSNKLVDMDHPRHPHSGCRTVLRLHRALHWLQLFLDGLRTSSEDARTSTLCSEAYNATLANYHSWIVRQAVTVAFCALPSRKVFLEAMNMESTEQAVEMLGEALPFIEHVYDISQKLYAEHSLLDLP 216
                                    17        27        37        47        57        67        77        87       100       110       120       130       140       150       160       170       180       190       200       210      
                                                                                                                   96|                                                                                                                    
                                                                                                                   100                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbr B   8 FNLKVVLVSFKQCLTDKGEVLLDHYIAGWKGLVRFLNSLGAVFSFISKDVVAKLQIMERLRSSPQSEHYTSLQSMVAYEVSNKLVDMDHHPRHPHSGCRTVLRLHRALHWLQLFLDGLRTSSEDARTSTLCSEAYNATLANYHSWIVRQAVTVAFCALPSRKVFLEAMNMESTEQAVEMLGEALPFIEHVYDISQKLYAEHSLLDLP 216
                                    17        27        37        47        57        67        77        87        99       109       119       129       139       149       159       169       179       189       199       209       
                                                                                                                   96|                                                                                                                     
                                                                                                                    99                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbr C   8 FNLKVVLVSFKQCLTDKGEVLLDHYIAGWKGLVRFLNSLGAVFSFISKDVVAKLQIMERLRSSPQSEHYTSLQSMVAYEVSNKLVDMDHRHPHSGCRTVLRLHRALHWLQLFLDGLRTSSEDARTSTLCSEAYNATLANYHSWIVRQAVTVAFCALPSRKVFLEAMNMESTEQAVEMLGEALPFIEHVYDISQKLYAEHSLLDLP 216
                                    17        27        37        47        57        67        77        87       101       111       121       131       141       151       161       171       181       191       201       211     
                                                                                                                   96|                                                                                                                   
                                                                                                                   101                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbr D   8 FNLKVVLVSFKQCLTDKGEVLLDHYIAGWKGLVRFLNSLGAVFSFISKDVVAKLQIMERLRSSPQSEHYTSLQSMVAYEVSNKLVDMDHPRHPHSGCRTVLRLHRALHWLQLFLDGLRTSSTSTLCSEAYNATLANYHSWIVRQAVTVAFCALPSRKVFLEAMNMESTEQAVEMLGEALPFIEHVYDISQKLYAEHSLLDLP 216
                                    17        27        37        47        57        67        77        87       100       110       120       130||     144       154       164       174       184       194       204       214  
                                                                                                                   96|                            131|                                                                                
                                                                                                                   100                             136                                                                                


Chain E from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbr E   8 FNLKVVLVSFKQCLTDKGEVLLDHYIAGWKGLVRFLNSLGAVFSFISKDVVAKLQIMERLRSSPQSEHYTSLQSMVAYEVSNKLVDMDHHPRHPHSGCRTVLRLHRALHWLQLFLDGLRTSSEDARTSTLCSEAYNATLANYHSWIVRQAVTVAFCALPSRKVFLEAMNMESTEQAVEMLGEALPFIEHVYDISQKLYAEHSLLDLP 216
                                    17        27        37        47        57        67        77        87        99       109       119       129       139       149       159       169       179       189       199       209       
                                                                                                                   96|                                                                                                                     
                                                                                                                    99                                                                                                                     


Chain F from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbr F   8 FNLKVVLVSFKQCLTDKGEVLLDHYIAGWKGLVRFLNSLGAVFSFISKDVVAKLQIMERLRSSPQSEHYTSLQSMVAYEVSNKLVDMDHHPHSGCRTVLRLHRALHWLQLFLDGLRTSSERTSTLCSEAYNATLANYHSWIVRQAVTVAFCALPSRKVFLEAMNMESTEQAVEMLGEALPFIEHVYDISQKLYAEHSLLDLP 216
                                    17        27        37        47        57        67        77        87       102       112       122       132|      144       154       164       174       184       194       204       214  
                                                                                                                   96|                           132|                                                                                 
                                                                                                                   102                            135                                                                                 


Chain G from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbr G   7 DFNLKVVLVSFKQCLTDKGEVLLDHYIAGWKGLVRFLNSLGAVFSFISKDVVAKLQIMERLRSSPQSEHYTSLQSMVAYEVSNKLVDRHPHSGCRTVLRLHRALHWLQLFLDGLRTSSEDARTSTLCSEAYNATLANYHSWIVRQAVTVAFCALPSRKVFLEAMNMESTEQAVEMLGEALPFIEHVYDISQKLYAEHSLLDLP 216
                                    16        26        36        46        56        66        76        86      |103       113       123       133       143       153       163       173       183       193       203       213   
                                                                                                                 93|                                                                                                                   
                                                                                                                 101                                                                                                                   


Chain H from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kbr H   8 FNLKVVLVSFKQCLTDKGEVLLDHYIAGWKGLVRFLNSLGAVFSFISKDVVAKLQIMERLRSSPQSEHYTSLQSMVAYEVSNKLVDMDHRHPHSGCRTVLRLHRALHWLQLFLDGLRTSSERTSTLCSEAYNATLANYHSWIVRQAVTVAFCALPSRKVFLEAMNMESTEQAVEMLGEALPFIEHVYDISQKLYAEHSLLDLP 216
                                    17        27        37        47        57        67        77        87       101       111       121       131||     143       153       163       173       183       193       203       213   
                                                                                                                   96|                            132|                                                                                 
                                                                                                                   101                             135
   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 '|'

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

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

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

(-) Gene Ontology  (21, 21)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4k80 4k84 4k85 4k8n 4kbs 4kf6