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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST SEC14 HOMOLOG SFH1 IN COMPLEX WITH PHOSPHATIDYLCHOLINE
 
Authors :  E. A. Ortlund, G. Schaaf, M. R. Redinbo, V. Bankaitis
Date :  31 Oct 07  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sec14, Golgi, Phospholipid, Phosphatidylcholine, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Schaaf, E. A. Ortlund, K. R. Tyeryar, C. J. Mousley, K. E. Ile, T. A. Garrett, J. Ren, M. J. Woolls, C. R. Raetz, M. R. Redinbo, V. A. Bankaitis
Functional Anatomy Of Phospholipid Binding And Regulation O Phosphoinositide Homeostasis By Proteins Of The Sec14 Superfamily
Mol. Cell V. 29 191 2008
PubMed-ID: 18243114  |  Reference-DOI: 10.1016/J.MOLCEL.2007.11.026

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN YKL091C
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28_SFH1
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: BY4741

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
16PL2Ligand/Ion(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
2GOL1Ligand/IonGLYCEROL
3PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
16PL1Ligand/Ion(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
2GOL1Ligand/IonGLYCEROL
3PO43Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
16PL1Ligand/Ion(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
2GOL-1Ligand/IonGLYCEROL
3PO43Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:221 , GLY A:222 , PHE A:223 , SER A:224 , HOH A:463BINDING SITE FOR RESIDUE PO4 A 311
2AC2SOFTWARELYS A:95 , ASN A:301 , GLY A:304 , HOH A:428BINDING SITE FOR RESIDUE PO4 A 312
3AC3SOFTWAREGLY A:246 , SER A:247 , SER A:248 , HOH A:420 , HOH A:504BINDING SITE FOR RESIDUE PO4 A 313
4AC4SOFTWARETYR A:109 , TYR A:113 , TYR A:124 , LEU A:128 , ILE A:131 , MET A:136 , TYR A:137 , THR A:140 , THR A:141 , MET A:145 , TYR A:153 , SER A:175 , THR A:177 , TYR A:195 , ILE A:196 , MET A:211 , THR A:238 , HOH A:350 , HOH A:365 , HOH A:386 , HOH A:417BINDING SITE FOR RESIDUE 6PL A 314
5AC5SOFTWAREVAL A:271 , LEU A:272 , PRO A:275 , ASP A:277 , HOH A:448 , HOH A:506BINDING SITE FOR RESIDUE GOL A 315
6AC6SOFTWAREPHE B:221 , GLY B:222 , SER B:224BINDING SITE FOR RESIDUE PO4 B 311
7AC7SOFTWARELYS B:95 , ASN B:301 , GLY B:304 , LYS B:305 , HOH B:349BINDING SITE FOR RESIDUE PO4 B 312
8AC8SOFTWAREGLY B:246 , SER B:247 , SER B:248 , HOH B:484 , HOH B:487 , HOH B:496BINDING SITE FOR RESIDUE PO4 B 313
9AC9SOFTWARETYR B:109 , TYR B:113 , TYR B:124 , LEU B:128 , ILE B:131 , LEU B:133 , TYR B:137 , MET B:145 , LEU B:149 , GLU B:152 , TYR B:153 , SER B:175 , THR B:177 , ALA B:189 , TYR B:195 , ILE B:196 , ARG B:210 , MET B:211 , PHE B:214 , HOH B:365 , HOH B:427 , HOH B:448BINDING SITE FOR RESIDUE 6PL B 314

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B7Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B7Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B7Q)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRAL_TRIOPS50191 CRAL-TRIO lipid binding domain profile.YKJ1_YEAST101-274
 		  2A:101-274
B:101-274
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRAL_TRIOPS50191 CRAL-TRIO lipid binding domain profile.YKJ1_YEAST101-274
 		  1A:101-274
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRAL_TRIOPS50191 CRAL-TRIO lipid binding domain profile.YKJ1_YEAST101-274
 		  1-
B:101-274

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL091C1YKL091C.1XI:270294-269362933YKJ1_YEAST1-3103102A:4-310
B:3-309		307
307

(-) 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:307
 aligned with YKJ1_YEAST | P33324 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
           YKJ1_YEAST     4 SILDTYPQICSPNALPGTPGNLTKEQEEALLQFRSILLEKNYKERLDDSTLLRFLRARKFDINASVEMFVETERWREEYGANTIIEDYENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFEELGGINLKKMYKITTEKQMLRNLVKEYELFATYRVPACSRRAGYLIETSCTVLDLKGISLSNAYHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHNPNDKFYYSDIGPWRDPRYIGPEGEIPNIFGKFTVTS 310
               SCOP domains d3b7qa1 A:4-94 automated matches                                                           d3b7qa2 A:95-310 automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 3b7qA01 A:4-82                                                                 3b7qA02 A:83-310 Phosphatidylinositol Transfer Protein Sec14p                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh................hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhhheee...hhhhhhhhhhhhhhhhhhhh..........hhhhh..hhhhhhhhh.........hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------CRAL_TRIO  PDB: A:101-274 UniProt: 101-274                                                                                                                                    ------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-310 UniProt: 1-310 [INCOMPLETE]                                                                                                                                                                                                                                                                  Transcript 1
                 3b7q A   4 SILDTYPQICSPNALPGTPGNLTKEQEEALLQFRSILLEKNYKERLDDSTLLRFLRARKFDINASVEMFVETERWREEYGANTIIEDYENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFEELGGINLKKMYKITTEKQMLRNLVKEYELFATYRVPACSRRAGYLIETSCTVLDLKGISLSNAYHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHNPNDKFYYSDIGPWRDPRYIGPEGEIPNIFGKFTVTS 310
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       


Chain B from PDB  Type:PROTEIN  Length:307
 aligned with YKJ1_YEAST | P33324 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:307
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       
           YKJ1_YEAST     3 TSILDTYPQICSPNALPGTPGNLTKEQEEALLQFRSILLEKNYKERLDDSTLLRFLRARKFDINASVEMFVETERWREEYGANTIIEDYENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFEELGGINLKKMYKITTEKQMLRNLVKEYELFATYRVPACSRRAGYLIETSCTVLDLKGISLSNAYHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHNPNDKFYYSDIGPWRDPRYIGPEGEIPNIFGKFTVT 309
               SCOP domains d3b7qb1 B:3-94 automated matches                                                            d3b7qb2 B:95-309 automated matches                                                                                                                                                                                      SCOP domains
               CATH domains 3b7qB01 B:3-82 N-terminal domain of phosphatidylinositol transfer protein sec14p3b7qB02 B:83-309 Phosphatidylinositol Transfer Protein Sec14p                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh................hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeeee.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhhheee...hhhhhhhhhh.....hhhhh..........hhhhh..hhhhh.............hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------CRAL_TRIO  PDB: B:101-274 UniProt: 101-274                                                                                                                                    ----------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-309 UniProt: 1-310 [INCOMPLETE]                                                                                                                                                                                                                                                                  Transcript 1
                 3b7q B   3 TSILDTYPQICSPNALPGTPGNLTKEQEEALLQFRSILLEKNYKERLDDSTLLRFLRARKFDINASVEMFVETERWREEYGANTIIEDYENNKEAEDKERIKLAKMYPQYYHHVDKDGRPLYFEELGGINLKKMYKITTEKQMLRNLVKEYELFATYRVPACSRRAGYLIETSCTVLDLKGISLSNAYHVLSYIKDVADISQNYYPERMGKFYIIHSPFGFSTMFKMVKPFLDPVTVSKIFILGSSYKKELLKQIPIENLPVKYGGTSVLHNPNDKFYYSDIGPWRDPRYIGPEGEIPNIFGKFTVT 309
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B7Q)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YKJ1_YEAST | P33324)
molecular function
    GO:0031210    phosphatidylcholine binding    Interacting selectively and non-covalently with phosphatidylcholine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of choline.
    GO:0008525    phosphatidylcholine transporter activity    Enables the directed movement of phosphatidylcholine into, out of or within a cell, or between cells. Phosphatidylcholine refers to a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0008526    phosphatidylinositol transporter activity    Enables the directed movement of phosphatidylinositol into, out of or within a cell, or between cells. Phosphatidylinositol refers to any glycophospholipids with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  3b7q
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 Related Entries

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

UniProtKB/Swiss-Prot
        YKJ1_YEAST | P33324: 3b74 3b7n 3b7z 3q8g

(-) Related Entries Specified in the PDB File

3b74 CRYSTAL STRUCTURE OF YEAST SEC14 HOMOLOG SFH1 IN COMPLEX WITH PHOSPHATIDYLETHANOLAMINE
3b7n CRYSTAL STRUCTURE OF YEAST SEC14 HOMOLOG SFH1 IN COMPLEX WITH PHOSPHATIDYLINOSITOL
3b7z