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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SEC13-SEC16 BLADE-INSERTED COMPLEX FROM PICHIA PASTORIS
 
Authors :  C. Mcmahon, P. D. Jeffrey, F. M. Hughson
Date :  18 Jun 13  (Deposition) - 02 Oct 13  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Propeller, Copii, Vesicle Coat Budding, Nuclear Pore Complex Proteins, Cop-Coated Vesicles, Endoplasmic Reticulum, Ace1, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Bharucha, Y. Liu, E. Papanikou, C. Mcmahon, M. Esaki, P. D. Jeffrey, F. M. Hughson, B. S. Glick
Sec16 Influences Transitional Er Sites By Regulating Rather Than Organizing Copii.
Mol Biol Cell V. 24 3406 2013
PubMed-ID: 24006484  |  Reference-DOI: 10.1091/MBC.E13-04-0185

(-) Compounds

Molecule 1 - SEC16,PROTEIN TRANSPORT PROTEIN SEC13
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-289, UNP RESIDUES 1030-1076,UNP RESIDUES 2- 289, UNP RESIDUES 1030-1076,UNP RESIDUES 2-289, UNP RESIDUES 1030- 1076,UNP RESIDUES 2-289, UNP RESIDUES 1030-1076
    Gene: SEC16, SEC13, PAS_CHR1-3_0057
    Organism Common: YEAST
    Organism Scientific: KOMAGATAELLA PASTORIS, KOMAGATAELLA PHAFFII (STRAIN GS115 / ATCC 20864)
    Organism Taxid: 4922, 644223
    Strain: GS115 / ATCC 20864

 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, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:2132 , ILE A:2157 , EDO A:2406BINDING SITE FOR RESIDUE CA A 2401
02AC2SOFTWAREEDO A:2405 , HOH A:2510 , HOH A:2537 , HOH A:2557 , HOH A:2562 , HOH A:2570 , HOH A:2576BINDING SITE FOR RESIDUE CA A 2402
03AC3SOFTWAREARG A:1052 , ALA A:2071 , TRP A:2072 , HOH A:2563BINDING SITE FOR RESIDUE CL A 2403
04AC4SOFTWARETRP A:2265 , HOH A:2605BINDING SITE FOR RESIDUE CL A 2404
05AC5SOFTWAREGLN A:2069 , ALA A:2162 , SER A:2163 , ASP A:2212 , VAL A:2213 , CA A:2402 , HOH A:2537 , HOH A:2573 , HOH A:2576BINDING SITE FOR RESIDUE EDO A 2405
06AC6SOFTWARESER A:2132 , ASP A:2133 , ILE A:2157 , CA A:2401 , EDO A:2407BINDING SITE FOR RESIDUE EDO A 2406
07AC7SOFTWAREASP A:2133 , LYS A:2135 , EDO A:2406BINDING SITE FOR RESIDUE EDO A 2407
08AC8SOFTWAREPHE A:1048 , SER A:2264 , ALA A:2273 , SER A:2275 , HOH A:2639BINDING SITE FOR RESIDUE EDO A 2408
09AC9SOFTWAREASP A:2029 , TYR A:2030 , TYR A:2031 , HOH A:2533BINDING SITE FOR RESIDUE EDO A 2409
10BC1SOFTWARESER B:2132 , ILE B:2157BINDING SITE FOR RESIDUE CA B 2401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L9O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile B:2167 -Ser B:2168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L9O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L9O)

(-) Exons   (0, 0)

(no "Exon" information available for 4L9O)

(-) 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:330
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................eeeeee..eeeee..ee.....ee.eeeee...eeeee......eeeeee.....eeeeee...eeeeee..eeeeeee.....eeeeee.hhhhheeeeeee....eeeeeee..eeeeeeee......eeeeee.hhhhh.eeeeee...eeeeee.........eeee.....eeeeee.......eeeeee....eeeeeee....eeeeeeee......eeeeee.......eeeeeee....eeeeee......eeeee.........eeeeee......eeeee....eeeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4l9o A 1027 SHMTAPVVRNPRTQFPIFHWCRGGKALSMLPKFDTYGQSKVEINIVGSGSVTIGNAHDDLIHDAVLDYYGRRLATCSSDKTIKIFEIQRLVETLIGHEGPVWQVAWAHPKFGVILASCSYDGKVLIWKEDNGVWNKVAEHSVHQASVNSVSWAPHEYGPVLLCASSDGKISIVEFKDGGALEPIVIQGHAIGVNAASWAPISNTRRFVSGGCDNLVKIWRYDDAAKTFIEEEAFQGHSDWVRDVAWSPSRLSKSYIATASQDRTVLIWTKDGKSNKWEKQPLTKEKFPDVCWRASWSLSGNVLAISGGDNKVTLWKENIQGKWESAGEVD 2299
                                  1036||    1050      1060      1070      1086|     2022      2032      2042      2056      2066      2076      2086      2096      2106      2116      2126      2136      2146      2156      2166 ||   2179      2189      2199      2209      2219      2229      2239      2249      2259      2269      2279      2289      2299
                                   1037|                                1078|||                                2049|                                                                                                              2168|                                                                                                                               
                                    1042                                 1085||                                 2054                                                                                                               2172                                                                                                                               
                                                                          1086|                                                                                                                                                                                                                                                                                       
                                                                           2013                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeeeee...eeeeee...eeee......eeeeee.....eeeeee...eeeeeeee..eeeeeeeee.....eeeeee.hhhhheeeeeee....eeeeee....eeeeeee......eeeeee.hhhhh.eeeeee...eeeeee......eeee.....eeeeee.......eeeeee....eeeeeee....eeeeeeee......eeeeee.......eeeeeee....eeeeee.......eeee.........eeeeee......eeeee....eeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4l9o B 1043 TQFPIFHWCRGGKALSMLPKFKVEINIVGGSVTIGNAHDDLIHDAVLDYYGRRLATCSSDKTIKIFEIDGENQRLVETLIGHEGPVWQVAWAHPKFGVILASCSYDGKVLIWKEDNGVWNKVAEHSVHQASVNSVSWAPHEYGPVLLCASSDGKISIVEFGALEPIVIQGHAIGVNAASWAPISNTRRFVSGGCDNLVKIWRYDDAAKTFIEEEAFQGHSDWVRDVAWSPSRLSKSYIATASQDRTVLIWTKDGKSNKWEKQPLTKEKFPDVCWRASWSLSGNVLAISGGDNKVTLWKENIQGKWESAGEV 2298
                                  1052      1062||    1085||    2021      2031      2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141|     2154      2164   || 2177      2187      2197      2207      2217      2227      2237      2247      2257      2267      2277      2287      2297 
                                             1063|   1077|||                                                                                                                            2141|                   2168|                                                                                                                              
                                              1070    1085||                                                                                                                             2145                    2172                                                                                                                              
                                                       1086|                                                                                                                                                                                                                                                                                       
                                                        2013
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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 4L9O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L9O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L9O)

(-) Gene Ontology  (11, 11)

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