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(-) Description

Title :  STRUCTURE OF THE SECA-SECY COMPLEX WITH A TRANSLOCATING POLYPEPTIDE SUBSTRATE
 
Authors :  L. Li, E. Park, J. Ling, J. Ingram, H. Ploegh, T. A. Rapoport
Date :  18 Nov 15  (Deposition) - 09 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.70
Chains :  Asym./Biol. Unit :  A,E,V,Y
Keywords :  Secy, Seca, Atpase, Channel, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Li, E. Park, J. Ling, J. Ingram, H. Ploegh, T. A. Rapoport
Crystal Structure Of A Substrate-Engaged Secy Protein-Translocation Channel.
Nature V. 531 395 2016
PubMed-ID: 26950603  |  Reference-DOI: 10.1038/NATURE17163

(-) Compounds

Molecule 1 - PROTEIN TRANSLOCASE SUBUNIT SECA, INSERTION PEPTIDE CHIMERA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SECA, DIV+, BSU35300
    Organism Scientific: BACILLUS SUBTILIS (STRAIN 168), SYNTHETIC CONSTRUCT, BACILLUS SUBTILIS
    Organism Taxid: 224308, 32630
    Strain: 168
 
Molecule 2 - PROTEIN TRANSLOCASE SUBUNIT SECY
    Chains: Y
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SECY, GTNG_0125
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS (STRAIN NG80- 2)
    Organism Taxid: 420246
    Strain: NG80-2
 
Molecule 3 - PREPROTEIN TRANSLOCASE SECE SUBUNIT
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GTNG_0091
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS (STRAIN NG80- 2)
    Organism Taxid: 420246
    Strain: NG80-2
 
Molecule 4 - AYC08
    Chains: V
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: VICUGNA PACOS
    Organism Taxid: 30538

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : AEVY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric/Biological Unit (4, 21)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION
3MG1Ligand/IonMAGNESIUM ION
4TBR18Ligand/IonHEXATANTALUM DODECABROMIDE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREADP A:1003binding site for residue MG A 1001
02AC2SOFTWARETHR A:102 , GLY A:103 , ASP A:492 , ADP A:1003binding site for residue BEF A 1002
03AC3SOFTWAREMET A:79 , PHE A:80 , PHE A:82 , GLN A:85 , GLY A:103 , GLY A:105 , LYS A:106 , THR A:107 , LEU A:108 , ASP A:492 , ARG A:528 , GLN A:529 , MG A:1001 , BEF A:1002binding site for residue ADP A 1003
04AC4SOFTWAREASP A:591 , GLN A:595 , GLN A:598 , TYR A:599 , GLU Y:103 , ARG Y:106binding site for residue TBR A 1004
05AC5SOFTWAREGLU A:798 , MET A:801 , GLU A:802 , PRO Y:263binding site for residue TBR A 1005
06AC6SOFTWARETHR A:251 , ASP A:253 , THR A:256 , VAL A:298 , ALA A:299 , MET A:300 , GLU A:544 , ARG A:547binding site for residue TBR A 1006
07AC7SOFTWARELYS A:302 , ASP A:303 , GLU A:443 , LYS A:447 , LYS A:462binding site for residue TBR A 1007
08AC8SOFTWAREHIS A:43 , GLU A:47 , GLU A:50binding site for residue TBR A 1008
09AC9SOFTWARETHR A:120 , HIS A:202 , ASP A:276 , GLU A:365 , LYS A:366binding site for residue TBR A 1009
10AD1SOFTWAREGLU A:625 , GLU A:628 , ASN A:629 , MET A:689 , ILE A:693binding site for residue TBR A 1010
11AD2SOFTWARELYS A:723 , ASP A:726 , HIS A:809 , SER A:813binding site for residue TBR A 1011
12AD3SOFTWAREASP A:773 , GLU A:778 , GLU A:780 , SER Y:289 , ARG Y:301 , ARG Y:302binding site for residue TBR A 1012
13AD4SOFTWARELYS A:229 , LYS A:232 , TYR A:234 , ALA A:285 , HIS A:288 , HIS A:289 , GLU A:348binding site for residue TBR A 1013
14AD5SOFTWAREGLU A:309 , ASP A:310 , LYS A:325 , LYS A:462 , HIS A:464 , GLU A:465binding site for residue TBR A 1014
15AD6SOFTWAREGLU A:443 , SER A:446 , LYS A:450 , VAL A:458binding site for residue TBR A 1015
16AD7SOFTWAREGLU A:34 , GLU A:71 , ARG A:74 , ARG A:75binding site for residue TBR A 1016
17AD8SOFTWARETHR A:376 , GLU A:379 , LYS A:583 , GLU A:586 , PHE A:590 , MET Y:104 , ARG Y:107binding site for residue TBR A 1017
18AD9SOFTWAREARG A:14 , GLU A:378 , GLU A:379 , GLN A:388binding site for residue TBR A 1018
19AE1SOFTWAREGLU A:50 , GLU A:53 , PRO Y:242binding site for residue TBR Y 501
20AE2SOFTWAREPHE A:804 , GLU Y:417binding site for residue TBR Y 502
21AE3SOFTWAREARG A:553 , LYS Y:94 , GLU Y:97binding site for residue TBR Y 503

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:775 -Y:60
2V:22 -V:95

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EUL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EUL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EUL)

(-) Exons   (0, 0)

(no "Exon" information available for 5EUL)

(-) 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:746
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhh.eeeeehhhhhhhhhhhh...hhhhh......eeeeehhhhhhh......eeeeee......hhhhhhhhh................hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......eeee..eeeee......ee.......hhhhhhhhhh.......eeeeeeehhhhhhh....eeeee.hhhhhhhhhhhh....eee.........ee...eee..hhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh.....eee......hhhhhhhhhh....eeee.hhhh........hhhhh..eeee.....hhhhhhhhhhh........eeeeeee..hhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eul A  14 RTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDEIVENMIKSSLERAIAAYMLELIMDRIITKYNEKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRGSKKTAIAIAVALAGFATVASYAQYEDGCSGELERQHTFAGGPGAPLREYQMEGFAMFEHMIESIEDEVAKFVMKA 825
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 ||    257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487||     499       509       519       529       539       549       559       569       579       589       599       609       619|      634       685       695   ||  711       721       731       741 ||    756       766       776       786    || 799       809       819      
                                                                                                                                                                                                                                                                 245|                                                                                                                                                                                                                                           488|                                                                                                                             619|              642|            699|                                  743|                                       791|                              
                                                                                                                                                                                                                                                                  250                                                                                                                                                                                                                                            491                                                                                                                              625               684             706                                   749                                        795                              


Chain E from PDB  Type:PROTEIN  Length:56
                                                                                        
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 5eul E   2 QRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRL  57
                                    11        21        31        41        51      


Chain V from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...ee.....eeeeeee.......eeeee.........eeeeee....ee........eeeeee...eeeeeee...hhhhheeeeeeee............eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 5eul V   1 QVQLVETGGGLVQPGGSLRLSCGASGSIFNYAMGWYRQAPGKQREVVARIATDDSTMYPDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYYQRTVMSQPYWGQGTQVTVS 116
                                    10        20        30|       41        51        61        71        81        91       101       111     
                                                        30|                                                                                    
                                                         32                                                                                    


Chain Y from PDB  Type:PROTEIN  Length:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.....hhhhhh............................hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.eeeee....eeeee....hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eul Y  13 DIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFCGGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVLGFIQALGMSYGFNNLAGGMLIQNPIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGISIIIFAGIVSGIPTILNQIYAIVRLLLVALAVVAVIVGVIYIQQAFRKIPIQSTHLPLKVNPVIFAVSFLIAPPTIASFFGTNDRRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYVTRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQLVKRHYRGFIK 430
                                    22        32        42        52        62        72        82        92       102       112       122       132       142 ||    153       163       173       183       193      |216       226       236       260      |275       285       295|      310       320       330       340       350       360       370       380       390       400       410       420       430
                                                                                                                                                             144|                                                   200|                           244|     267|                   295|                                                                                                                                 
                                                                                                                                                              146                                                    214                            259      273                    301
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5EUL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EUL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EUL)

(-) Gene Ontology  (18, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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        SECA_BACSU | P28366: 1m6n 1m74 1tf2 1tf5 2ibm 3dl8 3iqm 3iqy 3jv2

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