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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ATP-BOUND GET3-GET4-GET5 COMPLEX FROM S.CEREVISIAE
 
Authors :  H. B. Gristick, W. M. Clemons Jr.
Date :  21 Mar 14  (Deposition) - 09 Apr 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  5.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Tail-Anchored Targeting, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. B. Gristick, M. Rao, J. W. Chartron, M. E. Rome, S. O. Shan, W. M. Clemons
Crystal Structure Of Atp-Bound Get3-Get4-Get5 Complex Reveals Regulation Of Get3 By Get4.
Nat. Struct. Mol. Biol. V. 21 437 2014
PubMed-ID: 24727835  |  Reference-DOI: 10.1038/NSMB.2813

(-) Compounds

Molecule 1 - ATPASE GET3
    Chains: A, B
    EC Number: 3.6.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET33B
    Expression System Strain: BL21GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-354
    Gene: ARR4, D2371, GET3, GET3 YDL100C, YDL100C
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: ARSENICAL PUMP-DRIVING ATPASE, ARSENITE-STIMULATED ATPASE, GOLGI TO ER TRAFFIC PROTEIN 3, GUIDED ENTRY OF TAIL-ANCHORED PROTEINS 3
 
Molecule 2 - GOLGI TO ER TRAFFIC PROTEIN 4
    Chains: E, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET33B
    Expression System Strain: BL21GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 11-290
    Gene: GET4, GET4 YOR164C, O3580, YOR164C
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: GUIDED ENTRY OF TAIL-ANCHORED PROTEINS 4
 
Molecule 3 - UBIQUITIN-LIKE PROTEIN MDY2
    Chains: F, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET33B
    Expression System Strain: BL21GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-54
    Gene: GET5, GET5 MDY2 YOL111C, MDY2, TMA24, YOL111C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: GOLGI TO ER TRAFFIC PROTEIN 5, MATING-DEFICIENT PROTEIN 2, TRANSLATION MACHINERY-ASSOCIATED PROTEIN 24

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:27 , GLY A:28 , GLY A:30 , LYS A:31 , THR A:32 , THR A:33 , ASN A:61 , ASN A:272 , LEU A:316 , GLU A:320 , ILE A:321 , PHE A:330 , MG A:402 , LYS B:26 , GLY B:27 , PRO B:169 , GLU B:245 , LEU B:247BINDING SITE FOR RESIDUE ATP A 401
2AC2SOFTWARELYS A:31 , THR A:32 , ASP A:166 , ATP A:401BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWARECYS A:285 , CYS A:288 , CYS B:285 , CYS B:288BINDING SITE FOR RESIDUE ZN A 403
4AC4SOFTWARELYS A:26 , GLY A:27 , PRO A:169 , GLU A:245 , LEU A:247 , GLY B:27 , GLY B:28 , GLY B:30 , LYS B:31 , THR B:32 , THR B:33 , ASN B:61 , ASN B:272 , GLY B:319 , GLU B:320 , ILE B:321 , PHE B:330 , MG B:402BINDING SITE FOR RESIDUE ATP B 401
5AC5SOFTWARETHR B:32 , ASP B:166 , ATP B:401BINDING SITE FOR RESIDUE MG B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PWX)

(-) 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh....eeee......hhhhhhh.......ee......eee...hhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhh........hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pwx A   5 VEPNLHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTVPAHNLSDAFGEKFGKDARKVTGMNNLSCMEIDPSAALKDMALADLTGSIPGIDEALSFMEVMKHIKRQEQGEGETFDTVIFDTAPTGHTLRFLQLPNTLSKLLEKFISGKLNELKANVETIRQQFTDPDLTTFVCVCISEFLSLYETERLIQELISYDMDVNSIIVNQLLFAECKRCQARWKMQKKYLDQIDELYEDFHVVKMPLCAGEIRGLNNLTKFSQFLNKEYNPITDGKVIYELED 352
                                    14        24        34        44        54        64        74        84        94  ||   131       141       151       161       171       181       212       222       232       242       252       262       272     ||288       298       308       318       328       338       348    
                                                                                                                       97|                                                              190|                                                               278|                                                                   
                                                                                                                       125                                                               212                                                                285                                                                   


Chain B from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh....eeee......hhhhhhh.......ee......eee...hhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pwx B   5 VEPNLHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTVPAHNLSDAFGEKFGKDARKVTGMNNLSCMEIDPSAALKDMNDMALADLTGSIPGIDEALSFMEVMKHIKRQEQGEGETFDTVIFDTAPTGHTLRFLQLPNTLSKLLEKFVDISGKLNELKANVETIRQQFTDPDLTTFVCVCISEFLSLYETERLIQELISYDMDVNSIIVNQLLFAECKRCQARWKMQKKYLDQIDELYEDFHVVKMPLCAGEIRGLNNLTKFSQFLNKEYNPITDGKVIYELED 352
                                    14        24        34        44        54        64        74        84        94     ||128       138       148       158       168       178       188 ||    217       227       237       247       257       267       277||     293       303       313       323       333       343         
                                                                                                                         100|                                                              190|                                                                 278|                                                                   
                                                                                                                          125                                                               210                                                                  285                                                                   


Chain C from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pwx C  15 KTLQRFENKIKAGDYYEAHQTLRTIANRYVRSKSYEHAIELISQGALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGTHDSMIKYVDLLWDWLCQVDDIEDSTVAEFFSRLVFNYLFISNISFAHESKDIFLERFIEKFHPKYEKIDKNGYEIVFFEDYSDLNFLQLLLITCQTADASYFLNLKNHYLDFSQAYKSELEFLGQEYFN 290
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284      


Chain D from PDB  Type:PROTEIN  Length:52
                                                                                    
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 4pwx D   3 TSASGPEHEFVSKFLTLATLTEPKLPKSYTKPLKDVTNLGVPLPTLKYKYKQ  54
                                    12        22        32        42        52  


Chain E from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pwx E  14 AKTLQRFENKIKAGDYYEAHQTLRTIANRYVRSKSYEHAIELISQGALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGTHDSMIKYVDLLWDWLCQVDDIEDSTVAEFFSRLVFNYLFISNISFAHESKDIFLERFIEKFHPKYEKIDKNGYEIVFFEDYSDLNFLQLLLITCQTADASYFLNLKNHYLDFSQAYKSELEFLGQEYFN 290
                                    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       


Chain F from PDB  Type:PROTEIN  Length:52
                                                                                    
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 4pwx F   3 TSASGPEHEFVSKFLTLATLTEPKLPKSYTKPLKDVTNLGVPLPTLKYKYKQ  54
                                    12        22        32        42        52
   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 4PWX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 44)

Asymmetric/Biological Unit(hide GO term definitions)

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  4pwx
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  GET3_YEAST | Q12154
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  GET4_YEAST | Q12125
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  MDY2_YEAST | Q12285
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  3.6.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        GET3_YEAST | Q12154: 2woj 3a36 3a37 3b2e 3h84 3idq 3sja 3sjb 3sjc 3sjd 3vlc 3zs8 3zs9 4xtr 4xvu 4xwo 5bw8 5bwk
        GET4_YEAST | Q12125: 2wpv 3lku 5bw8 5bwk
        MDY2_YEAST | Q12285: 2lnz 2lxa 2lxc 2wpv 3lku 3vej 3zdm 4a20 4asw 4goc 5bw8 5bwk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4PWX)