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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE SNARE VAM3 AND THE HOPS VPS33-VPS16 SUBCOMPLEX FROM CHAETOMIUM THERMOPHILUM
 
Authors :  R. W. Baker, P. D. Jeffrey, F. M. Hughson
Date :  04 Jun 15  (Deposition) - 05 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Membrane Trafficking, Sm Protein, Hops Complex, Thermophile, Snare Domain, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. W. Baker, P. D. Jeffrey, M. Zick, B. P. Phillips, W. T. Wickner, F. M. Hughson
A Direct Role For The Sec1/Munc18-Family Protein Vps33 As A Template For Snare Assembly.
Science V. 349 1111 2015
PubMed-ID: 26339030  |  Reference-DOI: 10.1126/SCIENCE.AAC7906
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SM (SEC1/MUNC18-LIKE) PROTEIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQLINKH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CTHT_0057760
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
    Synonym: VPS33
 
Molecule 2 - PUTATIVE VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQLINKH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CTHT_0026760
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
    Synonym: VPS16
 
Molecule 3 - SNAP RECEPTOR-LIKE PROTEIN
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQLINKH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SNARE DOMAIN
    Gene: CTHT_0015850
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
    Synonym: VAM3

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5BUZ)

(-) Sites  (0, 0)

(no "Site" information available for 5BUZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BUZ)

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Val A:112 -Pro A:113
2Ala A:222 -Gly A:223
3Gly A:558 -Ala A:559
4Pro B:530 -Arg B:531
5Asp B:599 -Gly B:600
6Gly B:652 -Asn B:653
7Ile B:770 -Pro B:771
8Val D:112 -Pro D:113
9Ala D:222 -Gly D:223
10Pro E:530 -Arg E:531
11Asp E:599 -Gly E:600
12Gly E:652 -Asn E:653
13Ile E:770 -Pro E:771

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BUZ)

(-) 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:605
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh...hhhhhhhh.eeeeee.hhh.......eeeeeee..hhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhh.......eeee.....eeee..eee....hhhhhhhh...hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeee.hhhhhhhhh...hhhhhhhhhh.....eeee.....eeee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhh...............hhhhhhhhh.............hhhhh.....hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeeee.....eeeeeeee...hhhhhhhhhhhhhhh...eeeeeee....hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5buz A   5 AGFDAEQVRDKARKDLLHLLEGVRGKKNLVIEKDLAGPLGVIVKASTLRDYGVDNFFFLENKNTGTSQRNIVFIARGESVRNAHAIAAQIKRIQRESQTSHDFHIFWVPRRTLFSDKVLEEAGVLGDANISELPLYFFPLERDVLSLELNDSFRDLYLAKDPTPVFLLSRALMGIQKKHGLFPRIIGKGENAKRVADLLSRMRQELLAGEEAGESDRAGLSPSTTIESVIIIDREVDFVTPLLTQLTYEGLIDEYFGIQNNQTDVDAVRKRKIQLDGSDSLYSQLRDANFAIVGSLLNTVARRLKSDYESRHNTKTTAELKEFVKKLPGYQAEQQSLKIHSNIAEEIINYTRTEIFNKLLEVQQNLAAGADPSSQFDSIEELVARDTPLPQVLRLLCLYSCISGGIKTKELDHFRRLVLQGYGHQHLLTLHNLERLQMFLSKSSPLASMITMSGSSGGPDQKTNYTYLRKQLRLIVDEVNEQDPNDIAYVYSGYAPLSIRLVQCVLQKQYLLSITKGSGGGAQGWKGFEEIVKHARGPTFDEIQKGDKKTVFVVFVGGITFTEIAALRFIAKQEEARRNIVICTTSIINGNRMMNAAIETATFEK 658
                                    14        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       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       557       567       577    || 603       613       623       633       643       653     
                                                                                                                                                                                                                                                                                                     272|                                                                                                                                                                                                                                                      545|                       582|                                                           
                                                                                                                                                                                                                                                                                                      296                                                                                                                                                                                                                                                       556                        599                                                           


Chain B from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhh...........hhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5buz B 505 SFEVIARTAYEEGRTRLATELLNHEPRAGRQVPLLLSMEEDELALDKAIESGDTDLIYFVIHQLRRKLPLASFFRVVSSRPTASAMVEALARNSDGDGNEDTALLKDLYYQDDRRLDGASVFIREALQQPETRTASDKLDLAANLLQGNQKEHVFELGALKEAKMLLRMQETFERDLTDSFVGLSVNQTMFKLIKLGYHGRAKKIQSEFKVPERVAWWIRLQALVAKRDWNEIEEISRQRKSPIGWEPFFNQVLQAGNPRLAATFIPKCTNLEPGQTITMYEKCGMRVKAAEEAVRLKDTEAWNRLLEAAGRNTAEGREIERLG 828
                                   514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824    


Chain C from PDB  Type:PROTEIN  Length:38
                                                                      
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 5buz C 188 EIRNIEQGVSDLNVLFQQVAQLVAEQGEVLDTIERNVE 225
                                   197       207       217        


Chain D from PDB  Type:PROTEIN  Length:605
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh...hhhhhhhh.eeeeee.hhh.......eeeeeee..hhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhh.......eeee.....eeee..eee....hhhhhhhh...hhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeee.hhhhhhhhh...hhhhhhhhhh.....eeee.....eeee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhh...............hhhhhhhhh.............hhhhh.....hhhhhhhhhhhhhhhhhhh.............hhhhhh.....eeeee.....eeeeeeee...hhhhhhhhhhhhhhh...eeeeeee....hhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5buz D   5 AGFDAEQVRDKARKDLLHLLEGVRGKKNLVIEKDLAGPLGVIVKASTLRDYGVDNFFFLENKNTGTSQRNIVFIARGESVRNAHAIAAQIKRIQRESQTSHDFHIFWVPRRTLFSDKVLEEAGVLGDANISELPLYFFPLERDVLSLELNDSFRDLYLAKDPTPVFLLSRALMGIQKKHGLFPRIIGKGENAKRVADLLSRMRQELLAGEEAGESDRAGLSPSTTIESVIIIDREVDFVTPLLTQLTYEGLIDEYFGIQNNQTDVDAVRKRKIQLDGSDSLYSQLRDANFAIVGSLLNTVARRLKSDYESRHNTKTTAELKEFVKKLPGYQAEQQSLKIHSNIAEEIINYTRTEIFNKLLEVQQNLAAGADPSSQFDSIEELVARDTPLPQVLRLLCLYSCISGGIKTKELDHFRRLVLQGYGHQHLLTLHNLERLQMFLSKSSPLASMITMSGSSGGPDQKTNYTYLRKQLRLIVDEVNEQDPNDIAYVYSGYAPLSIRLVQCVLQKQYLLSITKGSGGGAQGWKGFEEIVKHARGPTFDEIQKGDKKTVFVVFVGGITFTEIAALRFIAKQEEARRNIVICTTSIINGNRMMNAAIETATFEK 658
                                    14        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       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       557       567       577    || 603       613       623       633       643       653     
                                                                                                                                                                                                                                                                                                     272|                                                                                                                                                                                                                                                      545|                       582|                                                           
                                                                                                                                                                                                                                                                                                      296                                                                                                                                                                                                                                                       556                        599                                                           


Chain E from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhh...........hhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5buz E 505 SFEVIARTAYEEGRTRLATELLNHEPRAGRQVPLLLSMEEDELALDKAIESGDTDLIYFVIHQLRRKLPLASFFRVVSSRPTASAMVEALARNSDGDGNEDTALLKDLYYQDDRRLDGASVFIREALQQPETRTASDKLDLAANLLQGNQKEHVFELGALKEAKMLLRMQETFERDLTDSFVGLSVNQTMFKLIKLGYHGRAKKIQSEFKVPERVAWWIRLQALVAKRDWNEIEEISRQRKSPIGWEPFFNQVLQAGNPRLAATFIPKCTNLEPGQTITMYEKCGMRVKAAEEAVRLKDTEAWNRLLEAAGRNTAEGREIERLG 828
                                   514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824    


Chain F from PDB  Type:PROTEIN  Length:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 5buz F 186 EEEIRNIEQGVSDLNVLFQQVAQLVAEQGEVLDTIERNVE 225
                                   195       205       215       225
   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 5BUZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 13)

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  Cis Peptide Bonds
    Ala A:222 - Gly A:223   [ RasMol ]  
    Ala D:222 - Gly D:223   [ RasMol ]  
    Asp B:599 - Gly B:600   [ RasMol ]  
    Asp E:599 - Gly E:600   [ RasMol ]  
    Gly A:558 - Ala A:559   [ RasMol ]  
    Gly B:652 - Asn B:653   [ RasMol ]  
    Gly E:652 - Asn E:653   [ RasMol ]  
    Ile B:770 - Pro B:771   [ RasMol ]  
    Ile E:770 - Pro E:771   [ RasMol ]  
    Pro B:530 - Arg B:531   [ RasMol ]  
    Pro E:530 - Arg E:531   [ RasMol ]  
    Val A:112 - Pro A:113   [ RasMol ]  
    Val D:112 - Pro D:113   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/TrEMBL
        G0S6M7_CHATD | G0S6M7: 4kmo 5bv0 5bv1
        G0SCM5_CHATD | G0SCM5: 4jc8 4kmo 5bv0 5bv1

(-) Related Entries Specified in the PDB File

4kmo 4KMO CONTAINS THE SAME VPS33-VPS16 CONSTRUCT AS A HETERODIMER WITHOUT THE VAM3 SNARE BOUND
5bv0
5bv1