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(-) Description

Title :  VIRA-RAB1 COMPLEX STRUCTURE
 
Authors :  F. Shao, Y. Zhu
Date :  16 Jun 12  (Deposition) - 05 Sep 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  A,B,C,D,E,F  (2x)
Keywords :  Alpha-Beta Fold, Rab1-Gap Complex, Rab1, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Dong, Y. Zhu, Q. Lu, L. Hu, Y. Zheng, F. Shao
Structurally Distinct Bacterial Tbc-Like Gaps Link Arf Gtpase To Rab1 Inactivation To Counteract Host Defenses.
Cell(Cambridge, Mass. ) V. 150 1029 2012
PubMed-ID: 22939626  |  Reference-DOI: 10.1016/J.CELL.2012.06.050

(-) Compounds

Molecule 1 - CYSTEINE PROTEASE-LIKE VIRA
    ChainsA, C, E
    EC Number3.4.22.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-2
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCP0181, PWR501_0191, VIRA
    Organism ScientificSHIGELLA FLEXNERI
    Organism Taxid623
    Strain301
    SynonymEFFECTOR PROTEIN VIRA
 
Molecule 2 - RAS-RELATED PROTEIN RAB-1A
    ChainsB, D, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRAB1, RAB1A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymYPT1-RELATED PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF
Biological Unit 4 (2x)ABCDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1AF33Ligand/IonALUMINUM FLUORIDE
2GDP3Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1AF31Ligand/IonALUMINUM FLUORIDE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1AF31Ligand/IonALUMINUM FLUORIDE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1AF31Ligand/IonALUMINUM FLUORIDE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (2, 12)
No.NameCountTypeFull Name
1AF36Ligand/IonALUMINUM FLUORIDE
2GDP6Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:188 , GLN A:280 , SER B:20 , GLY B:21 , LYS B:24 , SER B:42 , THR B:43 , THR B:67 , GLY B:69 , GDP B:202 , MG B:203 , HOH B:301 , HOH B:303BINDING SITE FOR RESIDUE AF3 B 201
2AC2SOFTWAREARG A:188 , ARG A:191 , ASP B:19 , GLY B:21 , VAL B:22 , GLY B:23 , LYS B:24 , SER B:25 , CYS B:26 , TYR B:36 , ASN B:124 , LYS B:125 , ASP B:127 , LEU B:128 , SER B:154 , ALA B:155 , LYS B:156 , AF3 B:201 , MG B:203 , HOH B:302 , HOH B:303BINDING SITE FOR RESIDUE GDP B 202
3AC3SOFTWARESER B:25 , THR B:43 , AF3 B:201 , GDP B:202 , HOH B:302 , HOH B:303BINDING SITE FOR RESIDUE MG B 203
4AC4SOFTWAREARG C:188 , GLN C:280 , HOH C:501 , SER D:20 , GLY D:21 , LYS D:24 , SER D:42 , THR D:43 , THR D:67 , GLY D:69 , GDP D:202 , MG D:203 , HOH D:302BINDING SITE FOR RESIDUE AF3 D 201
5AC5SOFTWAREARG C:188 , ARG C:191 , ASP D:19 , GLY D:21 , VAL D:22 , GLY D:23 , LYS D:24 , SER D:25 , CYS D:26 , TYR D:36 , ASN D:124 , LYS D:125 , ASP D:127 , LEU D:128 , SER D:154 , ALA D:155 , LYS D:156 , AF3 D:201 , MG D:203 , HOH D:302BINDING SITE FOR RESIDUE GDP D 202
6AC6SOFTWARESER D:25 , THR D:43 , AF3 D:201 , GDP D:202 , HOH D:301 , HOH D:302BINDING SITE FOR RESIDUE MG D 203
7AC7SOFTWAREARG E:188 , GLN E:280 , HOH E:501 , SER F:20 , GLY F:21 , LYS F:24 , THR F:43 , THR F:67 , GLY F:69 , GDP F:202 , MG F:203BINDING SITE FOR RESIDUE AF3 F 201
8AC8SOFTWAREARG E:188 , ARG E:191 , ASP F:19 , GLY F:21 , VAL F:22 , GLY F:23 , LYS F:24 , SER F:25 , CYS F:26 , TYR F:36 , ASN F:124 , LYS F:125 , ASP F:127 , LEU F:128 , SER F:154 , ALA F:155 , LYS F:156 , AF3 F:201 , MG F:203 , HOH F:302BINDING SITE FOR RESIDUE GDP F 202
9AC9SOFTWARESER F:25 , THR F:43 , AF3 F:201 , GDP F:202 , HOH F:301 , HOH F:302BINDING SITE FOR RESIDUE MG F 203

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:253 -E:355
2A:355 -C:253
3C:355 -E:253

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:40 -Pro A:41
2Gly C:40 -Pro C:41
3Gly E:40 -Pro E:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FMB)

(-) 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh.ee.........eeeeeee..eeeeeeee..eeeeeeee..eeeeee.hhhhhhhhhhh....ee......eeeeeee........hhhhhhhhhhh.eee...............hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh...............hhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee......eeeeeeeeeeee....eeeeeeeeeeee......hhhhhhhhhhhhhheeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmb A  40 GPLGSIYSPHETLAEKHSEKKLMDSFSPSLSQDKMDGEFAHANIDGISIRLCLNKGICSVFYLDGDKIQSTQLSSKEYNNLLSSLPPKQFNLGKVHTITAPVSGNFKTHKPAPEVIETAINCCTSIIPNDDYFHVKDTDFNSVWHDIYRDIRASDSNSTKIYFNNIEIPLKLIADLINELGINEFIDSKKELQMLSYNQVNKIINSNFPQQDLCFQTEKLLFTSLFQDPAFISALTSAFWQSLHITSSSVEHIYAQIMSENIENRLNFMPEQRVINNCGHIIKINAVVGGRAYEVSSSILPSHITCNGVGINKIETSYLVHAGTLPSSEGLRNAIPPESRQVSFAIISPDV 400
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       339       349       359       369       379       389       399 
                                                                                                                                                                                                                                                                                                                         327|                                                              
                                                                                                                                                                                                                                                                                                                          338                                                              

Chain B from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.....hhhhhhhhhhh.............eeeeeee......eeeeeee...hhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhh....eeee......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmb B   6 PEYDALFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM 176
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 

Chain C from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhheee.........eeeeeee..eeeeeeee..eeeeeeee..eeeeee.hhhhhhhhhhh....ee......eeeeeee........hhhhhhhhhhh.eee...............hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh...............hhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee.....eeeeeeeeeeee....eeeeeeeeeeee......hhhhhhhhhhhhhheeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmb C  40 GPLGSIYSPHETLAEKHSEKKLMDSFSPSLSQDKMDGEFAHANIDGISIRLCLNKGICSVFYLDGDKIQSTQLSSKEYNNLLSSLPPKQFNLGKVHTITAPVSGNFKTHKPAPEVIETAINCCTSIIPNDDYFHVKDTDFNSVWHDIYRDIRASDSNSTKIYFNNIEIPLKLIADLINELGINEFIDSKKELQMLSYNQVNKIINSNFPQQDLCFQTEKLLFTSLFQDPAFISALTSAFWQSLHITSSSVEHIYAQIMSENIENRLNFMPEQRVINNCGHIIKINAVVPRAYEVSSSILPSHITCNGVGINKIETSYLVHAGTLPSSEGLRNAIPPESRQVSFAIISPDV 400
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       340       350       360       370       380       390       400
                                                                                                                                                                                                                                                                                                                          328|                                                            
                                                                                                                                                                                                                                                                                                                           340                                                            

Chain D from PDB  Type:PROTEIN  Length:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.....hhhhhhhhhhh.............eeeeeee......eeeeeee...hhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhh....eeee......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmb D   6 PEYDALFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM 176
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 

Chain E from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhheee.........eeeeeee..eeeeeeee..eeeeeeee..eeeeee.hhhhhhhhhhh....ee......eeeeeee........hhhhhhhhhhh.eee...............hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh...............hhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee.....eeeeeeeeeeee....eeeeeeeeeeee......hhhhhhhhhhhhhheeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmb E  40 GPLGSIYSPHETLAEKHSEKKLMDSFSPSLSQDKMDGEFAHANIDGISIRLCLNKGICSVFYLDGDKIQSTQLSSKEYNNLLSSLPPKQFNLGKVHTITAPVSGNFKTHKPAPEVIETAINCCTSIIPNDDYFHVKDTDFNSVWHDIYRDIRASDSNSTKIYFNNIEIPLKLIADLINELGINEFIDSKKELQMLSYNQVNKIINSNFPQQDLCFQTEKLLFTSLFQDPAFISALTSAFWQSLHITSSSVEHIYAQIMSENIENRLNFMPEQRVINNCGHIIKINAVVPRAYEVSSSILPSHITCNGVGINKIETSYLVHAGTLPSSEGLRNAIPPESRQVSFAIISPDV 400
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       340       350       360       370       380       390       400
                                                                                                                                                                                                                                                                                                                          328|                                                            
                                                                                                                                                                                                                                                                                                                           340                                                            

Chain F from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....hhhhhhhhhhh.............eeeeeee......eeeeeee...hhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhh....eeee......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmb F   7 EYDALFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM 176
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

   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 4FMB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 44)

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  VIRA_SHIFL | Q7BU69
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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB1A_HUMAN | P628202fol 2wwx 3l0i 3sfv 3tkl 4fmc 4fmd 4fme 4iru 4jvs
        VIRA_SHIFL | Q7BU693eb8 3ee1

(-) Related Entries Specified in the PDB File

4fma 4fmc 4fmd 4fme