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(-) Description

Title :  EBOV SGP IN COMPLEX WITH VARIABLE FAB DOMAINS OF IGGS C13C6 AND BDBV91
 
Authors :  J. Pallesen, C. D. Murin, N. De Val, C. A. Cottrell, K. M. Hastie, H. L. Tu M. L. Fusco, A. I. Flyak, L. Zeitlin, J. E. Crowe Jr. , K. G. Andersen, E. O. Saphire, A. B. Ward
Date :  09 Jun 16  (Deposition) - 07 Sep 16  (Release) - 07 Sep 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  5.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Ebola Virus Secreted Glycoprotein, Sgp, Antibodies, Viral Protein- Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Pallesen, C. D. Murin, N. De Val, C. A. Cottrell, K. M. Hastie, H. L. Turner, M. L. Fusco, A. I. Flyak, L. Zeitlin, J. E. Crowe, K. G. Andersen, E. O. Saphire, A. B. Ward
Structures Of Ebola Virus Gp And Sgp In Complex With Therapeutic Antibodies.
Nat Microbiol V. 1 16128 2016
PubMed-ID: 27562261  |  Reference-DOI: 10.1038/NMICROBIOL.2016.128

(-) Compounds

Molecule 1 - BDBV91 VARIABLE FAB DOMAIN LIGHT CHAIN
    Chains: C, H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - BDBV91 VARIABLE FAB DOMAIN HEAVY CHAIN
    Chains: B, G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - C13C6 VARIABLE FAB DOMAIN HEAVY CHAIN
    Chains: D, I
    Engineered: YES
    Expression System: NICOTIANA BENTHAMIANA
    Expression System Taxid: 4100
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - C13C6 VARIABLE FAB DOMAIN LIGHT CHAIN
    Chains: E, J
    Engineered: YES
    Expression System: NICOTIANA BENTHAMIANA
    Expression System Taxid: 4100
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 5 - EBOLA SECRETED GLYCOPROTEIN
    Chains: A, F
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Common: FRUIT FLY
    Expression System Taxid: 7227
    Gene: GP
    Organism Common: ZEBOV
    Organism Scientific: ZAIRE EBOLAVIRUS
    Organism Taxid: 128952
    Strain: MAYINGA-76

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5KEM)

(-) SS Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1A:108 -A:135
2A:121 -A:147
3B:22 -B:92
4C:23 -C:88
5D:22 -D:92
6E:23 -E:88
7F:108 -F:135
8F:121 -F:147
9G:22 -G:92
10H:23 -H:88
11I:22 -I:92
12J:23 -J:88

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Ser C:7 -Pro C:8
2Ser C:94 -Pro C:95
3Lys B:12 -Pro B:13
4His B:35 -Trp B:36
5Gly D:8 -Gly D:9
6Tyr E:94 -Pro E:95
7Ser H:7 -Pro H:8
8Ser H:94 -Pro H:95
9Lys G:12 -Pro G:13
10His G:35 -Trp G:36
11Gly I:8 -Gly I:9
12Tyr J:94 -Pro J:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KEM)

(-) 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:232
                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee.hhhh....hhhhhh...........eee..ee..eeeeeeee......................eeeeeeee.........ee.....eeee..eee.ee......eeeee......hhhhhhhhh..........hhhhh.....eeeeeeee.....eeeee....eee........hhhhhhhhhh.............eee..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kem A   53 CRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTT  284
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...ee........eeee.............eee......ee..ee......eehhhhhh..eeee.......eeeee........eeee......................eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                5kem B    1 QVQLVQSGAELKPPGASVKVSCKPSGYTFTDYYIHWVRQAPGQGLEWMGWINPKSGETHYAQKFRGWVTLTRDTSISTTYMDLTRLKSDDTAVYFCARGDLETTIFFYNAVDVWGQGTLVT  110
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109 
                                                                              52A                            82A||               100A||||||          
                                                                                                              82B|                100B|||||          
                                                                                                               82C                 100C||||          
                                                                                                                                    100D|||          
                                                                                                                                     100E||          
                                                                                                                                      100F|          
                                                                                                                                       100G          


Chain C from PDB  Type:PROTEIN  Length:107
                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee......eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhhheeeee........eee...ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                5kem C    1 DIQMTQSPSSLSASVGDRVTITCRATESIGIYLNWYQRKPGKAPNLLIFATSSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYFCQQGFSSPFSFGQGTRLEIK  107
                                    10        20        30        40        50        60        70        80        90       100       


Chain D from PDB  Type:PROTEIN  Length:121
                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........ee..............eeee..eeee.hhhhhhh..eeee....eeeeee...hhhhh..........................ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                5kem D    1 DVKLLESGGGLVQPGGSLKLSCAASGFSLSTSGVGVGWFRQPSGKGLEWLALIWWDDDKYYNPSLKSQLSISKDFSRNQVFLKISNVDIADTATYYCARRDPFGYDNAMGYWGQGTSVTVS  112
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||101       111 
                                                             35A|                                             82A||               100A|||            
                                                              35B                                              82B|                100B||            
                                                                                                                82C                 100C|            
                                                                                                                                     100D            


Chain E from PDB  Type:PROTEIN  Length:107
                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee............eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                5kem E    1 DIVMTQSPLSLSTSVGDRVSLTCKASQNVGTAVAWYQQKPGQSPKLLIYSASNRYTGVPDRFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGAGTKLELR  107
                                    10        20        30        40        50        60        70        80        90       100       


Chain F from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee.hhhh....hhhhhh...........eee..ee..eeeeeeee......................eeeeeeee.........ee.....eeee..eee.ee......eeeee......hhhhhhhhh..........hhhhh.....eeeeeeee.....eeeee....eee........hhhhhhhhhh.............eee..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5kem F   53 CRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTT  284
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  


Chain G from PDB  Type:PROTEIN  Length:121
                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...ee........eeee.............eee......ee..ee......eehhhhhh..eeee.......eeeee........eeee......................eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                5kem G    1 QVQLVQSGAELKPPGASVKVSCKPSGYTFTDYYIHWVRQAPGQGLEWMGWINPKSGETHYAQKFRGWVTLTRDTSISTTYMDLTRLKSDDTAVYFCARGDLETTIFFYNAVDVWGQGTLVT  110
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109 
                                                                              52A                            82A||               100A||||||          
                                                                                                              82B|                100B|||||          
                                                                                                               82C                 100C||||          
                                                                                                                                    100D|||          
                                                                                                                                     100E||          
                                                                                                                                      100F|          
                                                                                                                                       100G          


Chain H from PDB  Type:PROTEIN  Length:107
                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee......eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhhheeeee........eee...ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                5kem H    1 DIQMTQSPSSLSASVGDRVTITCRATESIGIYLNWYQRKPGKAPNLLIFATSSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYFCQQGFSSPFSFGQGTRLEIK  107
                                    10        20        30        40        50        60        70        80        90       100       


Chain I from PDB  Type:PROTEIN  Length:121
                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........ee..............eeee..eeee.hhhhhhh..eeee....eeeeee...hhhhh..........................ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                5kem I    1 DVKLLESGGGLVQPGGSLKLSCAASGFSLSTSGVGVGWFRQPSGKGLEWLALIWWDDDKYYNPSLKSQLSISKDFSRNQVFLKISNVDIADTATYYCARRDPFGYDNAMGYWGQGTSVTVS  112
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||101       111 
                                                             35A|                                             82A||               100A|||            
                                                              35B                                              82B|                100B||            
                                                                                                                82C                 100C|            
                                                                                                                                     100D            


Chain J from PDB  Type:PROTEIN  Length:107
                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee............eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                5kem J    1 DIVMTQSPLSLSTSVGDRVSLTCKASQNVGTAVAWYQQKPGQSPKLLIYSASNRYTGVPDRFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGAGTKLELR  107
                                    10        20        30        40        50        60        70        80        90       100
   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 5KEM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly D:8 - Gly D:9   [ RasMol ]  
    Gly I:8 - Gly I:9   [ RasMol ]  
    His B:35 - Trp B:36   [ RasMol ]  
    His G:35 - Trp G:36   [ RasMol ]  
    Lys B:12 - Pro B:13   [ RasMol ]  
    Lys G:12 - Pro G:13   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Ser C:94 - Pro C:95   [ RasMol ]  
    Ser H:7 - Pro H:8   [ RasMol ]  
    Ser H:94 - Pro H:95   [ RasMol ]  
    Tyr E:94 - Pro E:95   [ RasMol ]  
    Tyr J:94 - Pro J:95   [ RasMol ]  
 

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  VGP_EBOZM | Q05320
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 Related Entries

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

UniProtKB/Swiss-Prot
        VGP_EBOZM | Q05320: 2ebo 2rlj 3csy 5fhc 5hj3 5jq3 5jq7 5jqb 5kel 5ken

(-) Related Entries Specified in the PDB File

5kel 5ken