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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PROTECTIVE HUMAN ANTIBODIES 100 AND 114 IN COMPLEX WITH EBOLA VIRUS FUSION GLYCOPROTEIN (GP)
 
Authors :  M. S. A. Gilman, J. S. Mclellan
Date :  21 Dec 15  (Deposition) - 16 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  6.70
Chains :  Asym./Biol. Unit :  A,B,H,J,K,L
Keywords :  Ig Domain, Fab, Immune System, Fusion, Ebola Virus, Glycoprotein, Gp, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Misasi, M. S. Gilman, M. Kanekiyo, M. Gui, A. Cagigi, S. Mulangu, D. Corti, J. E. Ledgerwood, A. Lanzavecchia, J. Cunningham, J. J. Muyembe-Tamfun, U. Baxa, B. S. Graham, Y. Xiang, N. J. Sullivan, J. S. Mclellan
Structural And Molecular Basis For Ebola Virus Neutralization By Protective Human Antibodies.
Science V. 351 1343 2016
PubMed-ID: 26917592  |  Reference-DOI: 10.1126/SCIENCE.AAD6117

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN
    Chains: J
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293 CELLS
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 502-599
    Gene: GP
    Organism Common: ZEBOV
    Organism Scientific: ZAIRE EBOLAVIRUS (STRAIN MAYINGA-76)
    Organism Taxid: 128952
    Strain: MAYINGA-76
    Synonym: GP1,2,GP
 
Molecule 2 - ENVELOPE GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN
    Chains: K
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293 CELLS
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 1-302,UNP RESIDUES 1-302
    Gene: GP
    Organism Common: ZEBOV
    Organism Scientific: ZAIRE EBOLAVIRUS
    Organism Taxid: 128952
    Strain: MAYINGA-76
    Synonym: GP1,2,GP,GP1,2,GP
 
Molecule 3 - ANTIBODY 100 FAB HEAVY CHAIN
    Cell: PBMC
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293 CELLS
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - ANTIBODY 100 FAB LIGHT CHAIN
    Cell: PBMC
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293 CELLS
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 5 - ANTIBODY 114 FAB LIGHT CHAIN
    Cell: PBMC
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293 CELLS
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 6 - ANTIBODY 114 FAB HEAVY CHAIN
    Cell: PBMC
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293 CELLS
    Expression System Taxid: 9606
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABHJKL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5FHC)

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:193
5H:22 -H:92
6H:140 -H:196
7J:511 -J:556
8K:108 -K:135
9K:121 -K:147
10L:23 -L:88
11L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Phe A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Tyr B:140 -Pro B:141
4Ser L:7 -Pro L:8
5Ala L:94 -Pro L:95
6Tyr L:140 -Pro L:141
7Phe H:146 -Pro H:147
8Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FHC)

(-) 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:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.....eeeeeee...hhhh.eeeeeee......eeeeeee.....ee.......eeeeee....eeeeee...hhhhheeeeeeeeeeee....eeeeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fhc A    1 QVQLQESGPGLVKPSDTLSLTCTVSGGSLSSFYWSWIRQPPGKGLEWIGYIYYSGSPNYSPSLESRVTMSVDTTRNQISLKLDSVTAADTAVYYCVRASRSYYWGSYRPTAFDSWGQGTLVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G||     108       118       134       144       154       164       174       184       194       204       214 
                                                                                                            82A||               100A||||||||                       126|                                                                                  
                                                                                                             82B|                100B|||||||                        133                                                                                  
                                                                                                              82C                 100C||||||                                                                                                             
                                                                                                                                   100D|||||                                                                                                             
                                                                                                                                    100E||||                                                                                                             
                                                                                                                                     100F|||                                                                                                             
                                                                                                                                      100G||                                                                                                             
                                                                                                                                       100H|                                                                                                             
                                                                                                                                        100I                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee..hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeee...eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fhc B    2 YELTQPLSVSVSPGQTAIFTCSGDNLGDKYVCWFQQRPGQSPMLLIYQDNKRPSGIPERFSGSNSGNTATLTISGTQSTDEADYYCQTWDSTVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                   |12        22        32        42        52        62        72        82        92 ||    103   |   112       122       132       142       152       162       172       182       192       202       
                                   9|                                                                                 94|       106A                                                                                                       
                                   11                                                                                  96                                                                                                                  


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeeee....eeeeeee.....eee.......eeeeeehhh.eeeeee...hhhh.eeeeeeee.......eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fhc H    1 EVQLVESGGGLIQPGGSLRLSCAASGFALRMYDMHWVRQTIDKRLEWVSAVGPSGDTYYADSVKGRFAVSRENAKNSLSLQMNSLTAGDTAIYYCVRSDRGVAGLFDSWGQGILVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50        60        70        80  |||   87        97   ||| 104       114       124  ||   139       149       159       169       179       189       199       209     
                                                                                                            82A||               100A||                        127|                                                                                 
                                                                                                             82B|                100B|                         133                                                                                 
                                                                                                              82C                 100C                                                                                                             


Chain J from PDB  Type:PROTEIN  Length:98
                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee......................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                5fhc J  502 EAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGG  599
                                   511       521       531       541       551       561       571       581       591        


Chain K from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeeee............hhh.eeeeeee.hhhh...hhhhhhhheeee......eee..eee.eeeeeeeeee....................eeeeeeeeee......eeee....eeee..eee.......eeeeeeeeeee......eeeeeeee.......eeeee....eeee.....hhhhhhhhhhhhhhhh.......eeeee.....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fhc K   33 IPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNRSEELSFS  309
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      |216       226       236       246       256       266       276 ||    309
                                                                                                                                                                                      189|                                                             278|       
                                                                                                                                                                                       214                                                              302       


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fhc L    2 IQMTQSPSSLSASVGDRITITCRASQAFDNYVAWYQQRPGKVPKLLISAASALHAGVPSRFSGSGSGTHFTLTISSLQPEDVATYYCQNYNSAPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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 5FHC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Cis Peptide Bonds
    Ala L:94 - Pro L:95   [ RasMol ]  
    Glu A:148 - Pro A:149   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe A:146 - Pro A:147   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  5fhc
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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 5hj3 5jq3 5jq7 5jqb 5kel 5kem 5ken

(-) Related Entries Specified in the PDB File

5fha 5fhb