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(-) Description

Title :  CRYSTAL STRUCTURE OF AN UNBOUND KZ52 NEUTRALIZING ANTI-EBOLAVIRUS ANTIBODY.
 
Authors :  J. E. Lee, M. L. Fusco, D. M. Abelson, A. J. Hessell, D. R. Burton, E. O. Sap
Date :  12 Aug 09  (Deposition) - 27 Oct 09  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  H,L,M,N
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  M,N  (1x)
Keywords :  Antibody Fragment (Fab), Immunoglobulin Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Lee, M. L. Fusco, D. M. Abelson, A. J. Hessell, D. R. Burton, E. O. Saphire
Techniques And Tactics Used In Determining The Structure Of The Trimeric Ebolavirus Glycoprotein.
Acta Crystallogr. , Sect. D V. 65 1162 2009
PubMed-ID: 19923712  |  Reference-DOI: 10.1107/S0907444909032314

(-) Compounds

Molecule 1 - KZ52 ANTIBODY FRAGMENT HEAVY CHAIN
    Chains: H, M
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - KZ52 ANTIBODY FRAGMENT LIGHT CHAIN
    Chains: L, N
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HLMN
Biological Unit 1 (1x): HL  
Biological Unit 2 (1x):   MN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE H:27 , THR H:28 , ASN H:31 , TYR H:32BINDING SITE FOR RESIDUE SO4 H 229
02AC2SOFTWARESER H:52 , SER H:52A , SER H:53 , GLY H:100ABINDING SITE FOR RESIDUE SO4 H 230
03AC3SOFTWARESER H:112 , SER H:113 , ARG N:108BINDING SITE FOR RESIDUE SO4 H 231
04AC4SOFTWAREGLN H:39 , ALA H:40 , GLY H:44 , GLU H:46BINDING SITE FOR RESIDUE GOL H 232
05AC5SOFTWARELYS L:39 , GLN L:42 , LYS L:45 , GOL L:213BINDING SITE FOR RESIDUE SO4 L 212
06AC6SOFTWAREGLN L:37 , LYS L:39 , LYS L:45 , LEU L:47 , ASP L:82 , SO4 L:212BINDING SITE FOR RESIDUE GOL L 213
07AC7SOFTWAREARG L:108 , SER M:113BINDING SITE FOR RESIDUE SO4 M 229
08AC8SOFTWAREPHE M:27 , THR M:28 , ASN M:31 , TYR M:32BINDING SITE FOR RESIDUE SO4 M 230
09AC9SOFTWARESER M:52 , SER M:52A , SER M:53 , THR M:100 , GLY M:100ABINDING SITE FOR RESIDUE SO4 M 231
10BC1SOFTWAREALA M:40 , GLY M:44 , GLU M:46BINDING SITE FOR RESIDUE GOL M 232
11BC2SOFTWARELYS N:39 , GLN N:42 , LYS N:45 , GOL N:213BINDING SITE FOR RESIDUE SO4 N 212
12BC3SOFTWAREGLN N:37 , LYS N:39 , LYS N:45 , ASP N:82 , SO4 N:212BINDING SITE FOR RESIDUE GOL N 213

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194
5M:22 -M:92
6M:142 -M:208
7N:23 -N:88
8N:134 -N:194

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe H:148 -Pro H:149
2Glu H:150 -Pro H:151
3Ser L:7 -Pro L:8
4Ala L:94 -Pro L:95
5Tyr L:140 -Pro L:141
6Phe M:148 -Pro M:149
7Glu M:150 -Pro M:151
8Ser N:7 -Pro N:8
9Ala N:94 -Pro N:95
10Tyr N:140 -Pro N:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3INU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3INU)

(-) Exons   (0, 0)

(no "Exon" information available for 3INU)

(-) 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 H from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3inuH01 H:1-113 Immunoglobulins                                                                                              3inuH02 H:114-228 Immunoglobulins                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee............eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3inu H    1 EVQLLESGGGLVKPGGSLRLSCAASGFTLINYRMNWVRQAPGKGLEWVSSISSSSSYIHYADSVKGRFTISRDNAENSLYLQMNSLRAEDTAVYYCVREGPRATGYSMADVFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128     ||140       150   ||||165   ||  176   ||  187       197  |||  210       220 ||   
                                                                              52A                            82A||               100A|||||||                               134|              154|||    169|      180|               200||              222|   
                                                                                                              82B|                100B||||||                                137               156||     171       182                203|               225   
                                                                                                               82C                 100C|||||                                                   157|                                   205                     
                                                                                                                                    100D||||                                                    162                                                           
                                                                                                                                     100E|||                                                                                                                  
                                                                                                                                      100F||                                                                                                                  
                                                                                                                                       100G|                                                                                                                  
                                                                                                                                        100H                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d3inul1 L:1-107 automated matches                                                                                d3inul2 L:108-211 automated matches                                                                      SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3inuL02 L:108-211 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeee........eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3inu L    1 ELVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKSYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSAPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNR  211
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
                                                     27A|||||                                                                                                                                                                                        
                                                      27B||||                                                                                                                                                                                        
                                                       27C|||                                                                                                                                                                                        
                                                        27D||                                                                                                                                                                                        
                                                         27E|                                                                                                                                                                                        
                                                          27F                                                                                                                                                                                        


Chain M from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3inuM01 M:1-113 Immunoglobulins                                                                                              3inuM02 M:114-227 Immunoglobulins                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee............eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh..eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3inu M    1 EVQLLESGGGLVKPGGSLRLSCAASGFTLINYRMNWVRQAPGKGLEWVSSISSSSSYIHYADSVKGRFTISRDNAENSLYLQMNSLRAEDTAVYYCVREGPRATGYSMADVFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118       128     ||140       150   ||||165   ||  176   ||  187       197  |||  210       220 ||  
                                                                              52A                            82A||               100A|||||||                               134|              154|||    169|      180|               200||              222|  
                                                                                                              82B|                100B||||||                                137               156||     171       182                203|               225  
                                                                                                               82C                 100C|||||                                                   157|                                   205                    
                                                                                                                                    100D||||                                                    162                                                          
                                                                                                                                     100E|||                                                                                                                 
                                                                                                                                      100F||                                                                                                                 
                                                                                                                                       100G|                                                                                                                 
                                                                                                                                        100H                                                                                                                 


Chain N from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d3inun1 N:1-107 automated matches                                                                                d3inun2 N:108-211 automated matches                                                                      SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3inuN02 N:108-211 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeee........eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3inu N    1 ELVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKSYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSAPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNR  211
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
                                                     27A|||||                                                                                                                                                                                        
                                                      27B||||                                                                                                                                                                                        
                                                       27C|||                                                                                                                                                                                        
                                                        27D||                                                                                                                                                                                        
                                                         27E|                                                                                                                                                                                        
                                                          27F
   Legend:   → Mismatch (orange background)
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  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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3INU)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3INU)

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3csy CRYSTAL STRUCTURE OF THE TRIMERIC PREFUSION EBOLA VIRUS GLYCOPROTEIN IN COMPLEX WITH A NEUTRALIZING ANTIBODY FROM A HUMAN SURVIVOR