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(-) Description

Title :  CRYSTAL STRUCTURE OF DH511.12P FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
 
Authors :  G. Ofek, L. Wu, C. S. Lougheed, L. D. Williams, N. I. Nicely, B. F. Haynes
Date :  02 Dec 16  (Deposition) - 15 Feb 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Hiv-1, Neutralizing, Antibody, Gp41, Mper, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. D. Williams, G. Ofek, S. Schatzle, J. R. Mcdaniel, X. Lu, N. I. Nicely L. Wu, C. S. Lougheed, T. Bradley, M. K. Louder, K. Mckee, R. T. Bailer, S. O'Dell, I. S. Georgiev, M. S. Seaman, R. J. Parks, D. J. Marshall, K. Anasti, G. Yang, X. Nie, N. L. Tumba, K. Wiehe, K. Wagh, B. Korber, T. B. Kepler, S. M. Alam, L. Morris, G. Kamanga, M. S. Cohen, M. Bonsignori, S. -M. Xia, D. C. Montefiori, G. Kelsoe, F. Gao, J. R. Mascola, M. A. Moody, K. O. Saunders, H. -X. Liao, G. D. Tomaras, G. Georgiou, B. F. Haynes
Potent And Broad Hiv Neutralizing Antibodies In Memory B Cells And Plasma
Sci Immunol 2017
PubMed: search  |  Reference-DOI: 10.1126/SCIIMMUNOL.AAL2200

(-) Compounds

Molecule 1 - DH511.12P FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 EMBRYONIC KIDNEY CELLS
    Expression System Taxid: 9606
    Fragment: FRAGMENT OF ANTIGEN BINDING
    Gene: IGG HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DH511.12P FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293 EMBRYONIC KIDNEY CELLS
    Expression System Taxid: 9606
    Fragment: FRAGMENT OF ANTIGEN BINDING
    Gene: IGG LIGHT CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GP41 MPER PEPTIDE
    Chains: A
    Engineered: YES
    Fragment: GP41 656-683
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: GP41 MPER PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5U3N)

(-) Sites  (0, 0)

(no "Site" information available for 5U3N)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly H:54 -Pro H:55
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Ser L:7 -Pro L:8
5Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U3N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3N)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3N)

(-) 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:23
                                                        
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                5u3n A  662 ELDKWASLWNWFDITNWLWYIRK  684
                                   671       681   


Chain H from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee........eeeee..hhhhheeeeeee.....eeeeeee.hhhhh..eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeeeee..hhhhh..eeeeeeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5u3n H    1 QVQLVQSGGGLVKPGGSLTPSCVTSGFTFSNTWMSWVRQTPGKGLEWVARISRVGDGPIIDYAAPVKGRFIISRDDSRNTLFLHMNNLKTEDTAVYYCTADEGAPILRFFEWGYYNYYMDVWGKGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||101       111       121       131       141       151       161       171       181       191       201       211    
                                                                              52A||                            82A||               100A|||||100J|||                                                                                                                   
                                                                               52B|                             82B|                100B|||||100K||                                                                                                                   
                                                                                52C                              82C                 100C|||||100L|                                                                                                                   
                                                                                                                                      100D|||||100M                                                                                                                   
                                                                                                                                       100E||||                                                                                                                       
                                                                                                                                        100F|||                                                                                                                       
                                                                                                                                         100G||                                                                                                                       
                                                                                                                                          100H|                                                                                                                       
                                                                                                                                           100I                                                                                                                       


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee.............eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u3n L    1 DIRLTQSPSSLSASVGDRITITCRASQSIKDYLNWYKHRPGEAPKLLIYSASKLRSGVSSRFSGSGYGSAFTLTISSLQPEDFATYYCQESYSSVPMYIFGQGTKVDLKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208     
                                                                                                                         95A|                                                                                                                      
                                                                                                                          95B
   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 5U3N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3N)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 5u3n)
 
  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Gly H:54 - Pro H:55   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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        ENV_HV1B9 | Q73372: 4r4h 5u3k 5u3l 5u3m 5u3o

(-) Related Entries Specified in the PDB File

5u3j CRYSTAL STRUCTURE OF DH511.1 FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
5u3k CRYSTAL STRUCTURE OF DH511.2 FAB IN COMPLEX WITH HIV-1 GP41 MPER 662-683 PEPTIDE
5u3l CRYSTAL STRUCTURE OF DH511.2 FAB IN COMPLEX WITH HIV-1 GP41 MPER 670-683 PEPTIDE
5u3m CRYSTAL STRUCTURE OF DH511.11P FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
5u3o CRYSTAL STRUCTURE OF DH511.2_K3 FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
5u3p CRYSTAL STRUCTURE OF DH511.4 FAB