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(-) Description

Title :  CRYSTAL STRUCTURE OF DH511.2_K3 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 :  1.76
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 - DH511.2_K3 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Expression System Variant: HEK 293
    Gene: IGG HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DH511.2_K3 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Expression System Variant: HEK 293
    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 5U3O)

(-) Sites  (0, 0)

(no "Site" information available for 5U3O)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:216 -L:214
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U3O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3O)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3O)

(-) 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:17
                                                  
               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
                5u3o A  669 KWNWFDITNWLWYIRKK  685
                                   678       


Chain H from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeeeeeee..hhhhh..eeeeeeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u3o H    1 QVQLVQSGGGLVKPGGSLTLSCSASGFFFDNSWMGWVRQAPGKGLEWVGRIRRLKDGATGEYGAAVKDRFTISRDDSRNMLYLHMRTLKTEDSGTYYCTMDEGTPVTRFLEWGYFYYYMAVWGRGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC  216
                                    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:216
                                                                                                                                                                                                                                                         
               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..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5u3o L    1 DIQMTQSPSFLYGSVGDRVTITCRASQNIKDYLNWYQQRPGRAPRLLIYAASNLQSGVPSRFSGSGYGTDFTLIISSLQPEDFATYFCQESYSSTPTHIFGLGTKLEKKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    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 5U3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3O)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ 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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 Related Entries

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        ENV_HV1B9 | Q73372: 4r4h 5u3k 5u3l 5u3m 5u3n

(-) 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
5u3n CRYSTAL STRUCTURE OF DH511.12P FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
5u3p CRYSTAL STRUCTURE OF DH511.4 FAB