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(-) Description

Title :  CRYSTAL STRUCTURE OF DH511.2 FAB IN COMPLEX WITH HIV-1 GP41 MPER 670-683 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 :  2.17
Chains :  Asym. Unit :  A,B,C,H,L,P
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  A,B,C  (1x)
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 FAB HEAVY CHAIN
    Chains: H, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Taxid: 9606
    Gene: IGG HEAVY CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DH511.2 FAB LIGHT CHAIN
    Chains: L, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Taxid: 9606
    Gene: IGG LIGHT CHAIN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GP41 MPER PEPTIDE
    Chains: P, C
    Engineered: YES
    Fragment: GP41 656-683
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: GP41 MPER 670-683 PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCHLP
Biological Unit 1 (1x):    HLP
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5U3L)

(-) Sites  (0, 0)

(no "Site" information available for 5U3L)

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:194
5H:22 -H:92
6L:23 -L:88
7L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric 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
5Phe A:146 -Pro A:147
6Glu A:148 -Pro A:149
7Ser B:7 -Pro B:8
8Tyr B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U3L)

(-) Exons   (0, 0)

(no "Exon" information available for 5U3L)

(-) 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 A from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhhh..eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeeee..hhhhh..eeeeeeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh...eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u3l A    1 QVQLVQSGGGLVKPGGSLTLSCSASGFFFDNSWMGWVRQAPGKGLEWVGRIRRLKDGATGEYGAAVKDRFTISRDDSRNMLYLHMRTLKTEDSGTYYCTMDEGTPVTRFLEWGYFYYYMAVWGRGTTVIVSSASTKGPSVFPLAGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTTYICNVNHKPSNTKVDKRVEP  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||101       111       121   ||  138       148       158       168       178       188  ||   199       209    
                                                                              52A||                            82A||               100A|||||100J|||                      125|                                                       191|                    
                                                                               52B|                             82B|                100B|||||100K||                       133                                                        193                    
                                                                                52C                              82C                 100C|||||100L|                                                                                                         
                                                                                                                                      100D|||||100M                                                                                                         
                                                                                                                                       100E||||                                                                                                             
                                                                                                                                        100F|||                                                                                                             
                                                                                                                                         100G||                                                                                                             
                                                                                                                                          100H|                                                                                                             
                                                                                                                                           100I                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.............eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u3l B    1 DIVMTQSPSSVSASVGDRVTITCRASQNIRDYLNWYQHKPGGSPRLLIYAASTLQTGVPSRFSGSGSGNLFTLTITNLQPEDFATYYCQENYNTIPSLSFGQGTKVDIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208   
                                                                                                                         95A|                                                                                                                    
                                                                                                                          95B                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:19
                                                    
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                5u3l C  667 KKKWNWFDITNWLWYIRKK  685
                                   676         


Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeeeeeee..hhhhh..eeeeeeee...eeeee........eeeee........eeeeeeeeee.....eeee........eee...ee.....eeeeeeeee....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u3l H    1 QVQLVQSGGGLVKPGGSLTLSCSASGFFFDNSWMGWVRQAPGKGLEWVGRIRRLKDGATGEYGAAVKDRFTISRDDSRNMLYLHMRTLKTEDSGTYYCTMDEGTPVTRFLEWGYFYYYMAVWGRGTTVIVSSASTKGPSVFPLAPSSSTSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSYICNVNHKPSNTKVDKRVEP  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||101       111       121      |132|      144       154       164       174       184  ||   200       210   
                                                                              52A||                            82A||               100A|||||100J|||                         128| ||                                                 187|                   
                                                                               52B|                             82B|                100B|||||100K||                          130 ||                                                  194                   
                                                                                52C                              82C                 100C|||||100L|                            132|                                                                        
                                                                                                                                      100D|||||100M                             135                                                                        
                                                                                                                                       100E||||                                                                                                            
                                                                                                                                        100F|||                                                                                                            
                                                                                                                                         100G||                                                                                                            
                                                                                                                                          100H|                                                                                                            
                                                                                                                                           100I                                                                                                            


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.............eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5u3l L    1 DIVMTQSPSSVSASVGDRVTITCRASQNIRDYLNWYQHKPGGSPRLLIYAASTLQTGVPSRFSGSGSGNLFTLTITNLQPEDFATYYCQENYNTIPSLSFGQGTKVDIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B                                                                                                                     


Chain P from PDB  Type:PROTEIN  Length:19
                                                    
               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
                5u3l P  667 KKKWNWFDITNWLWYIRKK  685
                                   676
   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 5U3L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U3L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U3L)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    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 ]  
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        ENV_HV1B9 | Q73372: 4r4h 5u3k 5u3m 5u3n 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
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
5u3o CRYSTAL STRUCTURE OF DH511.2_K3 FAB IN COMPLEX WITH HIV-1 GP41 MPER PEPTIDE
5u3p CRYSTAL STRUCTURE OF DH511.4 FAB