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(-) Description

Title :  2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL ANTIBODY 11F10 IN COMPLEX WITH HIV-1 GP41
 
Authors :  G. Ofek, F. J. Guenaga, W. R. Schief, J. Skinner, D. Baker, R. Wyatt, P. D.
Date :  15 Jan 10  (Deposition) - 29 Sep 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
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, Gp-41, Monoclonal Antibody, 2F5, Scaffold, Epitope, Transplant, Graft, Re-Elcitation, Envelope Protein, Immune System, Vaccine Design (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Ofek, F. J. Guenaga, W. R. Schief, J. Skinner, D. Baker, R. Wyatt, P. D. Kwong
Elicitation Of Structure-Specific Antibodies By Epitope Scaffolds.
Proc. Natl. Acad. Sci. Usa V. 107 17880 2010
PubMed-ID: 20876137  |  Reference-DOI: 10.1073/PNAS.1004728107

(-) Compounds

Molecule 1 - 11F10 ANTIBODY HEAVY CHAIN
    Cell: HYBRIDOMA
    Cell Line: MYELOMA CELL LINE FO
    Chains: H, A
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - 11F10 ANTIBODY LIGHT CHAIN
    Cell: HYBRIDOMA
    Cell Line: MYELOMA CELL LINE FO
    Chains: L, B
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 3 - ENVELOPE GLYCOPROTEIN GP41
    Chains: P, C
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: HIV-1 GP41 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NH22Mod. Amino AcidAMINO GROUP
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (0, 0)

(no "Site" information available for 3LEX)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:139 -A:194
3B:23 -B:88
4B:134 -B:194
5H:22 -H:92
6H:139 -H:194
7L:23 -L:93
8L:139 -L:199

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Asn H:96 -Tyr H:97
2Phe H:145 -Pro H:146
3Glu H:147 -Pro H:148
4Trp H:187 -Pro H:188
5Thr L:7 -Pro L:8
6Phe L:99 -Pro L:100
7Tyr L:145 -Pro L:146
8Asn A:96 -Tyr A:97
9Phe A:145 -Pro A:146
10Glu A:147 -Pro A:148
11Trp A:187 -Pro A:188
12Thr B:7 -Pro B:8
13Phe B:94 -Pro B:95
14Tyr B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LEX)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee......................................hhh....................hhhhh..........................................................................................................hhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lex A   1 DVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWSWIRQFPGNKLEWMGYINYSGYTSYNPSLKSRISITRDTSENQFFLQLHSVTPEDTATYFCAYGNYLPAYWGQGTLVTVSAAKTTAPSVYPLAPVGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG 213
                                    10        20        30     |  39        49        59        69        79   |||  86        96       106       116       126|      141       151       161       171       181       191       201       211  
                                                             35A                                             82A||                                         126|                                                                                 
                                                                                                              82B|                                          132                                                                                 
                                                                                                               82C                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee..........................................................hhhhh.....................................hhhhhhh.......................................................hhhhh........................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lex B   1 DVVMTQTPLSLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLASGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGTHFPWTFGGYTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
                                                     27A||||                                                                                                                                                                                           
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:9
 aligned with Q9IJQ0_9HIV1 | Q9IJQ0 from UniProtKB/TrEMBL  Length:122

    Alignment length:9
         Q9IJQ0_9HIV1   100 LLELDKWAG 108
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3lex C 660 LLELDKWAx 668
                                    |
                                  668-NH2


Chain H from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lex H   1 DVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWSWIRQFPGNKLEWMGYINYSGYTSYNPSLKSRISITRDTSENQFFLQLHSVTPEDTATYFCAYGNYLPAYWGQGTLVTVSAAKTTAPSVYPLAPVGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG 213
                                    10        20        30     |  39        49        59        69        79   |||  86        96       106       116       126|      141       151       161       171       181       191       201       211  
                                                             35A                                             82A||                                         126|                                                                                 
                                                                                                              82B|                                          132                                                                                 
                                                                                                               82C                                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee..........................................................hhhhh.....................................hhhhhhh.......................................................hhhhh........................hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lex L   1 DVVMTQTPLSLSVTIGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLASGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGTHFPWTFGGYTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    10        20       30C||      40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                                                     28A||||                                                                                                                                                                                           
                                                      29B|||                                                                                                                                                                                           
                                                       30C||                                                                                                                                                                                           
                                                        31D|                                                                                                                                                                                           
                                                         32E                                                                                                                                                                                           


Chain P from PDB  Type:PROTEIN  Length:9
 aligned with Q9IJQ0_9HIV1 | Q9IJQ0 from UniProtKB/TrEMBL  Length:122

    Alignment length:9
         Q9IJQ0_9HIV1   100 LLELDKWAG 108
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
           Pfam domains (1) GP41-3le- Pfam domains (1)
           Pfam domains (2) GP41-3le- Pfam domains (2)
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3lex P 660 LLELDKWAx 668
                                    |
                                  668-NH2
   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 3LEX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LEX)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: GP41] (22)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain C,P   (Q9IJQ0_9HIV1 | Q9IJQ0)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9IJQ0_9HIV1 | Q9IJQ0: 3ley

(-) Related Entries Specified in the PDB File

1tji CRYSTAL STRUCTURE OF THE BROADLY NEUTRALIZING ANTI-HIV-1 ANTIBODY 2F5 IN COMPLEX WITH A GP41 17MER
3les 2F5 EPITOPE SCAFFOLD ES2
3lev HIV-1 ANTIBODY 2F5 IN COMPLEX WITH EPITOPE SCAFFOLD ES2
3ley 2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL ANTIBODY 6A7 IN COMPLEX WITH HIV-1 GP41