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(-) Description

Title :  2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL ANTIBODY 6A7 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 :  1.99
Chains :  Asym./Biol. Unit :  H,L,P
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 - 6A7 ANTIBODY HEAVY CHAIN
    Cell: HYBRIDOMA
    Cell Line: MYELOMA CELL LINE FO
    Chains: H
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - 6A7 ANTIBODY LIGHT CHAIN
    Cell: HYBRIDOMA
    Cell Line: MYELOMA CELL LINE FO
    Chains: L
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 3 - ENVELOPE GLYCOPROTEIN GP41
    Chains: P
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: HIV-1 GP41 PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
2ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS H:163 , HOH H:244 , ASN L:143 , HOH L:268BINDING SITE FOR RESIDUE ZN H 222
2AC2SOFTWAREASP H:1 , HOH H:275 , HOH H:288 , HIS L:98 , HOH L:321BINDING SITE FOR RESIDUE ZN H 223
3AC3SOFTWAREGLU L:190 , HIS L:194 , HOH L:290BINDING SITE FOR RESIDUE ZN L 233

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:139 -H:194
3L:23 -L:93
4L:139 -L:199

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LEY)

(-) 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 H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               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
                 3ley H   1 DVQLQESGPGLVKPSQSLSLTCTVTGYLITTDYAWNWIRQFPGNKLEWMGYISYSGFTSYNPSLKSQISITRDTSKNQFFLQLNSVTTEDTATYYCAFGNYLPAYWGQGTLVTVSAAKTTAPSVYPLAPVCGGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTI 216
                                    10        20        30     |  39        49        59        69        79   |||  86        96       106       116       126 ||    139       149       159       169       179       189       199       209       
                                                             35A                                             82A||                                           128|                                                                                    
                                                                                                              82B|                                            132                                                                                    
                                                                                                               82C                                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee...eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ley L   1 DVVMTQTPLSLSVTLGQPASISCKSSQSLLDSDGKTYLNWLLQRPGQSPKRLIYLVSKLASGVPDRFTGSGSGTDFTLKINRVEAEDLGIYYCWQGTHFPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKSPIVKSFNRNEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   ||  213      
                                                                                                                                                                                                                                     204|           
                                                                                                                                                                                                                                      208           


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 GP41-3le- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3ley 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 3LEY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain 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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  Q9IJQ0_9HIV1 | Q9IJQ0
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 Related Entries

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

UniProtKB/TrEMBL
        Q9IJQ0_9HIV1 | Q9IJQ0: 3lex

(-) 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
3lex 2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL ANTIBODY 11F10 IN COMPLEX WITH HIV-1 GP41