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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 BROADLY NEUTRALIZING ANTIBODY PGT152
 
Authors :  C. Blattner, I. A. Wilson
Date :  03 Dec 13  (Deposition) - 14 May 14  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immunoglobulin, Fab Fragment, Immune System, Hiv Envelope (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Blattner, J. H. Lee, K. Sliepen, R. Derking, E. Falkowska, A. T. De La Pena, A. Cupo, J. P. Julien, M. Van Gils, P. S. Lee, W. Peng, J. C. Paulson, P. Poignard, D. R. Burton, J. P. Moore, R. W. Sanders, I. A. Wilson, A. B. Ward
Structural Delineation Of A Quaternary, Cleavage-Dependent Epitope At The Gp41-Gp120 Interface On Intact Hiv-1 Env Trimers.
Immunity V. 40 669 2014
PubMed-ID: 24768348  |  Reference-DOI: 10.1016/J.IMMUNI.2014.04.008

(-) Compounds

Molecule 1 - PGT152 LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Taxid: 9606
    Mutation: YES
    Organism Common: HUMAN, HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - PGT152 HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Taxid: 9606
    Gene: DKFZP686P15220
    Organism Common: HUMAN, HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4NUJ)

(-) Sites  (0, 0)

(no "Site" information available for 4NUJ)

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr A:7 -Pro A:8
2Phe A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Ser B:127 -Ser B:128
5Phe B:146 -Pro B:147
6Glu B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NUJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NUJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4NUJ)

(-) 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:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nuj A    1 DIVMTQTPLSLSVDPGQPASISCKSSQSLRQSNGKTSLYWYQQKPGQSPQLLIFEVSNRFSGVSDRFVGSGSGTDFTLRISRVEAEDVGFYYCMQSKDFPLTFGGGTKVDLKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    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 B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee..............eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4nuj B    1 RVQLVESGGGVVQPGKSVRLSCVVSDFPFSKYPMYWVRQAPGKGLEWVAAISADAWHVVYSGSVQGRFLVSRDNSKNILYLEMNTLKIEDTAVYRCARMFQESGPPNYYYYSGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100N||||   106       116       126       136       146       156       166       176       186       196       206        
                                                                              52A                            82A||               100A|||||100R                                                                                                                  
                                                                                                              82B|                100B|||||||                                                                                                                   
                                                                                                               82C                 100K||||||                                                                                                                   
                                                                                                                                    100L|||||                                                                                                                   
                                                                                                                                     100M||||                                                                                                                   
                                                                                                                                      100N|||                                                                                                                   
                                                                                                                                       100O||                                                                                                                   
                                                                                                                                        100P|                                                                                                                   
                                                                                                                                         100Q
   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 4NUJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NUJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NUJ)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4NUJ)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4nuj)
 
  Cis Peptide Bonds
    Glu B:148 - Pro B:149   [ RasMol ]  
    Phe A:94 - Pro A:95   [ RasMol ]  
    Phe B:146 - Pro B:147   [ RasMol ]  
    Ser B:127 - Ser B:128   [ RasMol ]  
    Thr A:7 - Pro A:8   [ RasMol ]  
    Tyr A:140 - Pro A:141   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q6N089_HUMAN | Q6N089: 2oqj 3mnv 3qct 3qcu 3qcv 4nm4 4nm8 5ewi 5ug0
        Q8TCD0_HUMAN | Q8TCD0: 1hzh 1n0x 3mnv 3mnw 3mnz 3pgf 4d9q 4nug 4nwt 5viy 5vj6 5vod
UniProtKB/TrEMBL
        Q6N089_HUMAN | Q6N089: 1u6a 3cfj 3cfk 4hpy
        Q8TCD0_HUMAN | Q8TCD0: 3cfj 3cfk 4nwu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4NUJ)