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(-) Description

Title :  STRUCTURAL ANALYSIS OF THE UNMUTATED ANCESTOR OF THE HIV-1 ENVELOPE V2 REGION ANTIBODY CH58 ISOLATED FROM AN RV144 HIV-1 VACCINE EFFICACY TRIAL VACCINEE AND ASSOCIATED WITH DECREASED TRANSMISSION RISK
 
Authors :  N. I. Nicely, K. Wiehe, T. B. Kepler, F. H. Jaeger, S. M. Dennison, H. -X. L S. M. Alam, K. -K. Hwang, M. Bonsignori, S. Rerks-Ngarm, S. Nitayaphan P. Pitisuttithum, J. Kaewkungwal, M. L. Robb, R. J. O'Connell, N. L. Mi J. H. Kim, B. F. Haynes
Date :  07 Oct 14  (Deposition) - 12 Aug 15  (Release) - 02 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Antibody, Igg Fold, Immune System, Hiv-1 Gp120 V2 Region (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. I. Nicely, K. Wiehe, T. B. Kepler, F. H. Jaeger, S. M. Dennison, S. Rerks-Ngarm, S. Nitayaphan, P. Pitisuttithum, J. Kaewkungwal, M. L. Robb, R. J. O'Connell, N. L. Michael, J. H. Kim, H. X. Liao, S. Munir Alam, K. K. Hwang, M. Bonsignori, B. F. Haynes
Structural Analysis Of The Unmutated Ancestor Of The Hiv-1 Envelope V2 Region Antibody Ch58 Isolated From An Rv144 Vaccine Efficacy Trial Vaccinee.
Ebiomedicine V. 2 713 2015
PubMed-ID: 26288844  |  Reference-DOI: 10.1016/J.EBIOM.2015.06.016

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN
    Chains: P
    Engineered: YES
    Fragment: HIV-1 GP120 DERIVED PEPTIDE (UNP RESIDUES 160-177)
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synthetic: YES
 
Molecule 2 - CH58-UA FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: EXPI293
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - CH58-UA FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell: EXPI293
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4RIS)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:134 -L:193

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeeee....eeee........eeeeehhh.eeeeee...hhhhheeeeeeeeeee.......eeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ris H    1 EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARLGGRYYYDSSGYYYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||    107       117       127       137       147       157       167       177       187       197       207        
                                                                              52A                            82A||               100A||||||||                                                                                                                   
                                                                                                              82B|                100B|||||||                                                                                                                   
                                                                                                               82C                 100C||||||                                                                                                                   
                                                                                                                                    100D|||||                                                                                                                   
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee....eeeeeeee...hhhhh..eeeee......eeee.............eeeeee....eeeeeee..hhhhheeeeeeee....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ris L    1 NFMLTQPHSVSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSSPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSSWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                    11        21      ||29        39        49        59       |67        77        87        97      106A       116       126       136       146       156       166       176       186       196       206   
                                    9|              27A|                                     66A|                                     106A                                                                                                       
                                    11               27B                                      66B                                                                                                                                                


Chain P from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                4ris P  166 RDKKQKVHALFYKA  179
                                   175
   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 4RIS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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