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(-) Description

Title :  CRYSTAL STRUCTURE OF RV144-ELICITED ANTIBODY CH59 IN COMPLEX WITH V2 PEPTIDE
 
Authors :  J. S. Mclellan, J. Gorman, B. F. Haynes, P. D. Kwong
Date :  24 Oct 12  (Deposition) - 06 Feb 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Immunoglobulin, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. X. Liao, M. Bonsignori, S. M. Alam, J. S. Mclellan, G. D. Tomaras, M. A. Moody, D. M. Kozink, K. K. Hwang, X. Chen, C. Y. Tsao, P. Liu, X. Lu, R. J. Parks, D. C. Montefiori, G. Ferrari, J. Pollara, M. Rao, K. K. Peachman, S. Santra, N. L. Letvin, N. Karasavvas, Z. Y. Yang, K. Dai, M. Pancera, J. Gorman, K. Wiehe, N. I. Nicely, S. Rerks-Ngarm, S. Nitayaphan, J. Kaewkungwal, P. Pitisuttithum, J. Tartaglia, F. Sinangil, J. H. Kim, N. L. Michael, T. B. Kepler, P. D. Kwong, J. R. Mascola, G. J. Nabel, A. Pinter, S. Zolla-Pazner, B. F. Haynes
Vaccine Induction Of Antibodies Against A Structurally Heterogeneous Site Of Immune Pressure Within Hiv-1 Envelope Protein Variable Regions 1 And 2.
Immunity V. 38 176 2013
PubMed-ID: 23313589  |  Reference-DOI: 10.1016/J.IMMUNI.2012.11.011

(-) Compounds

Molecule 1 - CH59 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - CH59 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ENVELOPE GLYCOPROTEIN GP160
    Chains: P
    Engineered: YES
    Fragment: UNP RESIDUES 160-178
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: PEPTIDE DERIVED FROM HIV-1 GP120 V2 REGION
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR H:183 , SER L:114 , VAL L:115 , THR L:116 , LEU L:135 , ILE L:136 , SER L:137 , HOH L:632BINDING SITE FOR RESIDUE GOL L 301
2AC2SOFTWAREGLU L:83 , VAL L:106 , GLY L:107 , GLN L:108 , TYR L:140 , HOH L:418 , HOH L:422BINDING SITE FOR RESIDUE GOL L 302

(-) 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 4HPY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HPY)

(-) 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:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeee.hhhhh....ee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hpy H    2 VQLVESGGGLVQPGRSLRLSCAASGFTFDDGAMHWVRQAPGKGLEWVSGISWNSNIIAYADSVKGRFTISRDNAKNSLYLEMNSLRVEDTALYYCAKDSPRGELPLNYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||| 104       114       124       134       144       154       164       174       184       194       204         
                                                                             52A                            82A||               100A||                                                                                                                 
                                                                                                             82B|                100B|                                                                                                                 
                                                                                                              82C                 100C                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee.........eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee......eee...eeeee........eeeee..hhhhhh...eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hpy L    0 DSYELTQPPSVSVSPGQTARITCSGDALPKNYAYWYQQKSGQAPVLVIYEDSKRPSGIPERFSGSSSGTMATLTISGAQVEDEADYYCYSTDSSGNHRVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE  210
                                     9|       20        30        40        50        60        70        80        90     || 98       107       117       127       137       147       157       167       177       187       197       207   
                                     9|                                                                                  95A|        106A                                                                                                        
                                     11                                                                                   95B                                                                                                                    


Chain P from PDB  Type:PROTEIN  Length:11
                                            
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .....hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                4hpy P  168 KKQKVHALFYK  178
                                   177
   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 4HPY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 4nuj 5ewi 5ug0
        Q8N5F4_HUMAN | Q8N5F4: 4dag
        Q9WLG7_9HIV1 | Q9WLG7: 4hpo
UniProtKB/TrEMBL
        G9HS63_9HIV1 | G9HS63: 4hpo
        Q6N089_HUMAN | Q6N089: 1u6a 3cfj 3cfk

(-) Related Entries Specified in the PDB File

4hpo 4hqq