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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ANTI-HIV-1 GP120-REACTIVE ANTIBODY 17B
 
Authors :  C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, M. Farzan, P. D. Kwong
Date :  24 Dec 03  (Deposition) - 03 Feb 04  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hiv-1; Gp120; Cd4I; Antibodies; Tyrosine Sulfation; Vh-Gene Usage, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, H. Choe, M. Farzan, P. D. Kwong
Structural Basis Of Tyrosine Sulfation And Vh-Gene Usage In Antibodies That Recognize The Hiv Type 1 Coreceptor-Binding Site On Gp120
Proc. Natl. Acad. Sci. Usa V. 101 2706 2004
PubMed-ID: 14981267  |  Reference-DOI: 10.1073/PNAS.0308527100

(-) Compounds

Molecule 1 - FAB 17B LIGHT CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: HUMAN HERPESVIRUS 4
    Expression System Cell: IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
    Expression System Common: EPSTEIN-BARR VIRUS
    Expression System Taxid: 10376
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 17B HEAVY CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: HUMAN HERPESVIRUS 4
    Expression System Cell: IMMORTALIZED B-CELL CLONE FUSED WITH A MURINE B-CELL FUSION PARTNER
    Expression System Common: EPSTEIN-BARR VIRUS
    Expression System Taxid: 10376
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1RZ8)

(-) Sites  (0, 0)

(no "Site" information available for 1RZ8)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:140 -B:196
5C:23 -C:88
6C:134 -C:194
7D:22 -D:92
8D:140 -D:196

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Trp A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:146 -Pro B:147
5Glu B:148 -Pro B:149
6Ser C:7 -Pro C:8
7Trp C:94 -Pro C:95
8Tyr C:140 -Pro C:141
9Phe D:146 -Pro D:147
10Glu D:148 -Pro D:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RZ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RZ8)

(-) Exons   (0, 0)

(no "Exon" information available for 1RZ8)

(-) 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:214
                                                                                                                                                                                                                                                       
               SCOP domains d1rz8a1 A:1-109 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1rz8a2 A:110-212 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains 1rz8A01 A:1-108 Immunoglobulins                                                                               1rz8A02 A:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee........ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rz8 A    1 DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains d1rz8b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                                  d1rz8b2 B:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1rz8B01 B:1-113 Immunoglobulins                                                                                                 1rz8B02 B:114-213 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeeee....eeee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee..hhhhh.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1rz8 B    1 EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105       115       125       135       145       155       165       175       185       195       205        
                                                                              52A                            82A||               100A|||||100J|                                                                                                                 
                                                                                                              82B|                100B|||||100K                                                                                                                 
                                                                                                               82C                 100C||||||                                                                                                                   
                                                                                                                                    100D|||||                                                                                                                   
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d1rz8c1 C:1-109 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1rz8c2 C:110-212 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains 1rz8C01 C:1-108 Immunoglobulins                                                                               1rz8C02 C:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee........ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rz8 C    1 DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains d1rz8d1 D:1-113 Immunoglobulin heavy chain variable domain, VH                                                                  d1rz8d2 D:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1rz8D01 D:1-113 Immunoglobulins                                                                                                 1rz8D02 D:114-213 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeee.hhhh.eee.......eeeeee....eeeeee...hhhhheeeeeeeee..hhhhh.........ee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1rz8 D    1 EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105       115       125       135       145       155       165       175       185       195       205        
                                                                              52A                            82A||               100A|||||100J|                                                                                                                 
                                                                                                              82B|                100B|||||100K                                                                                                                 
                                                                                                               82C                 100C||||||                                                                                                                   
                                                                                                                                    100D|||||                                                                                                                   
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I
   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  (4, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1rz8A02A:109-211
1b1rz8A01A:1-108
1c1rz8C01C:1-108
1d1rz8B02B:114-213
1e1rz8D02D:114-213
1f1rz8B01B:1-113
1g1rz8D01D:1-113
1h1rz8C02C:109-211

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RZ8)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1RZ8)

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  Cis Peptide Bonds
    Glu B:148 - Pro B:149   [ RasMol ]  
    Glu D:148 - Pro D:149   [ RasMol ]  
    Phe B:146 - Pro B:147   [ RasMol ]  
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    Tyr C:140 - Pro C:141   [ RasMol ]  
 
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  1rz8
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1RZ8)

(-) Related Entries Specified in the PDB File

1rz7 1rzf 1rzg 1rzi 1rzj 1rzk