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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STABILIZED INNER DOMAIN OF CLADE A/E HIV-1 GP120 IN COMPLEX WITH THE ADCC MEDIATING ANTI-HIV-1 ANTIBODY A32
 
Authors :  W. D. Tolbert, N. Gohain, M. Pazgier
Date :  18 Feb 15  (Deposition) - 02 Mar 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,G,H,L
Biol. Unit 1:  G,H,L  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Adcc, Non-Neutralizing, Anti-Hiv-1 Env Antibody A32, Cd4I Antibody, Viral Glycoprotein Gp120, Hiv-1 Env, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. D. Tolbert, N. Gohain, M. Veillette, J. P. Chapleau, C. Orlandi, M. L. Visciano, M. Ebadi, A. L. Devico, T. R. Fouts, A. Finzi, G. K. Lewis M. Pazgier
Paring Down Hiv Env: Design And Crystal Structure Of A Stabilized Inner Domain Of Hiv-1 Gp120 Displaying A Major Adcc Target Of The A32 Region.
Structure V. 24 697 2016
PubMed-ID: 27041594  |  Reference-DOI: 10.1016/J.STR.2016.03.005

(-) Compounds

Molecule 1 - STABILIZED INNER DOMAIN OF CLADE A/E GP120
    Chains: G, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK GNT1- 293 CELLS
    Expression System Taxid: 9606
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: CLADE A/E
 
Molecule 2 - A32 ANTIBODY FAB HEAVY CHAIN
    Chains: H, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293 CELLS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - A32 ANTIBODY LIGHT CHAIN
    Chains: L, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293 CELLS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCGHL
Biological Unit 1 (1x):    GHL
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4YBL)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:54 -A:74
2A:65 -A:115
3A:218 -A:247
4A:228 -A:239
5B:22 -B:92
6B:140 -B:196
7C:23 -C:88
8C:134 -C:193
9G:54 -G:74
10G:65 -G:115
11G:218 -G:247
12G:228 -G:239
13H:22 -H:92
14H:140 -H:196
15L:23 -L:88
16L:134 -L:193

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Gly H:26 -Gly H:27
2Lys H:43 -Gly H:44
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Tyr L:140 -Pro L:141
6Tyr B:40 -Pro B:41
7Lys B:43 -Gly B:44
8Phe B:146 -Pro B:147
9Glu B:148 -Pro B:149
10Tyr C:140 -Pro C:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YBL)

(-) 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:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee.......hhhhhhhhhhhee......ee..............hhhhhhhhhhhhhhhhhh...eee....eeeee..............ee.........hhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ybl A   45 WKDADTTLFCASDAKAHETECHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQCLIPIHYCTPAGYVILKCNDFNGTGPCKNVSSVQCTHGIKPNIKDNWRSELYKYKVVQI  491
                                    54        64        74        84        94       104       114 ||    220       230|      242       252||     482         
                                                                                                 116|              230|                 253|                 
                                                                                                  213               233                  474                 


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...ee....eeeeeeeee.......eeeeeeee.....eeeeeeee....eee.......eeeeeehhh.eeeeeee..hhhhheeeeeeeee.......eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ybl B    2 VQLQESGPGLVKPSQTLSLSCTVSGSSSSGAHYWSWIRQYPGKGLEWIGYIHYSGNTYYNPSLKSRITISQHTSENQFSLKLNSVTVADTAVYYCARGTRLRTLRNAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    11        21   ||   32   ||   40        50        60        70        80  |||   87        97   ||||102       112       122       132       142       152       162       172       182       192       202       212  
                                                  25|      35A|                                             82A||               100A||||                                                                                                                  
                                                   27       35B                                              82B|                100B|||                                                                                                                  
                                                                                                              82C                 100C||                                                                                                                  
                                                                                                                                   100D|                                                                                                                  
                                                                                                                                    100E                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....eeeeeee...........eeeeee......eeee.............eeeee...eeeeeee..hhhhheeeeeeeee...eeee...eeeee........eeeee..hhhhhhh...eeeeeeeee......eeeee..eee...eee...ee.....eeeeeeee.hhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ybl C    4 VLTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQHHPGKAPKLIISEVNNRPSGVPDRFSGSKSGNTASLTVSGLQAEDEAEYYCSSYTDIHNFVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    13        23    ||| 30        40        50        60        70        80        90     |  99       108       118       128       138       148       158       168       178       188       198       208
                                                  27A||                                                                  95A        106A                                                                                                      
                                                   27B|                                                                                                                                                                                       
                                                    27C                                                                                                                                                                                       


Chain G from PDB  Type:PROTEIN  Length:126
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhh..ee......eee.....eeee.hhh....hhhhhhhhhhhhhh....eeee....eeeeee.....eeee..eeee.........hhhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ybl G   50 TTLFCASDAKAHETECHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQCLDPIPIHYCTPAGYVILKCNDFNGTGPCKNVSSVQCTHGIKPNIKDNWRSELYKYKVVQI  491
                                    59        69        79        89        99       109      |213       223      |235       245       475       485      
                                                                                            116|                230|                 253|                 
                                                                                             211                 233                  474                 


Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee.....eeeeeeee......eeeeeee....eee.......eeeeee....eeeeeee..hhhhheeeeeeeee.......eeeee...eeeee........eeeee...eeeeeeeeeee........hhhhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ybl H    1 QVQLQESGPGLVKPSQTLSLSCTVSGGSGAHYWSWIRQYPGKGLEWIGYIHYSGNTYYNPSLKSRITISQHTSENQFSLKLNSVTVADTAVYYCARGTRLRTLRNAFDIWGQGTMVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20       |33  ||    41        51        61        71        81 |||    88        98  |||||103       113       123  ||   140       150       160       170       180       190       200       210    
                                                      28| 35A|                                             82A||               100A||||                       126|                                                                                
                                                       32  35B                                              82B|                100B|||                        134                                                                                
                                                                                                             82C                 100C||                                                                                                           
                                                                                                                                  100D|                                                                                                           
                                                                                                                                   100E                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....eeeeeee...........eeeeee......eeee.............eeeee...eeeeeee..hhhhheeeeeeee.....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ybl L    4 VLTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQHHPGKAPKLIISEVNNRPSGVPDRFSGSKSGNTASLTVSGLQAEDEAEYYCSSYTDIHNFVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    13        23    ||| 30        40        50        60        70        80        90     |  99       108       118       128       138       148       158       168       178       188       198       208
                                                  27A||                                                                  95A        106A                                                                                                      
                                                   27B|                                                                                                                                                                                       
                                                    27C
   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 4YBL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    Glu B:148 - Pro B:149   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Gly H:26 - Gly H:27   [ RasMol ]  
    Lys B:43 - Gly B:44   [ RasMol ]  
    Lys H:43 - Gly H:44   [ RasMol ]  
    Phe B:146 - Pro B:147   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Tyr B:40 - Pro B:41   [ RasMol ]  
    Tyr C:140 - Pro C:141   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 
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 Related Entries

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        A0A0M3KKW9_9 | A0A0M3KKW9: 4s1q 4s1r 4s1s 4yc2 5cd5 5f96 5f9o 5f9w 5fcu 5kjr 5te6 5u6e

(-) Related Entries Specified in the PDB File

3tnm THE A32 FAB STRUCTURE.
4h8w THE CLADE A/E HIV-1 GP120 IN COMPLEX WITH THE N5-I5 FAB.
4rqh THE INNER DOMAIN OF CLADE A/E HIV-1 GP120 IN COMPLEX WITH THE JR4 FAB.
4yc2