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(-) Description

Title :  CRYSTAL STRUCTURE OF THE INNER DOMAIN OF CLADE A/E HIV-1 GP120 IN COMPLEX WITH THE ADCC-POTENT RHESUS MACAQUE ANTIBODY JR4
 
Authors :  N. Gohain, W. D. Tolbert, M. Pazgier
Date :  15 Dec 15  (Deposition) - 16 Mar 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  G,H,L
Keywords :  Hiv-1 Gp120, Viral Protein, 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 - CLADE A/E 93TH057 HIV-1 GP120 CORE
    Chains: G
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-140
    Gene: HIV-1 ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - JR4 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: RHESUS MACAQUE
    Organism Scientific: MACACA MULATTA
    Organism Taxid: 9544
 
Molecule 3 - JR4 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Common: RHESUS MACAQUE
    Organism Scientific: MACACA MULATTA
    Organism Taxid: 9544

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : GHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR L:80 , VAL L:106 , GLN L:108 , TYR L:140 , LYS L:166 , HOH L:426 , HOH L:429 , HOH L:490 , HOH L:546binding site for residue SO4 L 301
2AC2SOFTWARESER H:172 , THR L:157 , GLY L:158 , HOH L:435 , HOH L:510 , HOH L:514binding site for residue SO4 L 302
3AC3SOFTWARESER L:59 , ARG L:61binding site for residue SO4 L 303
4AC4SOFTWARELYS G:240 , ASN L:156 , THR L:157binding site for residue CL L 304
5AC5SOFTWAREVAL L:11 , SER L:12binding site for residue CL L 305
6AC6SOFTWARETHR L:209binding site for residue CL L 306
7AC7SOFTWAREASN G:234 , HOH G:603 , HOH G:609 , LEU H:45 , GLU H:46 , ASN H:60 , SER L:2binding site for Mono-Saccharide NAG G 501 bound to ASN G 234

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1G:54 -G:74
2G:218 -G:247
3G:228 -G:239
4H:22 -H:92
5H:140 -H:196
6L:23 -L:88
7L:134 -L:193

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro G:212 -Ile G:213
2Ser G:481 -Glu G:482
3Gly H:54 -Gly H:55
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FCU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FCU)

(-) Exons   (0, 0)

(no "Exon" information available for 5FCU)

(-) 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 G from PDB  Type:PROTEIN  Length:104
                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eee...............ee.....eeehhhhhhhhhhhhhhh....eee....eeeeee........eee..eeee.............eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                5fcu G   45 WKDADTTLFCASDTHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKRSELYKYKVVQI  491
                                    54  ||    77        87        97       107||     220       230       240       250 ||    487    
                                       57|                                  108|                                     252|           
                                        71                                   212                                      480           


Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...ee.....eeeeee.hhhhhh..eeeeeee......eeeeeee.....eee.hhhhh.eeeeee....eeeeee...hhhhheeeeeeeeeee....eeeeeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee......eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fcu H    1 EVQLVESGPGLVKPLETLSLTCAVPGGSIRRNYWSWIRQPPGKGLEWIGHSYGSGGSTNYNPSLESRVTLSVDTSKNLFSLKLTSVTAADTAVYYCARTVWYYTSGTHYFDHWGQGVLVTVSSASTKGPSVFPLAPSSSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSGTQTYVCNVNHKPSNTKVDKRVEI  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120       133       143       153       163       173       183  ||   196       206       
                                                                              52A                            82A||               100A|||||                         128|                                                   186|                       
                                                                                                              82B|                100B||||                          132                                                    190                       
                                                                                                               82C                 100C|||                                                                                                           
                                                                                                                                    100D||                                                                                                           
                                                                                                                                     100E|                                                                                                           
                                                                                                                                      100F                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee..........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeeehhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fcu L    2 SVLTQPPSVSAAPGQKVTISCSGSSSNIGRSYVSWYQQVPGAAPKLLIYDTNKRPSGVSDRFSGSKSGSSASLAITGLQTGDEADYYCGAWDGSLNVHIFGSGTKLTVLGQPKASPLVTLFPPSSEELQANKATLVCLISDFYPGVVKVAWKADGNSVNTGVETTTPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPT  209
                                   |12        22     || 30        40        50        60        70        80        90     || 98       107       117       127       137       147       157       167       177       187       197       207  
                                   9|              27A|                                                                  95A|        106A                                                                                                       
                                   11               27B                                                                   95B
   Legend:   → Mismatch (orange background)
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  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 5FCU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FCU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FCU)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5FCU)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Gly H:54 - Gly H:55   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Pro G:212 - Ile G:213   [ RasMol ]  
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        A0A0M3KKW9_9 | A0A0M3KKW9: 4s1q 4s1r 4s1s 4ybl 4yc2 5cd5 5f96 5f9o 5f9w 5kjr 5te6 5u6e

(-) Related Entries Specified in the PDB File

4h8w HIV-1 CLADE A/E 93TH057 (H375S) GP120 IN COMPLEX WITH N5-I5
4rfe JR4 FAB STRUCTURE
4rfn HIV-1 CLADE A/E 93TH057 (H375S) GP120 IN COMPLEX WITH JR4