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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-HIV-1 V3 FAB 4025 IN COMPLEX WITH CON A PEPTIDE
 
Authors :  X. P. Kong, J. Sampson
Date :  07 Nov 11  (Deposition) - 28 Dec 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Ig Domains, Antibody Fab, Antigen Binding, The Third Variable Region Of Hiv-1 Gp120, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Gorny, J. Sampson, H. Li, X. Jiang, M. Totrov, X. H. Wang, C. Williams, T. O'Neal, B. Volsky, L. Li, T. Cardozo, P. Nyambi, S. Zolla-Pazner, X. P. Kong
Human Anti-V3 Hiv-1 Monoclonal Antibodies Encoded By The Vh5-51/Vl Lambda Genes Define A Conserved Antigenic Structure.
Plos One V. 6 27780 2011
PubMed-ID: 22164215  |  Reference-DOI: 10.1371/JOURNAL.PONE.0027780

(-) Compounds

Molecule 1 - LIGHT CHAIN OF ANTI-HIV-1 V3 MONOCLONAL ANTIBODY 4025
    Chains: L
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB REGION OF THE HEAVY CHAIN OF ANTI-HIV-1 V3 MONOCLONAL ANTIBODY 4025
    Chains: H
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - GP120
    Chains: P
    Engineered: YES
    Fragment: UNP RESIDUES 30-52
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: SYNTHESIZED BASED ON HIV-1 STRAIN OF CONSENSUS CLADE A
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric/Biological Unit (3, 34)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2GOL19Ligand/IonGLYCEROL
3SO48Ligand/IonSULFATE ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR L:2 , ASN L:92 , SER L:93 , GLY L:94 , HOH L:427BINDING SITE FOR RESIDUE GOL L 212
02AC2SOFTWAREGLN L:37 , VAL L:45 , PRO L:59 , HOH L:271 , HOH L:302 , HOH L:364 , HOH L:397BINDING SITE FOR RESIDUE GOL L 213
03AC3SOFTWAREALA H:100 , TYR L:49 , ARG L:54 , PRO L:55 , SER L:56 , HOH L:252 , HOH L:333 , HOH L:350BINDING SITE FOR RESIDUE GOL L 214
04AC4SOFTWARETHR L:205 , ACT L:228 , HOH L:386 , THR P:303BINDING SITE FOR RESIDUE GOL L 215
05AC5SOFTWARETYR H:91 , GLN L:38 , LYS L:39 , GLY L:41 , GLN L:42 , HOH L:308 , HOH L:327 , HOH L:349BINDING SITE FOR RESIDUE GOL L 216
06AC6SOFTWAREHOH H:339 , SER L:121 , SER L:122 , HOH L:372BINDING SITE FOR RESIDUE GOL L 217
07AC7SOFTWARESER L:52 , LYS L:53 , ARG L:54 , SO4 L:224 , SO4 L:225 , HOH L:304 , HOH L:435 , HOH L:468BINDING SITE FOR RESIDUE GOL L 218
08AC8SOFTWAREHOH H:307 , HOH H:325 , GLN L:42 , ALA L:43 , VAL L:45 , HOH L:283 , HOH L:417BINDING SITE FOR RESIDUE GOL L 219
09AC9SOFTWAREHIS H:164 , GLN L:167 , SER L:168 , HOH L:341 , HOH L:464BINDING SITE FOR RESIDUE SO4 L 220
10BC1SOFTWAREPRO L:59 , ARG L:61 , GLN L:79 , ASP L:81 , HOH L:271BINDING SITE FOR RESIDUE SO4 L 221
11BC2SOFTWARESER L:40 , GLU L:83 , LYS L:103 , TYR L:172 , HOH L:359BINDING SITE FOR RESIDUE SO4 L 222
12BC3SOFTWAREPRO L:154 , VAL L:155 , LYS L:156 , ALA L:157BINDING SITE FOR RESIDUE SO4 L 223
13BC4SOFTWAREARG L:54 , SER L:63 , GOL L:218 , HOH L:249 , HOH L:276BINDING SITE FOR RESIDUE SO4 L 224
14BC5SOFTWARELYS L:53 , LYS L:186 , ARG L:189 , GOL L:218 , HOH L:435 , HOH L:468BINDING SITE FOR RESIDUE SO4 L 225
15BC6SOFTWARETHR L:18 , ARG L:20 , HOH L:434BINDING SITE FOR RESIDUE ACT L 226
16BC7SOFTWAREASN L:112 , THR L:114 , VAL L:115 , LYS L:204BINDING SITE FOR RESIDUE ACT L 227
17BC8SOFTWAREGLU L:198 , GLY L:199 , GLU L:203 , THR L:205 , GOL L:215 , HOH L:474 , ACT P:2BINDING SITE FOR RESIDUE ACT L 228
18BC9SOFTWAREALA H:125 , SER H:127 , ALA H:137 , LYS H:214 , HOH H:372 , HOH H:412 , LEU L:117 , PHE L:118 , PRO L:119BINDING SITE FOR RESIDUE GOL H 220
19CC1SOFTWARESER H:55 , ASP H:56 , THR H:57 , HOH H:247 , THR L:5 , GLN L:6 , THR L:100BINDING SITE FOR RESIDUE GOL H 221
20CC2SOFTWARESER H:130 , THR H:131 , SER H:132 , GLY H:133 , SER H:186 , SER H:187 , ACT H:233 , HOH H:426BINDING SITE FOR RESIDUE GOL H 222
21CC3SOFTWAREGLY H:65 , GLN H:66 , GLY H:67 , TRP H:82 , SER H:82A , SER H:82B , HOH H:368 , HOH H:443BINDING SITE FOR RESIDUE GOL H 223
22CC4SOFTWAREMET H:40 , LYS H:43 , GLY H:44 , GLU H:46 , HOH H:239 , HOH L:438BINDING SITE FOR RESIDUE GOL H 224
23CC5SOFTWARELYS H:117 , SER H:120 , ASP H:144 , HOH H:405 , LYS L:129 , HOH L:313BINDING SITE FOR RESIDUE GOL H 225
24CC6SOFTWARETYR H:27 , SER H:28 , PHE H:29 , SER H:30 , HOH H:323BINDING SITE FOR RESIDUE GOL H 226
25CC7SOFTWAREGLY H:118 , SER H:120 , VAL H:121 , PHE H:122 , THR H:205 , VAL H:207 , LYS H:209 , HOH H:248 , HOH H:329 , GLU L:123BINDING SITE FOR RESIDUE GOL H 227
26CC8SOFTWARELYS H:83 , ALA H:84 , SER H:85 , HOH H:343 , HOH H:373 , HOH H:479BINDING SITE FOR RESIDUE GOL H 228
27CC9SOFTWAREPRO H:41 , LEU H:170 , TYR H:176 , HOH H:319 , HOH H:370 , HOH H:480BINDING SITE FOR RESIDUE GOL H 229
28DC1SOFTWAREARG H:38 , SER H:62 , PHE H:63 , GLN H:66 , LYS H:83 , HOH H:299 , HOH H:333BINDING SITE FOR RESIDUE GOL H 230
29DC2SOFTWAREGLN H:171 , SER H:172 , HOH H:237 , HOH H:298 , HOH H:300 , HOH H:303 , GLY L:158 , GLU L:160 , SER L:179BINDING SITE FOR RESIDUE SO4 H 231
30DC3SOFTWARETYR H:27 , SER H:28 , TYR H:32 , HOH H:377 , ARG P:304BINDING SITE FOR RESIDUE SO4 H 232
31DC4SOFTWARESER H:127 , SER H:128 , LYS H:129 , SER H:186 , LEU H:189 , THR H:219 , GOL H:222BINDING SITE FOR RESIDUE ACT H 233
32DC5SOFTWARESER H:30 , LYS H:73BINDING SITE FOR RESIDUE ACT H 234
33DC6SOFTWAREGLY H:26 , HOH H:421BINDING SITE FOR RESIDUE ACT H 235
34DC7SOFTWAREACT L:228 , THR P:303 , HOH P:414BINDING SITE FOR RESIDUE ACT P 2

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:134 -L:193
5L:211 -H:216

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr L:140 -Pro L:141
2Ser H:132 -Gly H:133
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UJJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UJJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3UJJ)

(-) 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:230
                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeeee....eeee........eeeeehhh.eeeeee...hhhhheeeeeeee..hhhhh....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ujj H    1 EVQLVQSGAEVKKPGESLKISCKASGYSFSSYWIAWVRQMPGKGLEWMGFIYPADSDTRYSPSFQGQGTISADKSISTAYLQWSSLKASDTAMYYCAILGFWGANRGGGGMDVWGQGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKT  219
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109       119       129       139       149       159       169       179       189       199       209       219
                                                                              52A                            82A||               100A||||||                                                                                                                       
                                                                                                              82B|                100B|||||                                                                                                                       
                                                                                                               82C                 100C||||                                                                                                                       
                                                                                                                                    100D|||                                                                                                                       
                                                                                                                                     100E||                                                                                                                       
                                                                                                                                      100F|                                                                                                                       
                                                                                                                                       100G                                                                                                                       


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..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ujj L    1 SYELTQPPSVSVSPGQTARITCSGDALPEKYAYWYQQKSGQAPVLIIYEDSKRPSGIPERFSGSRSGTMATLTISGAQVDDEADYYCYSTNSGGTFFVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC  211
                                    11        21        31        41        51        61        71        81        91    ||  99       108       118       128       138       148       158       168       178       188       198       208   
                                    9|                                                                                  95A|        106A                                                                                                         
                                    11                                                                                   95B                                                                                                                     


Chain P from PDB  Type:PROTEIN  Length:17
 aligned with ENV_HV1V9 | Q9Q714 from UniProtKB/Swiss-Prot  Length:859

    Alignment length:17
                                   316       
           ENV_HV1V9    307 TRKSIRIGPGQAFYATG  323
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author .....eee..ee..... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                3ujj P  303 TRKSIRIGPGQAFYATG  321
                                  |314       
                                309|         
                                 312         


Chain P from PDB  Type:PROTEIN  Length:17
 aligned with Q9YXJ8_9HIV1 | Q9YXJ8 from UniProtKB/TrEMBL  Length:221

    Alignment length:17
                                    41       
        Q9YXJ8_9HIV1     32 TRKSIRIGPGQTFYATG   48
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author .....eee..ee..... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                3ujj P  303 TRKSIRIGPGQAFYATG  321
                                  |314       
                                309|         
                                 312
   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 3UJJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UJJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UJJ)

(-) Gene Ontology  (20, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (ENV_HV1V9 | Q9Q714)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

Chain P   (Q9YXJ8_9HIV1 | Q9YXJ8)
biological process
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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  Cis Peptide Bonds
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    Ser H:132 - Gly H:133   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  Q9YXJ8_9HIV1 | Q9YXJ8
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  ENV_HV1V9 | Q9Q714
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9YXJ8_9HIV1 | Q9YXJ8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3UJJ)

(-) Related Entries Specified in the PDB File

3uji