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(-) Description

Title :  CRYSTAL STRUCTURE OF UNLIGANDED HIV-1 CLADE C STRAIN C1086 GP120 CORE
 
Authors :  Y. D. Kwon, P. D. Kwong
Date :  17 Aug 11  (Deposition) - 04 Apr 12  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hiv-1 Gp120, Unliganded, Clade C1086, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. D. Kwon, A. Finzi, X. Wu, C. Dogo-Isonagie, L. K. Lee, L. R. Moore, S. D. Schmidt, J. Stuckey, Y. Yang, T. Zhou, J. Zhu, D. A. Vicic, A. K. Debnath, L. Shapiro, C. A. Bewley, J. R. Mascola, J. G. Sodroski, P. D. Kwong
Unliganded Hiv-1 Gp120 Core Structures Assume The Cd4-Bound Conformation With Regulation By Quaternary Interactions And Variable Loops.
Proc. Natl. Acad. Sci. Usa V. 109 5663 2012
PubMed-ID: 22451932  |  Reference-DOI: 10.1073/PNAS.1112391109

(-) Compounds

Molecule 1 - HIV-1 CLADE C1086 GP120
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: HIV-1 ENV
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:234 , ILE A:272 , LEU A:277 , HIS A:352BINDING SITE FOR RESIDUE NAG A 734
02AC2SOFTWAREASP A:211 , LYS A:252 , LEU A:261 , ASN A:262 , ASN A:446 , SER A:447 , NAG A:948BINDING SITE FOR RESIDUE NAG A 762
03AC3SOFTWAREASN A:276 , THR A:278 , ASN A:279 , THR B:278 , NAG B:776BINDING SITE FOR RESIDUE NAG A 776
04AC4SOFTWAREGLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLU A:290 , GLU A:348BINDING SITE FOR RESIDUE NAG A 789
05AC5SOFTWAREGLU A:335 , SER A:336 , ASN A:339 , TYR A:403 , ARG A:408 , SER A:409BINDING SITE FOR RESIDUE NAG A 839
06AC6SOFTWAREASN A:386 , SER A:388BINDING SITE FOR RESIDUE NAG A 886
07AC7SOFTWAREPRO A:363 , SER A:388 , ASP A:389 , ASN A:392 , ASN A:404 , THR A:406BINDING SITE FOR RESIDUE NAG A 892
08AC8SOFTWARESER A:291 , ASN A:448 , HOH A:518 , NAG A:762 , GLU B:290BINDING SITE FOR RESIDUE NAG A 948
09AC9SOFTWAREASN B:234 , THR B:236 , PRO B:238 , SER B:274BINDING SITE FOR RESIDUE NAG B 734
10BC1SOFTWAREASP B:211 , LYS B:252 , VAL B:254 , ASN B:262 , ASN B:446 , SER B:447BINDING SITE FOR RESIDUE NAG B 762
11BC2SOFTWARELYS A:97 , GLU A:275 , LYS A:282 , NAG A:776 , ASN B:276 , THR B:278BINDING SITE FOR RESIDUE NAG B 776
12BC3SOFTWAREHOH B:36 , GLU B:268 , GLU B:269 , ILE B:270 , ASN B:289 , GLU B:290 , GLU B:348 , HOH B:497BINDING SITE FOR RESIDUE NAG B 789
13BC4SOFTWAREHOH B:27 , ASN B:386 , SER B:388BINDING SITE FOR RESIDUE NAG B 886
14BC5SOFTWAREPRO B:363 , ASP B:389 , ASN B:392 , THR B:406 , GLY B:407BINDING SITE FOR RESIDUE NAG B 892

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:54 -A:74
2A:119 -A:205
3A:218 -A:247
4A:228 -A:239
5A:296 -A:331
6A:378 -A:445
7A:385 -A:418
8B:54 -B:74
9B:119 -B:205
10B:218 -B:247
11B:228 -B:239
12B:296 -B:331
13B:378 -B:445
14B:385 -B:418

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:78 -Pro A:79
2Asp B:78 -Pro B:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TGR)

(-) 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:346
 aligned with C6G099_9HIV1 | C6G099 from UniProtKB/TrEMBL  Length:849

    Alignment length:440
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478
         C6G099_9HIV1    39 VWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTPLCVTLNCTNVKGNESDTSEVMKNCSFKATTELKDKKHKVHALFYKLDVVPLNGNSSSSGEYRLINCNTSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNNTRKSIRIGPGQTFYATGDIIGNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDGGQSNETNDTETFRPGGGDMRDNWRSELYKYKVVEIK 478
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.......hhhhhhhhhhhee..............eeee...hhhhhhhhhhhhhhhhhhh...eeee.-------------------------------------------------------------------.eeee.............eee....eeeee........eeee....ee.............eee.........eee..........eeeeeeeeeeeeeee..-----------------------...eeeeeeehhhhhhhhhhhhhhhhh.....eeee......hhhhhheeeee..eeeee.......ee......ee.......eeeeeeeee.eee......eee........eeeeeeeeeeeeee....----..eeeeee.....hhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tgr A  44 VWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTG-------------------------------------------------------------------GSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPN-----------------------NIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDGGQ----NDTETFRPGGGDMRDNWRSELYKYKVVEIK 492
                                    53        63        73        83        93       103       113       123|        -         -         -         -         -         -       199       209       219       229       239       249       259       269       279       289       299|        -         -    |  330       340       350   ||  361       371       381       391       404       414       424       434       444       454     |   -|      472       482       492
                                                                                                          124                                                                 198                                                                                                   300                     325                          354|                                        399|                                                      460  463                             
                                                                                                                                                                                                                                                                                                                                          356                                         403                                                                                           


Chain B from PDB  Type:PROTEIN  Length:346
 aligned with C6G099_9HIV1 | C6G099 from UniProtKB/TrEMBL  Length:849

    Alignment length:440
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478
         C6G099_9HIV1    39 VWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTPLCVTLNCTNVKGNESDTSEVMKNCSFKATTELKDKKHKVHALFYKLDVVPLNGNSSSSGEYRLINCNTSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNNTRKSIRIGPGQTFYATGDIIGNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDGGQSNETNDTETFRPGGGDMRDNWRSELYKYKVVEIK 478
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.......hhhhhhhhhhhee..............eeee...hhhhhhhhhhhhhhhhhh....eeee.-------------------------------------------------------------------.eeee.............eee....eeee.........eeee....ee.............eee.........eeee.........eeeeeeeeeeeeeee..-----------------------...eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.......ee......ee.......eeeeeeee..eee......eee........eeeeeeeeeeeeee....----..eeeeee.....hhhhhhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tgr B  44 VWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTG-------------------------------------------------------------------GSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPN-----------------------NIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDGGQ----NDTETFRPGGGDMRDNWRSELYKYKVVEIK 492
                                    53        63        73        83        93       103       113       123|        -         -         -         -         -         -       199       209       219       229       239       249       259       269       279       289       299|        -         -    |  330       340       350   ||  361       371       381       391       404       414       424       434       444       454     |   -|      472       482       492
                                                                                                          124                                                                 198                                                                                                   300                     325                          354|                                        399|                                                      460  463                             
                                                                                                                                                                                                                                                                                                                                          356                                         403
   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 3TGR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (C6G099_9HIV1 | C6G099)
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: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: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.

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 Related Entries

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

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        C6G099_9HIV1 | C6G099: 3tgs 4i53 4lsv 5f4l 5f4p 5f4r 5f4u

(-) Related Entries Specified in the PDB File

3tgq 3tgs 3tgt 3tih