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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GERMLINE-TARGETING HIV-1 GP120 ENGINEERED OUTER DOMAIN, EOD-GT6
 
Authors :  J. -P. Julien, J. Jardine, W. R. Schief, I. A. Wilson
Date :  19 Mar 13  (Deposition) - 10 Apr 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hiv-1 Gp120, Cd4 Binding Site, Vrc01-Like Broadly Neutralizing Antibodies, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jardine, J. P. Julien, S. Menis, T. Ota, O. Kalyuzhniy, A. Mcguire, D. Sok, P. S. Huang, S. Macpherson, M. Jones, T. Nieusma, J. Mathison, D. Baker, A. B. Ward, D. R. Burton, L. Stamatatos, D. Nemazee, I. A. Wilson, W. R. Schief
Rational Hiv Immunogen Design To Target Specific Germline B Cell Receptors.
Science V. 340 711 2013
PubMed-ID: 23539181  |  Reference-DOI: 10.1126/SCIENCE.1234150

(-) Compounds

Molecule 1 - GERMLINE-TARGETING HIV-1 GP120 ENGINEERED OUTER DOMAIN, EOD-GT6
    Chains: A, B, C, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293S
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:18 , SER A:94BINDING SITE FOR RESIDUE NAG A 201
2AC2SOFTWAREHIS A:14 , SER A:16 , SER A:17 , ASN A:65 , THR B:56 , HOH B:301BINDING SITE FOR RESIDUE NAG A 202
3AC3SOFTWAREASN B:18 , SER B:94 , GLU B:96 , HOH B:320BINDING SITE FOR RESIDUE NAG B 201
4AC4SOFTWARETHR A:56 , HIS B:14 , SER B:16 , SER B:17 , VAL B:57 , ASN B:65BINDING SITE FOR RESIDUE NAG B 202
5AC5SOFTWAREASN C:18 , SER C:94BINDING SITE FOR RESIDUE NAG C 201
6AC6SOFTWAREHIS C:14 , CYS C:15 , SER C:16 , SER C:17 , VAL C:57 , ASN C:65 , HOH C:305BINDING SITE FOR RESIDUE NAG C 202
7AC7SOFTWAREASN D:18 , SER D:94 , GLU D:96BINDING SITE FOR RESIDUE NAG D 201
8AC8SOFTWAREHIS D:14 , SER D:17 , VAL D:57 , ASN D:65 , ASN D:150BINDING SITE FOR RESIDUE NAG D 202

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:7 -A:158
2A:15 -A:151
3A:51 -A:88
4A:99 -A:105
5B:7 -B:158
6B:15 -B:151
7B:51 -B:88
8B:99 -B:105
9C:7 -C:158
10C:15 -C:151
11C:51 -C:88
12C:99 -C:105
13D:7 -D:158
14D:15 -D:151
15D:51 -D:88
16D:99 -D:105

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Arg A:8 -Pro A:9
2Asp A:27 -Gly A:28
3Arg B:8 -Pro B:9
4Arg C:8 -Pro C:9
5Asp C:27 -Gly C:28
6Gly C:29 -Val C:30
7Arg D:8 -Pro D:9
8Asp D:170 -Ser D:171

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JPJ)

(-) 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:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhheeeeeeeeee........eeeeee.....................eee.........eee..........eeeeeeeeeeeee....eeeeehhhhhhhhhhhhhhhhhhhh..eeee............eeee....eeee.......eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jpj A   1 DTITLPCRPAPPPHCSSNITGLILTRDGGVSNDETEIFRPSGGDMRDIARCQIAGTVVSTQLFLNGSLAEEEVVIRSVDFRDNAKSICVQLDTSVEIDCTGAGHCDISRAKWDNTLKQIASKLREQFGDRTIIFKQSSGGDPEFVTHSFNCGGEFFYCDSTQLFDSTWFD 170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170


Chain B from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhheeeeeeeeee........eeeeee.................ee..eee.........eee..........eeeeeeeeeeeee....eeeeehhhhhhhhhhhhhhhhhhhh..eeee.........eeeee..eeeee.hhhhh.eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jpj B   1 DTITLPCRPAPPPHCSSNITGLILTRDGGVSNDETEIFRPSGGDMRDIARCQIAGTVVSTQLFLNGSLAEEEVVIRSVDFRDNAKSICVQLDTSVEIDCTGAGHCDISRAKWDNTLKQIASKLREQFGDRTIIFKQSSPEFVTHSFNCGGEFFYCDSTQLFDSTWFDST 172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       143       153       163         
                                                                                                                                                                   138|                              
                                                                                                                                                                    142                              


Chain C from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhheeeeeeeeee........eeeeee............eee.........eee..........eeeeeeeeeeeee....eeeeehhhhhhhhhhhhhhhhhhhh..eeee...eeeee....eeeee.hhhh.eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jpj C   1 DTITLPCRPAPPPHCSSNITGLILTRDGGVSNDETEIFRPSCQIAGTVVSTQLFLNGSLAEEEVVIRSVDFRDNAKSICVQLDTSVEIDCTGAGHCDISRAKWDNTLKQIASKLREQFGDRTIIFKQVTHSFNCGGEFFYCDSTQLFDSTWFDSTGT 174
                                    10        20        30        40||      59        69        79        89        99       109       119       129      |147       157       167       
                                                                   41|                                                                                  136|                             
                                                                    51                                                                                   145                             


Chain D from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee...hhhhheeeeeeeeee...eeeeee................eee.........eee..........eeeeeeeeeeeeeee..eeeeehhhhhhhhhhhhhhhhhhhh..eeee..........eeee....eeee.......eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jpj D   1 DTITLPCRPAPPPHCSSNITGLILTRDDETEIFRPSGGDMCQIAGTVVSTQLFLNGSLAEEEVVIRSVDFRDNAKSICVQLDTSVEIDCTGAGHCDISRAKWDNTLKQIASKLREQFGDRTIIFKQSSDPEFVTHSFNCGGEFFYCDSTQLFDSTWFDSTGT 174
                                    10        20      ||35        45|       60        70        80        90       100       110       120       130       142       152       162       172  
                                                     27|          45|                                                                                    138|                                 
                                                      33           51                                                                                     141
   Legend:   → Mismatch (orange background)
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  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 4JPJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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        ENV_HV1H2 | P04578: 1aik 1df4 1df5 1dlb 1g9m 1gc1 1gzl 1k33 1k34 1mzi 1opn 1opt 1opw 1rzj 2cmr 2me1 2mg1 2mg2 2mg3 2ny7 2pv6 2x7r 2xra 2zzo 3d0v 3dnl 3dnn 3dno 3dro 3idx 3idy 3j70 3tyg 3vie 4jpk 4ydv 4zto 5bn0 5c0r 5c0s 5cil 5cin 5cmu 5cmz 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6 5x08

(-) Related Entries Specified in the PDB File

4jpi 4jpk